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		Date	Author	Revision	Message
		8/30/17 10:15 PM	BenStoever	159	GitHub ReadMe corrected.	[more]
		Action Path Modified /trunk/README.md
		8/30/17 9:45 PM	BenStoever	158	GitHub ReadMe corrected.	[more]
		Action Path Modified /trunk/README.md
		8/30/17 9:29 PM	BenStoever	157	GitHub ReadMe extended.	[more]
		Action Path Modified /trunk/README.md
		8/30/17 8:51 PM	BenStoever	156	GitHub ReadMe edited. GitHub license file added.	[more]
		Action Path Added /trunk/LICENSE.md Modified /trunk/README.md
		8/10/17 12:25 PM	BenStoever	155	GitHub ReadMe edited.	[more]
		Action Path Modified /trunk Modified /trunk/README.md
		8/10/17 12:25 PM	BenStoever	154	GitHub ReadMe added.	[more]
		Action Path Modified /trunk Added /trunk/README.md
		1/25/17 6:53 PM	BenStoever	153	Debug outputs removed and TODO changed.	[more]
		Action Path Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/maxsequencepairmatch/MaxSequencePairMatchAligner.java
		1/25/17 4:42 PM	BenStoever	152	TODOs added.	[more]
		Action Path Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/ComparisonDocumentReader.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/maxsequencepairmatch/MaxSequencePairMatchAligner.java
		1/25/17 2:49 PM	BenStoever	151	Application description updated in copyright notices of test project.	[more]
		Action Path Modified /trunk/test/.settings/org.eclipse.jdt.ui.prefs Modified /trunk/test/src/NOTICE.txt Modified /trunk/test/src/info/bioinfweb/alignmentcomparator/CreateSequencesTest.java Modified /trunk/test/src/info/bioinfweb/alignmentcomparator/StringBuilderTest.java Modified /trunk/test/src/info/bioinfweb/alignmentcomparator/document/io/results/FastaReaderTest.java Modified /trunk/test/src/info/bioinfweb/alignmentcomparator/document/superalignment/AverageDegapedPositionAlignerTest.java
		1/25/17 2:49 PM	BenStoever	150	Application description updated in copyright notices of main project.	[more]
		Action Path Modified /trunk/main/.settings/org.eclipse.jdt.ui.prefs Modified /trunk/main/include/NOTICE.txt Modified /trunk/main/src/NOTICE.txt Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/Main.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/ComparedAlignment.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/Document.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/SuperalignedModelDecorator.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/UnlignedIndicesChangeListener.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/event/DocumentEvent.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/event/DocumentListener.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/ComparedAlignmentDataAdapter.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/ComparisonDocumentDataAdapter.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/ComparisonDocumentReader.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/IOConstants.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/ImportedAlignmentModelFactory.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/AverageDegapedPositionAligner.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/CompareAlgorithm.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/ExternalProgramAligner.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/MuscleProfileAligner.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/SuperAlignmentAlgorithm.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/maxsequencepairmatch/AlignmentNode.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/maxsequencepairmatch/MaxSequencePairMatchAligner.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/maxsequencepairmatch/ShiftQueues.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/undo/DocumentEdit.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/undo/InsertGapEdit.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/undo/InsertRemoveGapEdit.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/undo/RemoveGapEdit.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/AlignmentComparisonComponent.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/AlignmentComparisonPanelListener.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/AlignmentComparisonSelection.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/AveragePositionArea.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/MainFrame.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/ActionManagement.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/DocumentAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/InsertSupergapAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/RedoAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/RedoToAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/RemoveSupergapAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/SupergapAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/ToggleSynchronizeSelectionAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/UndoAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/UndoRedoToAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/UndoToAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/file/CompareAlignmentsAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/file/ExitAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/file/OpenResultsAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/file/SaveAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/file/SaveAsAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/help/AboutAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/help/WebsiteAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/AboutDialog.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/ConsoleOutputDialog.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/StartComparisonDialog.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/algorithmpanels/AlgorithmPreferencesPanel.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/algorithmpanels/AlgorithmPreferencesPanelFactory.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/algorithmpanels/AverageDegapedPositionPanel.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/algorithmpanels/MaxSequencePairMatchPanel.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/algorithmpanels/MuscleProfilePanel.java
		1/25/17 2:44 PM	BenStoever	149	License files added to include folder as expected by release manager.	[more]
		Action Path Added /trunk/main/include/APACHE-LICENSE.txt Added /trunk/main/include/GPL.txt Added /trunk/main/include/NOTICE.txt Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/maxsequencepairmatch/MaxSequencePairMatchAligner.java
		1/25/17 1:51 PM	BenStoever	148	Bug fix: Sequence index area moved to top again.	[more]
		Action Path Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/AlignmentComparisonComponent.java
		1/25/17 1:41 PM	BenStoever	147	Copyright information in test project updated.	[more]
		Action Path Modified /trunk/test/.settings/org.eclipse.jdt.ui.prefs Added /trunk/test/src/APACHE-LICENSE.txt Added /trunk/test/src/GPL.txt Added /trunk/test/src/NOTICE.txt Modified /trunk/test/src/info/bioinfweb/alignmentcomparator/CreateSequencesTest.java Modified /trunk/test/src/info/bioinfweb/alignmentcomparator/StringBuilderTest.java Modified /trunk/test/src/info/bioinfweb/alignmentcomparator/document/io/results/FastaReaderTest.java Modified /trunk/test/src/info/bioinfweb/alignmentcomparator/document/superalignment/AverageDegapedPositionAlignerTest.java
		1/25/17 1:37 PM	BenStoever	146	Copyright information updated.	[more]
		Action Path Modified /trunk/main/.settings/org.eclipse.jdt.ui.prefs Added /trunk/main/src/APACHE-LICENSE.txt Added /trunk/main/src/GPL.txt Added /trunk/main/src/NOTICE.txt Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/Main.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/ComparedAlignment.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/Document.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/SuperalignedModelDecorator.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/UnlignedIndicesChangeListener.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/event/DocumentEvent.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/event/DocumentListener.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/ComparedAlignmentDataAdapter.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/ComparisonDocumentDataAdapter.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/ComparisonDocumentReader.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/IOConstants.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/ImportedAlignmentModelFactory.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/AverageDegapedPositionAligner.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/CompareAlgorithm.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/ExternalProgramAligner.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/MuscleProfileAligner.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/SuperAlignmentAlgorithm.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/maxsequencepairmatch/AlignmentNode.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/maxsequencepairmatch/MaxSequencePairMatchAligner.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/maxsequencepairmatch/ShiftQueues.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/undo/DocumentEdit.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/undo/InsertGapEdit.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/undo/InsertRemoveGapEdit.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/undo/RemoveGapEdit.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/AlignmentComparisonComponent.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/AlignmentComparisonPanelListener.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/AlignmentComparisonSelection.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/AveragePositionArea.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/MainFrame.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/ActionManagement.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/DocumentAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/InsertSupergapAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/RedoAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/RedoToAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/RemoveSupergapAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/SupergapAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/ToggleSynchronizeSelectionAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/UndoAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/UndoRedoToAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/UndoToAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/file/CompareAlignmentsAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/file/ExitAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/file/OpenResultsAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/file/SaveAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/file/SaveAsAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/help/AboutAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/help/WebsiteAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/AboutDialog.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/ConsoleOutputDialog.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/StartComparisonDialog.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/algorithmpanels/AlgorithmPreferencesPanel.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/algorithmpanels/AlgorithmPreferencesPanelFactory.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/algorithmpanels/AverageDegapedPositionPanel.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/algorithmpanels/MaxSequencePairMatchPanel.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/algorithmpanels/MuscleProfilePanel.java
		1/25/17 1:22 PM	BenStoever	145	Comment related main menu entries removed. Copyright information in about dialog updated.	[more]
		Action Path Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/MainFrame.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/AboutDialog.java
		1/20/17 6:00 PM	BenStoever	144	Test project adjusted to recent changes.	[more]
		Action Path Deleted /trunk/test/src/info/bioinfweb/alignmentcomparator/document/io/results/ResultsReaderWriterTest.java
		1/20/17 5:58 PM	BenStoever	143	Current comment implementations removed. (Will be replaced by refactored version in the future.)	[more]
		Action Path Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/Document.java Deleted /trunk/main/src/info/bioinfweb/alignmentcomparator/document/comments Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/ComparedAlignmentDataAdapter.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/ComparisonDocumentReader.java Deleted /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/alignment Deleted /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/results Deleted /trunk/main/src/info/bioinfweb/alignmentcomparator/document/undo/AddCommentEdit.java Deleted /trunk/main/src/info/bioinfweb/alignmentcomparator/document/undo/AddRemoveCommentEdit.java Deleted /trunk/main/src/info/bioinfweb/alignmentcomparator/document/undo/ChangeCommentTextEdit.java Deleted /trunk/main/src/info/bioinfweb/alignmentcomparator/document/undo/CommentEdit.java Deleted /trunk/main/src/info/bioinfweb/alignmentcomparator/document/undo/MoveCommentEdit.java Deleted /trunk/main/src/info/bioinfweb/alignmentcomparator/document/undo/RemoveCommentEdit.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/AlignmentComparisonComponent.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/AlignmentComparisonSelection.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/ActionManagement.java Deleted /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/AddCommentAction.java Deleted /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/ChangeCommentTextAction.java Deleted /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/MoveCommentAction.java Deleted /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/edit/RemoveCommentAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/file/OpenResultsAction.java Deleted /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/comments
		1/20/17 5:46 PM	BenStoever	142	Tag for state before removing comment implementations created. (Future versions will have a refactored comment model. The current state is stored here, before comment-related implementations are temporarily removed from the application.)	[more]
		Action Path Added /tags/nonRelease/beforeRemovingComments (Copy from /trunk @ 141)
		1/20/17 5:44 PM	BenStoever	141	Intermediate commit in refactoring comment model.	[more]
		Action Path Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/comments/Comment.java Added /trunk/main/src/info/bioinfweb/alignmentcomparator/document/comments/CommentAnchor.java Added /trunk/main/src/info/bioinfweb/alignmentcomparator/document/comments/CommentAnchorList.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/comments/CommentList.java Deleted /trunk/main/src/info/bioinfweb/alignmentcomparator/document/comments/CommentPosition.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/comments/CommentPositionComparator.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/comments/SequencePositionAdapter.java Added /trunk/main/src/info/bioinfweb/alignmentcomparator/document/comments/SingleCommentAnchor.java (Copy from /trunk/main/src/info/bioinfweb/alignmentcomparator/document/comments/CommentPosition.java @ 133) Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/results/ResultsWriter.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/undo/MoveCommentEdit.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/AlignmentComparisonSelection.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/comments/SingleLineCommentPositioner.java
		12/10/16 10:23 AM	BenStoever	140	Adjustments to recent changes in JPhyloIO in test project.	[more]
		Action Path Modified /trunk/test/.classpath
		12/10/16 10:23 AM	BenStoever	139	Adjustments to recent changes in JPhyloIO. Stream in CompareAlignmentsAction closed.	[more]
		Action Path Modified /trunk/main/.classpath Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/file/CompareAlignmentsAction.java
		11/16/16 11:05 PM	BenStoever	138	Adjustments to recent changes in JPhyloIO.	[more]
		Action Path Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/StartComparisonDialog.java
		10/24/16 2:48 PM	BenStoever	137	Minor changes.	[more]
		Action Path Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/results/ResultsReader.java
		10/24/16 11:33 AM	BenStoever	136	Adjustments to recent changes in LibrAlign.	[more]
		Action Path Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/SuperalignedModelDecorator.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/io/ImportedAlignmentModelFactory.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/AverageDegapedPositionAligner.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/document/superalignment/maxsequencepairmatch/MaxSequencePairMatchAligner.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/file/CompareAlignmentsAction.java
		10/23/16 11:25 AM	BenStoever	135	Alignments can now be imported from all formats supported by JPhyloIO.	[more]
		Action Path Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/Main.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/actions/file/CompareAlignmentsAction.java Modified /trunk/main/src/info/bioinfweb/alignmentcomparator/gui/dialogs/StartComparisonDialog.java
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