X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=47b0694423ad6baf9f4a0d1a9ba756cc959c3901;hb=c63c9f4011573ca0e65befe9633a9380a829527b;hp=885aab25810b925766dd9793f5d20221b1e54fc9;hpb=a86ad83f39c98c9a06d08a1ba1fa8b529d30a63c;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 885aab2..47b0694 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -27,13 +27,15 @@ import jalview.commands.EditCommand.Action; import jalview.commands.EditCommand.Edit; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResults; -import jalview.datamodel.SearchResults.Match; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.SequenceAnnotationReport; +import jalview.schemes.CollectionColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.structure.SelectionListener; import jalview.structure.SelectionSource; @@ -59,7 +61,6 @@ import java.awt.event.MouseWheelListener; import java.util.ArrayList; import java.util.List; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; @@ -132,7 +133,7 @@ public class SeqPanel extends JPanel implements MouseListener, StructureSelectionManager ssm; - SearchResults lastSearchResults; + SearchResultsI lastSearchResults; /** * Creates a new SeqPanel object. @@ -676,7 +677,7 @@ public class SeqPanel extends JPanel implements MouseListener, * the start of the highlighted region. */ @Override - public void highlightSequence(SearchResults results) + public void highlightSequence(SearchResultsI results) { if (results == null || results.equals(lastSearchResults)) { @@ -785,7 +786,7 @@ public class SeqPanel extends JPanel implements MouseListener, seqARep.appendFeatures(tooltipText, rpos, features, this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } - if (tooltipText.length() == 6) // + if (tooltipText.length() == 6) // { setToolTipText(null); lastTooltip = null; @@ -910,7 +911,7 @@ public class SeqPanel extends JPanel implements MouseListener, * * @param results */ - private void setStatusMessage(SearchResults results) + private void setStatusMessage(SearchResultsI results) { AlignmentI al = this.av.getAlignment(); int sequenceIndex = al.findIndex(results); @@ -919,7 +920,7 @@ public class SeqPanel extends JPanel implements MouseListener, return; } SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence(); - for (Match m : results.getResults()) + for (SearchResultMatchI m : results.getResults()) { SequenceI seq = m.getSequence(); if (seq.getDatasetSequence() != null) @@ -1501,7 +1502,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (features != null && features.size() > 0) { - SearchResults highlight = new SearchResults(); + SearchResultsI highlight = new SearchResults(); highlight.addResult(sequence, features.get(0).getBegin(), features .get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); @@ -1565,10 +1566,10 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.getWrapAlignment() && seq > av.getAlignment().getHeight()) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.cannot_edit_annotations_in_wrapped_view"), MessageManager.getString("label.wrapped_view_no_edit"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -1588,19 +1589,11 @@ public class SeqPanel extends JPanel implements MouseListener, if (stretchGroup == null) { - stretchGroup = av.getAlignment().findGroup(sequence); - - if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) - && (res < stretchGroup.getEndRes())) - { - av.setSelectionGroup(stretchGroup); - } - else - { - stretchGroup = null; - } + stretchGroup = av.getAlignment().findGroup(sequence, res); + av.setSelectionGroup(stretchGroup); } - else if (!stretchGroup.getSequences(null).contains(sequence) + if (stretchGroup == null + || !stretchGroup.getSequences(null).contains(sequence) || (stretchGroup.getStartRes() > res) || (stretchGroup.getEndRes() < res)) { @@ -1662,13 +1655,13 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.getConservationSelected()) { - SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), + SliderPanel.setConservationSlider(ap, av.getViewportColourScheme(), "Background"); } if (av.getAbovePIDThreshold()) { - SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), + SliderPanel.setPIDSliderSource(ap, av.getViewportColourScheme(), "Background"); } if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) @@ -1740,15 +1733,15 @@ public class SeqPanel extends JPanel implements MouseListener, stretchGroup.cs.alignmentChanged(stretchGroup, av.getHiddenRepSequences()); + CollectionColourSchemeI groupColourScheme = stretchGroup.getGroupColourScheme(); + String name = stretchGroup.getName(); if (stretchGroup.cs.conservationApplied()) { - SliderPanel.setConservationSlider(ap, stretchGroup.cs, - stretchGroup.getName()); + SliderPanel.setConservationSlider(ap, groupColourScheme, name); } - else + if (stretchGroup.cs.getThreshold() > 0) { - SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, - stretchGroup.getName()); + SliderPanel.setPIDSliderSource(ap, groupColourScheme, name); } } PaintRefresher.Refresh(this, av.getSequenceSetId());