X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=bd8bb7cae1bbc623bb6c15ffe48222a5bbbf73b8;hb=dd81a4ab9d1ffc6168e7a041c7d488db37298cce;hp=2c9b7f6787de8a59f2bb3ce1e02a83642e71087b;hpb=2a4301b8fdda9f4e9d77473402d9b91b51009735;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 2c9b7f6..bd8bb7c 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.api.AlignViewportI; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.commands.EditCommand.Edit; @@ -37,7 +38,9 @@ import jalview.structure.SequenceListener; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; import jalview.util.Comparison; +import jalview.util.MappingUtils; import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; import java.awt.BorderLayout; import java.awt.Color; @@ -168,16 +171,17 @@ public class SeqPanel extends JPanel implements MouseListener, int res = 0; int x = evt.getX(); - if (av.wrapAlignment) + if (av.getWrapAlignment()) { - int hgap = av.charHeight; - if (av.scaleAboveWrapped) + int hgap = av.getCharHeight(); + if (av.getScaleAboveWrapped()) { - hgap += av.charHeight; + hgap += av.getCharHeight(); } - int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + + hgap + seqCanvas.getAnnotationHeight(); int y = evt.getY(); @@ -221,15 +225,16 @@ public class SeqPanel extends JPanel implements MouseListener, int seq = 0; int y = evt.getY(); - if (av.wrapAlignment) + if (av.getWrapAlignment()) { - int hgap = av.charHeight; - if (av.scaleAboveWrapped) + int hgap = av.getCharHeight(); + if (av.getScaleAboveWrapped()) { - hgap += av.charHeight; + hgap += av.getCharHeight(); } - int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + + hgap + seqCanvas.getAnnotationHeight(); y -= hgap; @@ -246,44 +251,6 @@ public class SeqPanel extends JPanel implements MouseListener, return seq; } - SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res) - { - Vector tmp = new Vector(); - SequenceFeature[] features = sequence.getSequenceFeatures(); - if (features != null) - { - for (int i = 0; i < features.length; i++) - { - if (av.featuresDisplayed == null - || !av.featuresDisplayed.containsKey(features[i].getType())) - { - continue; - } - - if (features[i].featureGroup != null - && seqCanvas.fr.featureGroups != null - && seqCanvas.fr.featureGroups - .containsKey(features[i].featureGroup) - && !((Boolean) seqCanvas.fr.featureGroups - .get(features[i].featureGroup)).booleanValue()) - { - continue; - } - - if ((features[i].getBegin() <= res) - && (features[i].getEnd() >= res)) - { - tmp.addElement(features[i]); - } - } - } - - features = new SequenceFeature[tmp.size()]; - tmp.copyInto(features); - - return features; - } - /** * When all of a sequence of edits are complete, put the resulting edit list * on the history stack (undo list), and reset flags for editing in progress. @@ -394,7 +361,7 @@ public class SeqPanel extends JPanel implements MouseListener, } endEditing(); - if (av.wrapAlignment) + if (av.getWrapAlignment()) { ap.scrollToWrappedVisible(seqCanvas.cursorX); } @@ -408,7 +375,7 @@ public class SeqPanel extends JPanel implements MouseListener, { ap.scrollUp(false); } - if (!av.wrapAlignment) + if (!av.getWrapAlignment()) { while (seqCanvas.cursorX < av.getColumnSelection() .adjustForHiddenColumns(av.startRes)) @@ -663,6 +630,7 @@ public class SeqPanel extends JPanel implements MouseListener, String lastMessage; + @Override public void mouseOverSequence(SequenceI sequence, int index, int pos) { String tmp = sequence.hashCode() + " " + index + " " + pos; @@ -693,6 +661,7 @@ public class SeqPanel extends JPanel implements MouseListener, { return this.ap == null ? null : this.ap.av; } + @Override public void updateColours(SequenceI seq, int index) { System.out.println("update the seqPanel colours"); @@ -760,14 +729,14 @@ public class SeqPanel extends JPanel implements MouseListener, } // use aa to see if the mouse pointer is on a - if (av.showSequenceFeatures) + if (av.isShowSequenceFeatures()) { int rpos; - SequenceFeature[] features = findFeaturesAtRes( + List features = ap.getFeatureRenderer().findFeaturesAtRes( sequence.getDatasetSequence(), rpos = sequence.findPosition(res)); seqARep.appendFeatures(tooltipText, rpos, features, - this.ap.seqPanel.seqCanvas.fr.minmax); + this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } if (tooltipText.length() == 6) // { @@ -830,35 +799,36 @@ public class SeqPanel extends JPanel implements MouseListener, int setStatusMessage(SequenceI sequence, int res, int seq) { int pos = -1; - StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " - + sequence.getName()); + StringBuilder text = new StringBuilder(32); + text.append("Sequence " + (seq + 1) + " ID: " + sequence.getName()); - Object obj = null; + String residue = null; + /* + * Try to translate the display character to residue name (null for gap). + */ + final String displayChar = String.valueOf(sequence.getCharAt(res)); if (av.getAlignment().isNucleotide()) { - obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) - + ""); - if (obj != null) + residue = ResidueProperties.nucleotideName.get(displayChar); + if (residue != null) { - text.append(" Nucleotide: "); + text.append(" Nucleotide: ").append(residue); } } else { - obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); - if (obj != null) + residue = "X".equalsIgnoreCase(displayChar) ? "STOP" + : ResidueProperties.aa2Triplet.get(displayChar); + if (residue != null) { - text.append(" Residue: "); + text.append(" Residue: ").append(residue); } } - if (obj != null) + if (residue != null) { pos = sequence.findPosition(res); - if (obj != "") - { - text.append(obj + " (" + pos + ")"); - } + text.append(" (").append(Integer.toString(pos)).append(")"); } ap.alignFrame.statusBar.setText(text.toString()); return pos; @@ -875,7 +845,7 @@ public class SeqPanel extends JPanel implements MouseListener, { if (mouseWheelPressed) { - int oldWidth = av.charWidth; + int oldWidth = av.getCharWidth(); // Which is bigger, left-right or up-down? if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt @@ -898,25 +868,25 @@ public class SeqPanel extends JPanel implements MouseListener, } av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize)); - av.charWidth = oldWidth; + av.setCharWidth(oldWidth); ap.fontChanged(); } else { - if (evt.getX() < lastMousePress.getX() && av.charWidth > 1) + if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1) { - av.charWidth--; + av.setCharWidth(av.getCharWidth() - 1); } else if (evt.getX() > lastMousePress.getX()) { - av.charWidth++; + av.setCharWidth(av.getCharWidth() + 1); } ap.paintAlignment(false); } FontMetrics fm = getFontMetrics(av.getFont()); - av.validCharWidth = fm.charWidth('M') <= av.charWidth; + av.validCharWidth = fm.charWidth('M') <= av.getCharWidth(); lastMousePress = evt.getPoint(); @@ -1420,21 +1390,21 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(null); } - SequenceFeature[] features = findFeaturesAtRes( + List features = seqCanvas.getFeatureRenderer().findFeaturesAtRes( sequence.getDatasetSequence(), sequence.findPosition(findRes(evt))); - if (features != null && features.length > 0) + if (features != null && features.size()> 0) { SearchResults highlight = new SearchResults(); - highlight.addResult(sequence, features[0].getBegin(), - features[0].getEnd()); + highlight.addResult(sequence, features.get(0).getBegin(), + features.get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); } - if (features != null && features.length > 0) + if (features != null && features.size()> 0) { seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[] - { sequence }, features, false, ap); + { sequence }, features.toArray(new SequenceFeature[features.size()]), false, ap); seqCanvas.highlightSearchResults(null); } @@ -1485,7 +1455,7 @@ public class SeqPanel extends JPanel implements MouseListener, startWrapBlock = wrappedBlock; - if (av.wrapAlignment && seq > av.getAlignment().getHeight()) + if (av.getWrapAlignment() && seq > av.getAlignment().getHeight()) { JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.cannot_edit_annotations_in_wrapped_view"), @@ -1549,16 +1519,16 @@ public class SeqPanel extends JPanel implements MouseListener, if (javax.swing.SwingUtilities.isRightMouseButton(evt)) { - SequenceFeature[] allFeatures = findFeaturesAtRes( + List allFeatures = ap.getFeatureRenderer().findFeaturesAtRes( sequence.getDatasetSequence(), sequence.findPosition(res)); Vector links = new Vector(); - for (int i = 0; i < allFeatures.length; i++) + for (SequenceFeature sf:allFeatures) { - if (allFeatures[i].links != null) + if (sf.links != null) { - for (int j = 0; j < allFeatures[i].links.size(); j++) + for (int j = 0; j < sf.links.size(); j++) { - links.addElement(allFeatures[i].links.elementAt(j)); + links.addElement(sf.links.elementAt(j)); } } } @@ -1868,52 +1838,68 @@ public class SeqPanel extends JPanel implements MouseListener, // handles selection messages... // TODO: extend config options to allow user to control if selections may be // shared between viewports. - if (av == source - || !av.followSelection - || (av.isSelectionGroupChanged(false) || av - .isColSelChanged(false)) - || (source instanceof AlignViewport && ((AlignViewport) source) - .getSequenceSetId().equals(av.getSequenceSetId()))) + boolean iSentTheSelection = (av == source + || (source instanceof AlignViewport && ((AlignmentViewport) source) + .getSequenceSetId().equals(av.getSequenceSetId()))); + if (iSentTheSelection || !av.followSelection) + { + return; + } + + /* + * Ignore the selection if there is one of our own pending. + */ + if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false)) + { + return; + } + + /* + * Check for selection in a view of which this one is a dna/protein + * complement. + */ + if (selectionFromTranslation(seqsel, colsel, source)) { return; } + // 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; - // if (!av.isSelectionGroupChanged(false)) + boolean repaint = false; + boolean copycolsel = true; + + SequenceGroup sgroup = null; + if (seqsel != null && seqsel.getSize() > 0) { - SequenceGroup sgroup = null; - if (seqsel != null && seqsel.getSize() > 0) + if (av.getAlignment() == null) { - if (av.getAlignment() == null) - { - jalview.bin.Cache.log.warn("alignviewport av SeqSetId=" - + av.getSequenceSetId() + " ViewId=" + av.getViewId() - + " 's alignment is NULL! returning immediatly."); - return; - } - sgroup = seqsel.intersect(av.getAlignment(), - (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); - if ((sgroup == null || sgroup.getSize() == 0) - || (colsel == null || colsel.size() == 0)) - { - // don't copy columns if the region didn't intersect. - copycolsel = false; - } + jalview.bin.Cache.log.warn("alignviewport av SeqSetId=" + + av.getSequenceSetId() + " ViewId=" + av.getViewId() + + " 's alignment is NULL! returning immediately."); + return; } - if (sgroup != null && sgroup.getSize() > 0) + sgroup = seqsel.intersect(av.getAlignment(), + (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); + if ((sgroup == null || sgroup.getSize() == 0) + || (colsel == null || colsel.size() == 0)) { - av.setSelectionGroup(sgroup); + // don't copy columns if the region didn't intersect. + copycolsel = false; } - else - { - av.setSelectionGroup(null); - } - av.isSelectionGroupChanged(true); - repaint = true; } + if (sgroup != null && sgroup.getSize() > 0) + { + av.setSelectionGroup(sgroup); + } + else + { + av.setSelectionGroup(null); + } + av.isSelectionGroupChanged(true); + repaint = true; + if (copycolsel) { // the current selection is unset or from a previous message @@ -1941,6 +1927,7 @@ public class SeqPanel extends JPanel implements MouseListener, av.isColSelChanged(true); repaint = true; } + if (copycolsel && av.hasHiddenColumns() && (av.getColumnSelection() == null || av.getColumnSelection() @@ -1948,11 +1935,52 @@ public class SeqPanel extends JPanel implements MouseListener, { System.err.println("Bad things"); } - if (repaint) + if (repaint) // always true! { // probably finessing with multiple redraws here PaintRefresher.Refresh(this, av.getSequenceSetId()); // ap.paintAlignment(false); } } + + /** + * If this panel is a cdna/protein translation view of the selection source, + * tries to map the source selection to a local one, and returns true. Else + * returns false. + * + * @param seqsel + * @param colsel + * @param source + */ + protected boolean selectionFromTranslation(SequenceGroup seqsel, + ColumnSelection colsel, SelectionSource source) + { + if (!(source instanceof AlignViewportI)) { + return false; + } + final AlignViewportI sourceAv = (AlignViewportI) source; + 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); + + PaintRefresher.Refresh(this, av.getSequenceSetId()); + + return true; + } }