X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=bd8bb7cae1bbc623bb6c15ffe48222a5bbbf73b8;hb=e07fc11d5aaf4d1237d83e5f7ea0909dea09902e;hp=4a43798975f89f99535fcf4f1523567d638e7a78;hpb=913c7db3eaf97959bcd34a7e96b64632b622edc8;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 4a43798..bd8bb7c 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -20,8 +20,10 @@ */ package jalview.gui; +import jalview.api.AlignViewportI; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; +import jalview.commands.EditCommand.Edit; import jalview.datamodel.ColumnSelection; import jalview.datamodel.SearchResults; import jalview.datamodel.Sequence; @@ -34,7 +36,11 @@ import jalview.structure.SelectionListener; import jalview.structure.SelectionSource; 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; @@ -245,22 +251,33 @@ public class SeqPanel extends JPanel implements MouseListener, return seq; } + /** + * 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. + */ void endEditing() { - if (editCommand != null && editCommand.getSize() > 0) + try + { + if (editCommand != null && editCommand.getSize() > 0) + { + ap.alignFrame.addHistoryItem(editCommand); + av.firePropertyChange("alignment", null, av.getAlignment() + .getSequences()); + } + } finally { - ap.alignFrame.addHistoryItem(editCommand); - av.firePropertyChange("alignment", null, av.getAlignment() - .getSequences()); + /* + * Tidy up come what may... + */ + startseq = -1; + lastres = -1; + editingSeqs = false; + groupEditing = false; + keyboardNo1 = null; + keyboardNo2 = null; + editCommand = null; } - - startseq = -1; - lastres = -1; - editingSeqs = false; - groupEditing = false; - keyboardNo1 = null; - keyboardNo2 = null; - editCommand = null; } void setCursorRow() @@ -640,6 +657,11 @@ public class SeqPanel extends JPanel implements MouseListener, } @Override + public VamsasSource getVamsasSource() + { + return this.ap == null ? null : this.ap.av; + } + @Override public void updateColours(SequenceI seq, int index) { System.out.println("update the seqPanel colours"); @@ -777,35 +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; @@ -926,7 +949,7 @@ public class SeqPanel extends JPanel implements MouseListener, } } - StringBuffer message = new StringBuffer(); + StringBuilder message = new StringBuilder(64); if (groupEditing) { message.append("Edit group:"); @@ -1151,8 +1174,8 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, - startres, startres - lastres, av.getAlignment(), true); + appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres + - lastres); } } else @@ -1167,8 +1190,8 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, - startres, lastres - startres, av.getAlignment(), true); + appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres + - startres); } } @@ -1189,8 +1212,8 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[] - { seq }, lastres, startres - lastres, av.getAlignment(), true); + appendEdit(Action.INSERT_GAP, new SequenceI[] + { seq }, lastres, startres - lastres); } } else @@ -1202,7 +1225,7 @@ public class SeqPanel extends JPanel implements MouseListener, { for (int j = lastres; j > startres; j--) { - if (!jalview.util.Comparison.isGap(seq.getCharAt(startres))) + if (!Comparison.isGap(seq.getCharAt(startres))) { endEditing(); break; @@ -1217,7 +1240,7 @@ public class SeqPanel extends JPanel implements MouseListener, int max = 0; for (int m = startres; m < lastres; m++) { - if (!jalview.util.Comparison.isGap(seq.getCharAt(m))) + if (!Comparison.isGap(seq.getCharAt(m))) { break; } @@ -1226,9 +1249,8 @@ public class SeqPanel extends JPanel implements MouseListener, if (max > 0) { - editCommand.appendEdit(Action.DELETE_GAP, - new SequenceI[] - { seq }, startres, max, av.getAlignment(), true); + appendEdit(Action.DELETE_GAP, new SequenceI[] + { seq }, startres, max); } } } @@ -1244,8 +1266,8 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - editCommand.appendEdit(Action.INSERT_NUC, new SequenceI[] - { seq }, lastres, startres - lastres, av.getAlignment(), true); + appendEdit(Action.INSERT_NUC, new SequenceI[] + { seq }, lastres, startres - lastres); } } } @@ -1280,22 +1302,37 @@ public class SeqPanel extends JPanel implements MouseListener, } } - editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1, - av.getAlignment(), true); + appendEdit(Action.DELETE_GAP, seq, blankColumn, 1); - editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, - av.getAlignment(), true); + appendEdit(Action.INSERT_GAP, seq, j, 1); } + /** + * Helper method to add and perform one edit action. + * + * @param action + * @param seq + * @param pos + * @param count + */ + protected void appendEdit(Action action, SequenceI[] seq, int pos, + int count) + { + + final Edit edit = new EditCommand().new Edit(action, seq, pos, count, + av.getAlignment().getGapCharacter()); + + editCommand.appendEdit(edit, av.getAlignment(), + true, null); + } + void deleteChar(int j, SequenceI[] seq, int fixedColumn) { - editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, - av.getAlignment(), true); + appendEdit(Action.DELETE_GAP, seq, j, 1); - editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1, - av.getAlignment(), true); + appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1); } /** @@ -1801,52 +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 @@ -1874,6 +1927,7 @@ public class SeqPanel extends JPanel implements MouseListener, av.isColSelChanged(true); repaint = true; } + if (copycolsel && av.hasHiddenColumns() && (av.getColumnSelection() == null || av.getColumnSelection() @@ -1881,11 +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; + } }