X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=ae4ae109d79173a5d5aac997ae3be802ca2aec6b;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=e488a32b7ca7d7285d7e4203385d7a96fe5aee38;hpb=10e637daad8983c41db8679baabea5563d7371f4;p=jalview.git diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index e488a32..ae4ae10 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -20,33 +20,39 @@ */ 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.ColumnSelection; import jalview.datamodel.SearchResults; +import jalview.datamodel.SearchResults.Match; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.schemes.ResidueProperties; +import jalview.structure.SelectionListener; import jalview.structure.SelectionSource; import jalview.structure.SequenceListener; import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; +import jalview.util.MappingUtils; import jalview.util.MessageManager; -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 + MouseListener, SequenceListener, SelectionListener { public SeqCanvas seqCanvas; @@ -109,6 +115,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, seqCanvas.addMouseListener(this); ssm = StructureSelectionManager.getStructureSelectionManager(av.applet); ssm.addStructureViewerListener(this); + ssm.addSelectionListener(this); seqCanvas.repaint(); } @@ -159,8 +166,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, void setCursorPosition() { - SequenceI sequence = av.getAlignment().getSequenceAt( - seqCanvas.cursorY); + SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1; scrollToVisible(); @@ -212,7 +218,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } endEditing(); - if (av.wrapAlignment) + if (av.getWrapAlignment()) { ap.scrollToWrappedVisible(seqCanvas.cursorX); } @@ -252,8 +258,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, void setSelectionAreaAtCursor(boolean topLeft) { - SequenceI sequence = av.getAlignment().getSequenceAt( - seqCanvas.cursorY); + SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); if (av.getSelectionGroup() != null) { @@ -393,41 +398,107 @@ public class SeqPanel extends Panel implements MouseMotionListener, return 1; } + /** + * Set status message in alignment panel + * + * @param sequence + * aligned sequence object + * @param res + * alignment column + * @param seq + * index of sequence in alignment + * @return position of res in sequence + */ void setStatusMessage(SequenceI sequence, int res, int seq) { - StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " - + sequence.getName()); - - Object obj = null; + // TODO remove duplication of identical gui method + StringBuilder text = new StringBuilder(32); + String seqno = seq == -1 ? "" : " " + (seq + 1); + text.append("Sequence" + seqno + " ID: " + sequence.getName()); + + 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) - { - text.append(" Residue: "); - } - } + residue = "X".equalsIgnoreCase(displayChar) ? "X" + : ResidueProperties.aa2Triplet.get(displayChar); + if (residue != null) + { + text.append(" Residue: ").append(residue); + } + } + + int pos = -1; + if (residue != null) + { + 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) + ")"); + // } + // } - if (obj != null) - { + ap.alignFrame.statusBar.setText(text.toString()); - if (obj != "") - { - text.append(obj + " (" + sequence.findPosition(res) + ")"); - } - } + } - ap.alignFrame.statusBar.setText(text.toString()); + /** + * Set the status bar message to highlight the first matched position in + * search results. + * + * @param results + */ + private void setStatusMessage(SearchResults results) + { + List matches = results.getResults(); + if (!matches.isEmpty()) + { + Match m = matches.get(0); + SequenceI seq = m.getSequence(); + int sequenceIndex = this.av.getAlignment().findIndex(seq); + /* + * Convert position in sequence (base 1) to sequence character array index + * (base 0) + */ + int start = m.getStart() - 1; + setStatusMessage(seq, start, sequenceIndex); + } } public void mousePressed(MouseEvent evt) @@ -538,16 +609,17 @@ public class SeqPanel extends Panel implements MouseMotionListener, 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(); @@ -596,15 +668,16 @@ public class SeqPanel extends Panel implements MouseMotionListener, 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; @@ -676,10 +749,17 @@ public class SeqPanel extends Panel implements MouseMotionListener, ap.alignFrame.repaint(); } } + setStatusMessage(results); seqCanvas.highlightSearchResults(results); } + @Override + public VamsasSource getVamsasSource() + { + return this.ap == null ? null : this.ap.av; + } + public void updateColours(SequenceI seq, int index) { System.out.println("update the seqPanel colours"); @@ -716,39 +796,38 @@ public class SeqPanel extends Panel implements MouseMotionListener, mouseOverSequence(sequence, res, respos); } - StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " - + sequence.getName()); + StringBuilder text = new StringBuilder(); + text.append("Sequence ").append(Integer.toString(seq + 1)) + .append(" ID: ").append(sequence.getName()); - Object obj = null; + String obj = null; + final String ch = String.valueOf(sequence.getCharAt(res)); if (av.getAlignment().isNucleotide()) { - obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) - + ""); + obj = ResidueProperties.nucleotideName.get(ch); if (obj != null) { - text.append(" Nucleotide: "); + text.append(" Nucleotide: ").append(obj); } } else { - obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); + obj = "X".equalsIgnoreCase(ch) ? "X" + : ResidueProperties.aa2Triplet.get(ch); if (obj != null) { - text.append(" Residue: "); + text.append(" Residue: ").append(obj); } } if (obj != null) { - if (obj != "") - { - text.append(obj + " (" + respos + ")"); - } + text.append(" (").append(Integer.toString(respos)).append(")"); } ap.alignFrame.statusBar.setText(text.toString()); - StringBuffer tooltipText = new StringBuffer(); + StringBuilder tooltipText = new StringBuilder(); SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence); if (groups != null) { @@ -759,7 +838,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (!groups[g].getName().startsWith("JTreeGroup") && !groups[g].getName().startsWith("JGroup")) { - tooltipText.append(groups[g].getName() + " "); + tooltipText.append(groups[g].getName()).append(" "); } if (groups[g].getDescription() != null) { @@ -849,7 +928,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, { if (mouseWheelPressed) { - int oldWidth = av.charWidth; + int oldWidth = av.getCharWidth(); // Which is bigger, left-right or up-down? if (Math.abs(evt.getY() - lastMousePress.y) > Math.abs(evt.getX() @@ -857,7 +936,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, { int fontSize = av.font.getSize(); - if (evt.getY() < lastMousePress.y && av.charHeight > 1) + if (evt.getY() < lastMousePress.y && av.getCharHeight() > 1) { fontSize--; } @@ -872,29 +951,29 @@ public class SeqPanel extends Panel implements MouseMotionListener, } av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize)); - av.charWidth = oldWidth; + av.setCharWidth(oldWidth); } else { - if (evt.getX() < lastMousePress.x && av.charWidth > 1) + if (evt.getX() < lastMousePress.x && av.getCharWidth() > 1) { - av.charWidth--; + av.setCharWidth(av.getCharWidth() - 1); } else if (evt.getX() > lastMousePress.x) { - av.charWidth++; + av.setCharWidth(av.getCharWidth() + 1); } - if (av.charWidth < 1) + if (av.getCharWidth() < 1) { - av.charWidth = 1; + av.setCharWidth(1); } } ap.fontChanged(); FontMetrics fm = getFontMetrics(av.getFont()); - av.validCharWidth = fm.charWidth('M') <= av.charWidth; + av.validCharWidth = fm.charWidth('M') <= av.getCharWidth(); lastMousePress = evt.getPoint(); @@ -960,15 +1039,18 @@ public class SeqPanel extends Panel implements MouseMotionListener, StringBuffer message = new StringBuffer(); if (groupEditing) { - message.append(MessageManager.getString("action.edit_group")).append(":"); + message.append(MessageManager.getString("action.edit_group")).append( + ":"); if (editCommand == null) { - editCommand = new EditCommand(MessageManager.getString("action.edit_group")); + editCommand = new EditCommand( + MessageManager.getString("action.edit_group")); } } else { - message.append(MessageManager.getString("label.edit_sequence")).append(" " + seq.getName()); + message.append(MessageManager.getString("label.edit_sequence")) + .append(" " + seq.getName()); String label = seq.getName(); if (label.length() > 10) { @@ -976,7 +1058,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, } if (editCommand == null) { - editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label})); + editCommand = new EditCommand(MessageManager.formatMessage( + "label.edit_params", new String[] + { label })); } } @@ -1178,8 +1262,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, } else { - editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, - startres, startres - lastres, av.getAlignment(), true); + editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, startres, + startres - lastres, av.getAlignment(), true); } } else @@ -1194,8 +1278,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, } else { - editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, - startres, lastres - startres, av.getAlignment(), true); + editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, startres, + lastres - startres, av.getAlignment(), true); } } @@ -1290,16 +1374,16 @@ public class SeqPanel extends Panel implements MouseMotionListener, editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1, av.getAlignment(), true); - editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, - av.getAlignment(), true); + editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(), + true); } void deleteChar(int j, SequenceI[] seq, int fixedColumn) { - editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, - av.getAlignment(), true); + editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, av.getAlignment(), + true); editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1, av.getAlignment(), true); @@ -1378,7 +1462,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, SequenceFeature[] allFeatures = findFeaturesAtRes(sequence, sequence.findPosition(res)); - Vector links = null; + Vector links = null; if (allFeatures != null) { for (int i = 0; i < allFeatures.length; i++) @@ -1387,7 +1471,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, { if (links == null) { - links = new Vector(); + links = new Vector(); } for (int j = 0; j < allFeatures[i].links.size(); j++) { @@ -1718,6 +1802,16 @@ public class SeqPanel extends Panel implements MouseMotionListener, { 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 @@ -1835,4 +1929,46 @@ public class SeqPanel extends Panel implements MouseMotionListener, ap.scrollTo(column, column, ap.av.startSeq, true, true); } + /** + * 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); + + ap.scalePanelHolder.repaint(); + ap.repaint(); + + return true; + } + }