X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=479b7468f99f8eec49fb1c88c857b38414c568a5;hb=ed87c8b39a1b48ef6bdf013106d8a667d559c4be;hp=ae4ae109d79173a5d5aac997ae3be802ca2aec6b;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index ae4ae10..479b746 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -20,21 +20,10 @@ */ package jalview.appletgui; -import java.awt.BorderLayout; -import java.awt.Font; -import java.awt.FontMetrics; -import java.awt.Panel; -import java.awt.Point; -import java.awt.event.InputEvent; -import java.awt.event.MouseEvent; -import java.awt.event.MouseListener; -import java.awt.event.MouseMotionListener; -import java.util.List; -import java.util.Vector; - import jalview.api.AlignViewportI; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; +import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResults.Match; @@ -50,6 +39,18 @@ import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; import jalview.util.MappingUtils; import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; + +import java.awt.BorderLayout; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Panel; +import java.awt.Point; +import java.awt.event.InputEvent; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.util.Vector; public class SeqPanel extends Panel implements MouseMotionListener, MouseListener, SequenceListener, SelectionListener @@ -431,8 +432,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, } else { - residue = "X".equalsIgnoreCase(displayChar) ? "X" - : ResidueProperties.aa2Triplet.get(displayChar); + residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*" + .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet + .get(displayChar)); if (residue != null) { text.append(" Residue: ").append(residue); @@ -445,36 +447,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, pos = sequence.findPosition(res); text.append(" (").append(Integer.toString(pos)).append(")"); } - // Object obj = null; - // if (av.getAlignment().isNucleotide()) - // { - // obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) - // + ""); - // if (obj != null) - // { - // text.append(" Nucleotide: "); - // } - // } - // else - // { - // obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); - // if (obj != null) - // { - // text.append(" Residue: "); - // } - // } - // - // if (obj != null) - // { - // - // if (obj != "") - // { - // text.append(obj + " (" + sequence.findPosition(res) + ")"); - // } - // } ap.alignFrame.statusBar.setText(text.toString()); - } /** @@ -482,25 +456,40 @@ public class SeqPanel extends Panel implements MouseMotionListener, * search results. * * @param results + * @return true if results were matched, false if not */ - private void setStatusMessage(SearchResults results) + private boolean setStatusMessage(SearchResults results) { - List matches = results.getResults(); - if (!matches.isEmpty()) + AlignmentI al = this.av.getAlignment(); + int sequenceIndex = al.findIndex(results); + if (sequenceIndex == -1) + { + return false; + } + SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence(); + for (Match m : results.getResults()) { - Match m = matches.get(0); SequenceI seq = m.getSequence(); - int sequenceIndex = this.av.getAlignment().findIndex(seq); + if (seq.getDatasetSequence() != null) + { + seq = seq.getDatasetSequence(); + } - /* - * Convert position in sequence (base 1) to sequence character array index - * (base 0) - */ - int start = m.getStart() - 1; - setStatusMessage(seq, start, sequenceIndex); + if (seq == ds) + { + /* + * Convert position in sequence (base 1) to sequence character array + * index (base 0) + */ + int start = m.getStart() - m.getSequence().getStart(); + setStatusMessage(seq, start, sequenceIndex); + return true; + } } + return false; } + @Override public void mousePressed(MouseEvent evt) { lastMousePress = evt.getPoint(); @@ -551,6 +540,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, return; } + @Override public void mouseClicked(MouseEvent evt) { SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt)); @@ -576,14 +566,15 @@ public class SeqPanel extends Panel implements MouseMotionListener, } if (features != null && features.length > 0) { - seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[] - { sequence }, features, false, ap); + seqCanvas.getFeatureRenderer().amendFeatures( + new SequenceI[] { sequence }, features, false, ap); seqCanvas.highlightSearchResults(null); } } } + @Override public void mouseReleased(MouseEvent evt) { mouseDragging = false; @@ -619,8 +610,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } int cHeight = av.getAlignment().getHeight() * av.getCharHeight() - + hgap - + seqCanvas.getAnnotationHeight(); + + hgap + seqCanvas.getAnnotationHeight(); int y = evt.getY(); y -= hgap; @@ -677,8 +667,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } int cHeight = av.getAlignment().getHeight() * av.getCharHeight() - + hgap - + seqCanvas.getAnnotationHeight(); + + hgap + seqCanvas.getAnnotationHeight(); y -= hgap; @@ -729,6 +718,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, String lastMessage; + @Override public void mouseOverSequence(SequenceI sequence, int index, int pos) { String tmp = sequence.hashCode() + index + ""; @@ -740,9 +730,10 @@ public class SeqPanel extends Panel implements MouseMotionListener, lastMessage = tmp; } + @Override public void highlightSequence(SearchResults results) { - if (av.followHighlight) + if (av.isFollowHighlight()) { if (ap.scrollToPosition(results, true)) { @@ -760,12 +751,14 @@ public class SeqPanel extends Panel implements MouseMotionListener, return this.ap == null ? null : this.ap.av; } + @Override public void updateColours(SequenceI seq, int index) { System.out.println("update the seqPanel colours"); // repaint(); } + @Override public void mouseMoved(MouseEvent evt) { int res = findRes(evt); @@ -812,8 +805,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, } else { - obj = "X".equalsIgnoreCase(ch) ? "X" - : ResidueProperties.aa2Triplet.get(ch); + obj = "X".equalsIgnoreCase(ch) ? "X" : ResidueProperties.aa2Triplet + .get(ch); if (obj != null) { text.append(" Residue: ").append(obj); @@ -897,13 +890,15 @@ public class SeqPanel extends Panel implements MouseMotionListener, for (int i = 0; i < features.length; i++) { if (av.getFeaturesDisplayed() == null - || !av.getFeaturesDisplayed().isVisible(features[i].getType())) + || !av.getFeaturesDisplayed().isVisible( + features[i].getType())) { continue; } if (features[i].featureGroup != null - && !seqCanvas.fr.checkGroupVisibility(features[i].featureGroup,false)) + && !seqCanvas.fr.checkGroupVisibility( + features[i].featureGroup, false)) { continue; } @@ -924,6 +919,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, Tooltip tooltip; + @Override public void mouseDragged(MouseEvent evt) { if (mouseWheelPressed) @@ -1059,8 +1055,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (editCommand == null) { editCommand = new EditCommand(MessageManager.formatMessage( - "label.edit_params", new String[] - { label })); + "label.edit_params", new String[] { label })); } } @@ -1294,14 +1289,14 @@ public class SeqPanel extends Panel implements MouseMotionListener, { for (int j = lastres; j < startres; j++) { - insertChar(j, new SequenceI[] - { seq }, fixedRight); + insertChar(j, new SequenceI[] { seq }, fixedRight); } } else { - editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[] - { seq }, lastres, startres - lastres, av.getAlignment(), true); + editCommand.appendEdit(Action.INSERT_GAP, + new SequenceI[] { seq }, lastres, startres - lastres, + av.getAlignment(), true); } } else @@ -1316,8 +1311,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, endEditing(); break; } - deleteChar(startres, new SequenceI[] - { seq }, fixedRight); + deleteChar(startres, new SequenceI[] { seq }, fixedRight); } } else @@ -1335,8 +1329,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (max > 0) { - editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[] - { seq }, startres, max, av.getAlignment(), true); + editCommand.appendEdit(Action.DELETE_GAP, + new SequenceI[] { seq }, startres, max, + av.getAlignment(), true); } } } @@ -1672,6 +1667,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, seqCanvas.repaint(); } + @Override public void mouseEntered(MouseEvent e) { if (oldSeq < 0) @@ -1686,6 +1682,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } } + @Override public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) @@ -1745,6 +1742,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, running = false; } + @Override public void run() { running = true; @@ -1789,6 +1787,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, /** * modify current selection according to a received message. */ + @Override public void selection(SequenceGroup seqsel, ColumnSelection colsel, SelectionSource source) { @@ -1797,7 +1796,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, // TODO: extend config options to allow user to control if selections may be // shared between viewports. if (av != null - && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignViewport) source) + && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignmentViewport) source) .getSequenceSetId().equals(av.getSequenceSetId())))) { return; @@ -1834,7 +1833,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, sgroup = seqsel.intersect(av.getAlignment(), (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); if ((sgroup == null || sgroup.getSize() == 0) - && (colsel == null || colsel.size() == 0)) + && (colsel == null || colsel.isEmpty())) { // don't copy columns if the region didn't intersect. copycolsel = false; @@ -1856,7 +1855,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, { // the current selection is unset or from a previous message // so import the new colsel. - if (colsel == null || colsel.size() == 0) + if (colsel == null || colsel.isEmpty()) { if (av.getColumnSelection() != null) { @@ -1941,22 +1940,24 @@ public class SeqPanel extends Panel implements MouseMotionListener, protected boolean selectionFromTranslation(SequenceGroup seqsel, ColumnSelection colsel, SelectionSource source) { - if (!(source instanceof AlignViewportI)) { + if (!(source instanceof AlignViewportI)) + { return false; } final AlignViewportI sourceAv = (AlignViewportI) source; - if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv) + if (sourceAv.getCodingComplement() != av + && av.getCodingComplement() != sourceAv) { return false; } - + /* * Map sequence selection */ SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av); av.setSelectionGroup(sg); av.isSelectionGroupChanged(true); - + /* * Map column selection */ @@ -1964,10 +1965,10 @@ public class SeqPanel extends Panel implements MouseMotionListener, av); av.setColumnSelection(cs); av.isColSelChanged(true); - + ap.scalePanelHolder.repaint(); ap.repaint(); - + return true; }