X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=6ca9499618fec362038f5999f4aaf01c822d99a5;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=700f82d4ebdb4a1d0f14794fd9f97475413b721d;hpb=c97f556291e878a0c8e82ebf521a07f67c90234a;p=jalview.git diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index 700f82d..6ca9499 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -432,8 +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); @@ -446,36 +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()); - } /** @@ -497,6 +470,10 @@ public class SeqPanel extends Panel implements MouseMotionListener, for (Match m : results.getResults()) { SequenceI seq = m.getSequence(); + if (seq.getDatasetSequence() != null) + { + seq = seq.getDatasetSequence(); + } if (seq == ds) { @@ -504,7 +481,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, * Convert position in sequence (base 1) to sequence character array * index (base 0) */ - int start = m.getStart() - 1; + int start = m.getStart() - m.getSequence().getStart(); setStatusMessage(seq, start, sequenceIndex); return true; } @@ -512,6 +489,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, return false; } + @Override public void mousePressed(MouseEvent evt) { lastMousePress = evt.getPoint(); @@ -562,6 +540,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, return; } + @Override public void mouseClicked(MouseEvent evt) { SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt)); @@ -587,14 +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; @@ -630,8 +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; @@ -688,8 +667,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } int cHeight = av.getAlignment().getHeight() * av.getCharHeight() - + hgap - + seqCanvas.getAnnotationHeight(); + + hgap + seqCanvas.getAnnotationHeight(); y -= hgap; @@ -740,6 +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 + ""; @@ -751,6 +730,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, lastMessage = tmp; } + @Override public void highlightSequence(SearchResults results) { if (av.isFollowHighlight()) @@ -771,12 +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); @@ -823,8 +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); @@ -908,13 +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; } @@ -935,6 +919,15 @@ public class SeqPanel extends Panel implements MouseMotionListener, Tooltip tooltip; + /** + * set when the current UI interaction has resulted in a change that requires + * overview shading to be recalculated. this could be changed to something + * more expressive that indicates what actually has changed, so selective + * redraws can be applied + */ + private boolean needOverviewUpdate; // TODO: refactor to avcontroller + + @Override public void mouseDragged(MouseEvent evt) { if (mouseWheelPressed) @@ -1070,8 +1063,7 @@ 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 })); } } @@ -1305,14 +1297,14 @@ 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 @@ -1327,8 +1319,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, endEditing(); break; } - deleteChar(startres, new SequenceI[] - { seq }, fixedRight); + deleteChar(startres, new SequenceI[] { seq }, fixedRight); } } else @@ -1346,8 +1337,9 @@ 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); } } } @@ -1537,9 +1529,11 @@ public class SeqPanel extends Panel implements MouseMotionListener, { return; } - - stretchGroup.recalcConservation(); // always do this - annotation has own - // state + // always do this - annotation has own state + // but defer colourscheme update until hidden sequences are passed in + boolean vischange = stretchGroup.recalcConservation(true); + // here we rely on stretchGroup == av.getSelection() + needOverviewUpdate |= vischange && av.isSelectionDefinedGroup(); if (stretchGroup.cs != null) { stretchGroup.cs.alignmentChanged(stretchGroup, @@ -1556,11 +1550,12 @@ public class SeqPanel extends Panel implements MouseMotionListener, stretchGroup.getName()); } } + PaintRefresher.Refresh(ap, av.getSequenceSetId()); + ap.paintAlignment(needOverviewUpdate); + needOverviewUpdate = false; changeEndRes = false; changeStartRes = false; stretchGroup = null; - PaintRefresher.Refresh(ap, av.getSequenceSetId()); - ap.paintAlignment(true); av.sendSelection(); } @@ -1612,6 +1607,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (res > (stretchGroup.getStartRes() - 1)) { stretchGroup.setEndRes(res); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } else if (changeStartRes) @@ -1619,6 +1615,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (res < (stretchGroup.getEndRes() + 1)) { stretchGroup.setStartRes(res); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } @@ -1652,6 +1649,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (stretchGroup.getSequences(null).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } else { @@ -1661,6 +1659,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } stretchGroup.addSequence(nextSeq, false); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } @@ -1683,6 +1682,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, seqCanvas.repaint(); } + @Override public void mouseEntered(MouseEvent e) { if (oldSeq < 0) @@ -1697,6 +1697,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } } + @Override public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) @@ -1756,6 +1757,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, running = false; } + @Override public void run() { running = true; @@ -1800,6 +1802,7 @@ 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) { @@ -1825,9 +1828,12 @@ public class SeqPanel extends Panel implements MouseMotionListener, // do we want to thread this ? (contention with seqsel and colsel locks, I // suspect) - // rules are: colsel is copied if there is a real intersection between - // sequence selection - boolean repaint = false, copycolsel = true; + /* + * only copy colsel if there is a real intersection between + * sequence selection and this panel's alignment + */ + boolean repaint = false; + boolean copycolsel = false; if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true)) { SequenceGroup sgroup = null; @@ -1844,11 +1850,9 @@ 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)) + if ((sgroup != null && sgroup.getSize() > 0)) { - // don't copy columns if the region didn't intersect. - copycolsel = false; + copycolsel = true; } } if (sgroup != null && sgroup.getSize() > 0) @@ -1867,7 +1871,7 @@ 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) { @@ -1952,33 +1956,34 @@ 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 */ ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv, av); av.setColumnSelection(cs); - av.isColSelChanged(true); - + ap.scalePanelHolder.repaint(); ap.repaint(); - + return true; }