X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=4fdb25a2913b927eacaf32162847de66f0aa27ee;hb=49665d43dbcc49a55d7d44fbf58a7c27ab0ae860;hp=3266fabf5631a665138d9e9f7feb574d451a8434;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 3266fab..4fdb25a 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -27,8 +27,9 @@ 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; @@ -59,7 +60,6 @@ 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; @@ -124,7 +124,7 @@ public class SeqPanel extends JPanel implements MouseListener, private final SequenceAnnotationReport seqARep; - StringBuffer tooltipText = new StringBuffer(); + StringBuilder tooltipText = new StringBuilder(); String tmpString; @@ -132,7 +132,7 @@ public class SeqPanel extends JPanel implements MouseListener, StructureSelectionManager ssm; - SearchResults lastSearchResults; + SearchResultsI lastSearchResults; /** * Creates a new SeqPanel object. @@ -676,7 +676,7 @@ 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 +785,7 @@ 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 +910,7 @@ 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 +919,7 @@ 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 +1501,7 @@ 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 +1565,10 @@ 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 +1588,11 @@ 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)) { @@ -1745,7 +1737,7 @@ public class SeqPanel extends JPanel implements MouseListener, SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()); } - else + if (stretchGroup.cs.getThreshold() > 0) { SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());