X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=d4300e4d8356f6ebe86d7f3935785790343c59de;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=4e625e14aede3537513b21ca3936654100209011;hpb=619cc880371f3228e6a1fb33c6bfb6e7a7e2622c;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 4e625e1..d4300e4 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -70,13 +70,16 @@ import javax.swing.ToolTipManager; public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener { - private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern.compile("<"); + private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern + .compile("<"); - String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column"); + String TOGGLE_LABELSCALE = MessageManager + .getString("label.scale_label_to_column"); String ADDNEW = MessageManager.getString("label.add_new_row"); - String EDITNAME = MessageManager.getString("label.edit_label_description"); + String EDITNAME = MessageManager + .getString("label.edit_label_description"); String HIDE = MessageManager.getString("label.hide_row"); @@ -86,7 +89,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, String OUTPUT_TEXT = MessageManager.getString("label.export_annotation"); - String COPYCONS_SEQ = MessageManager.getString("label.copy_consensus_sequence"); + String COPYCONS_SEQ = MessageManager + .getString("label.copy_consensus_sequence"); boolean resizePanel = false; @@ -253,8 +257,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, else if (evt.getActionCommand().equals(OUTPUT_TEXT)) { new AnnotationExporter().exportAnnotations(ap, - new AlignmentAnnotation[] - { aa[selectedRow] }); + new AlignmentAnnotation[] { aa[selectedRow] }); } else if (evt.getActionCommand().equals(COPYCONS_SEQ)) { @@ -547,9 +550,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, } else { - ap.getSeqPanel().ap.getIdPanel() - .highlightSearchResults(aa[selectedRow].groupRef - .getSequences(null)); + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults( + aa[selectedRow].groupRef.getSequences(null)); } return; } @@ -557,36 +559,45 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (evt.getClickCount() == 1) { - ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(Arrays - .asList(new SequenceI[] - { aa[selectedRow].sequenceRef })); + ap.getSeqPanel().ap + .getIdPanel() + .highlightSearchResults( + Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef })); } else if (evt.getClickCount() >= 2) { ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg!=null) + if (sg != null) { - // we make a copy rather than edit the current selection if no modifiers pressed + // we make a copy rather than edit the current selection if no + // modifiers pressed // see Enhancement JAL-1557 if (!(evt.isControlDown() || evt.isShiftDown())) { sg = new SequenceGroup(sg); sg.clear(); sg.addSequence(aa[selectedRow].sequenceRef, false); - } else { + } + else + { if (evt.isControlDown()) { sg.addOrRemove(aa[selectedRow].sequenceRef, true); - } else { - // notionally, we should also add intermediate sequences from last added sequence ? + } + else + { + // notionally, we should also add intermediate sequences from + // last added sequence ? sg.addSequence(aa[selectedRow].sequenceRef, true); } } - } else { + } + else + { sg = new SequenceGroup(); sg.setStartRes(0); - sg.setEndRes(ap.av.getAlignment().getWidth()-1); + sg.setEndRes(ap.av.getAlignment().getWidth() - 1); sg.addSequence(aa[selectedRow].sequenceRef, false); } ap.av.setSelectionGroup(sg); @@ -632,7 +643,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, { final String label = aa[selectedRow].label; JMenuItem hideType = new JMenuItem(); - String text = MessageManager.getString("label.hide_all") + " " + label; + String text = MessageManager.getString("label.hide_all") + " " + + label; hideType.setText(text); hideType.addActionListener(new ActionListener() { @@ -692,7 +704,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, pop.addSeparator(); // av and sequencegroup need to implement same interface for final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( - MessageManager.getString("label.ignore_gaps_consensus"), + MessageManager.getString("label.ignore_gaps_consensus"), (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef .getIgnoreGapsConsensus() : ap.av .isIgnoreGapsConsensus()); @@ -705,7 +717,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, { // TODO: pass on reference to ap so the view can be updated. aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); - ap.getAnnotationPanel().paint(ap.getAnnotationPanel().getGraphics()); + ap.getAnnotationPanel().paint( + ap.getAnnotationPanel().getGraphics()); } else { @@ -718,7 +731,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (aaa.groupRef != null) { final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - MessageManager.getString("label.show_group_histogram"), + MessageManager.getString("label.show_group_histogram"), aa[selectedRow].groupRef.isShowConsensusHistogram()); chist.addActionListener(new ActionListener() { @@ -737,7 +750,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(chist); final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( - MessageManager.getString("label.show_group_logo"), + MessageManager.getString("label.show_group_logo"), aa[selectedRow].groupRef.isShowSequenceLogo()); cprofl.addActionListener(new ActionListener() { @@ -756,7 +769,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(cprofl); final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( - MessageManager.getString("label.normalise_group_logo"), + MessageManager.getString("label.normalise_group_logo"), aa[selectedRow].groupRef.isNormaliseSequenceLogo()); cproflnorm.addActionListener(new ActionListener() { @@ -781,7 +794,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, else { final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram()); + MessageManager.getString("label.show_histogram"), + av.isShowConsensusHistogram()); chist.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -800,7 +814,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(chist); final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( - MessageManager.getString("label.show_logo"), av.isShowSequenceLogo()); + MessageManager.getString("label.show_logo"), + av.isShowSequenceLogo()); cprof.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -819,7 +834,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(cprof); final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( - MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo()); + MessageManager.getString("label.normalise_logo"), + av.isNormaliseSequenceLogo()); cprofnorm.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -855,11 +871,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ protected void copy_annotseqtoclipboard(SequenceI sq) { - SequenceI[] seqs = new SequenceI[] - { sq }; + SequenceI[] seqs = new SequenceI[] { sq }; String[] omitHidden = null; - SequenceI[] dseqs = new SequenceI[] - { sq.getDatasetSequence() }; + SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() }; if (dseqs[0] == null) { dseqs[0] = new Sequence(sq); @@ -875,8 +889,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, sq.getLength(), seqs); } - int[] alignmentStartEnd = new int[] - { 0, ds.getWidth() - 1 }; + int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 }; List hiddenCols = av.getColumnSelection().getHiddenColumns(); if (hiddenCols != null) { @@ -895,13 +908,14 @@ public class AnnotationLabels extends JPanel implements MouseListener, hiddenColumns = new ArrayList(); for (int[] region : av.getColumnSelection().getHiddenColumns()) { - hiddenColumns.add(new int[] - { region[0], region[1] }); + hiddenColumns.add(new int[] { region[0], region[1] }); } } - Desktop.jalviewClipboard = new Object[] - { seqs, ds, // what is the dataset of a consensus sequence ? need to flag + Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset + // of a consensus + // sequence ? need to + // flag // sequence as special. hiddenColumns }; } @@ -990,8 +1004,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, int ofontH = fontHeight; int sOffset = 0; int visHeight = 0; - int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap.getAnnotationPanel() - .getVisibleVRange() : null; + int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap + .getAnnotationPanel().getVisibleVRange() : null; if (clip && visr != null) { sOffset = visr[0];