X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=d1fb7dc9d651de9f74829be7a05814300af76a19;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=6cd5b702da5eb37da5e8b1476df8d68722938112;hpb=ed2283c5f54da377a2a2fdbdb7aec75ed7041714;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 6cd5b70..d1fb7dc 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,27 +20,11 @@ */ package jalview.gui; -import java.awt.BorderLayout; -import java.awt.Color; -import java.awt.Font; -import java.awt.FontMetrics; -import java.awt.Point; -import java.awt.event.MouseEvent; -import java.awt.event.MouseListener; -import java.awt.event.MouseMotionListener; -import java.awt.event.MouseWheelEvent; -import java.awt.event.MouseWheelListener; -import java.util.List; -import java.util.Vector; - -import javax.swing.JOptionPane; -import javax.swing.JPanel; -import javax.swing.ToolTipManager; - import jalview.api.AlignViewportI; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.commands.EditCommand.Edit; +import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResults.Match; @@ -60,6 +44,23 @@ import jalview.util.MappingUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Point; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.awt.event.MouseWheelEvent; +import java.awt.event.MouseWheelListener; +import java.util.List; +import java.util.Vector; + +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.ToolTipManager; + /** * DOCUMENT ME! * @@ -128,6 +129,8 @@ public class SeqPanel extends JPanel implements MouseListener, StructureSelectionManager ssm; + SearchResults lastSearchResults; + /** * Creates a new SeqPanel object. * @@ -167,6 +170,13 @@ public class SeqPanel extends JPanel implements MouseListener, int wrappedBlock = -1; + /** + * Returns the aligned sequence position (base 0) at the mouse position, or + * the closest visible one + * + * @param evt + * @return + */ int findRes(MouseEvent evt) { int res = 0; @@ -182,8 +192,7 @@ public class SeqPanel extends JPanel implements MouseListener, } int cHeight = av.getAlignment().getHeight() * av.getCharHeight() - + hgap - + seqCanvas.getAnnotationHeight(); + + hgap + seqCanvas.getAnnotationHeight(); int y = evt.getY(); y -= hgap; @@ -203,13 +212,18 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - if (x > seqCanvas.getWidth() + seqCanvas.getWidth()) + if (x > seqCanvas.getX() + seqCanvas.getWidth()) { // make sure we calculate relative to visible alignment, rather than // right-hand gutter x = seqCanvas.getX() + seqCanvas.getWidth(); } res = (x / av.getCharWidth()) + av.getStartRes(); + if (res > av.getEndRes()) + { + // moused off right + res = av.getEndRes(); + } } if (av.hasHiddenColumns()) @@ -235,8 +249,7 @@ public class SeqPanel extends JPanel implements MouseListener, } int cHeight = av.getAlignment().getHeight() * av.getCharHeight() - + hgap - + seqCanvas.getAnnotationHeight(); + + hgap + seqCanvas.getAnnotationHeight(); y -= hgap; @@ -644,11 +657,30 @@ public class SeqPanel extends JPanel implements MouseListener, lastMessage = tmp; } + /** + * Highlight the mapped region described by the search results object (unless + * unchanged). This supports highlight of protein while mousing over linked + * cDNA and vice versa. The status bar is also updated to show the location of + * the start of the highlighted region. + */ @Override public void highlightSequence(SearchResults results) { + if (results == null || results.equals(lastSearchResults)) + { + return; + } + lastSearchResults = results; + if (av.isFollowHighlight()) { + /* + * if scrollToPosition requires a scroll adjustment, this flag prevents + * another scroll event being propagated back to the originator + * + * @see AlignmentPanel#adjustmentValueChanged + */ + ap.setDontScrollComplement(true); if (ap.scrollToPosition(results, false)) { seqCanvas.revalidate(); @@ -663,6 +695,7 @@ public class SeqPanel extends JPanel implements MouseListener, { return this.ap == null ? null : this.ap.av; } + @Override public void updateColours(SequenceI seq, int index) { @@ -734,9 +767,9 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.isShowSequenceFeatures()) { int rpos; - List features = ap.getFeatureRenderer().findFeaturesAtRes( - sequence.getDatasetSequence(), - rpos = sequence.findPosition(res)); + List features = ap.getFeatureRenderer() + .findFeaturesAtRes(sequence.getDatasetSequence(), + rpos = sequence.findPosition(res)); seqARep.appendFeatures(tooltipText, rpos, features, this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } @@ -823,8 +856,9 @@ public class SeqPanel extends JPanel implements MouseListener, } 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); @@ -849,19 +883,31 @@ public class SeqPanel extends JPanel implements MouseListener, */ private void setStatusMessage(SearchResults results) { - List matches = results.getResults(); - if (!matches.isEmpty()) + AlignmentI al = this.av.getAlignment(); + int sequenceIndex = al.findIndex(results); + if (sequenceIndex == -1) + { + return; + } + 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; + } } } @@ -988,7 +1034,8 @@ public class SeqPanel extends JPanel implements MouseListener, message.append("Edit group:"); if (editCommand == null) { - editCommand = new EditCommand(MessageManager.getString("action.edit_group")); + editCommand = new EditCommand( + MessageManager.getString("action.edit_group")); } } else @@ -1001,7 +1048,8 @@ public class SeqPanel extends JPanel implements MouseListener, } 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 })); } } @@ -1239,14 +1287,13 @@ public class SeqPanel extends JPanel implements MouseListener, { for (int j = lastres; j < startres; j++) { - insertChar(j, new SequenceI[] - { seq }, fixedRight); + insertChar(j, new SequenceI[] { seq }, fixedRight); } } else { - appendEdit(Action.INSERT_GAP, new SequenceI[] - { seq }, lastres, startres - lastres); + appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres, + startres - lastres); } } else @@ -1263,8 +1310,7 @@ public class SeqPanel extends JPanel implements MouseListener, endEditing(); break; } - deleteChar(startres, new SequenceI[] - { seq }, fixedRight); + deleteChar(startres, new SequenceI[] { seq }, fixedRight); } } else @@ -1282,8 +1328,8 @@ public class SeqPanel extends JPanel implements MouseListener, if (max > 0) { - appendEdit(Action.DELETE_GAP, new SequenceI[] - { seq }, startres, max); + appendEdit(Action.DELETE_GAP, new SequenceI[] { seq }, + startres, max); } } } @@ -1293,14 +1339,13 @@ public class SeqPanel extends JPanel implements MouseListener, { for (int j = lastres; j < startres; j++) { - insertChar(j, new SequenceI[] - { seq }, fixedRight); + insertChar(j, new SequenceI[] { seq }, fixedRight); } } else { - appendEdit(Action.INSERT_NUC, new SequenceI[] - { seq }, lastres, startres - lastres); + appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres, + startres - lastres); } } } @@ -1356,8 +1401,7 @@ public class SeqPanel extends JPanel implements MouseListener, final Edit edit = new EditCommand().new Edit(action, seq, pos, count, av.getAlignment().getGapCharacter()); - editCommand.appendEdit(edit, av.getAlignment(), - true, null); + editCommand.appendEdit(edit, av.getAlignment(), true, null); } void deleteChar(int j, SequenceI[] seq, int fixedColumn) @@ -1423,21 +1467,23 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(null); } - List features = seqCanvas.getFeatureRenderer().findFeaturesAtRes( - sequence.getDatasetSequence(), - sequence.findPosition(findRes(evt))); + List features = seqCanvas.getFeatureRenderer() + .findFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(findRes(evt))); - if (features != null && features.size()> 0) + if (features != null && features.size() > 0) { SearchResults highlight = new SearchResults(); - highlight.addResult(sequence, features.get(0).getBegin(), - features.get(0).getEnd()); + highlight.addResult(sequence, features.get(0).getBegin(), features + .get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); } - if (features != null && features.size()> 0) + if (features != null && features.size() > 0) { - seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[] - { sequence }, features.toArray(new SequenceFeature[features.size()]), false, ap); + seqCanvas.getFeatureRenderer().amendFeatures( + new SequenceI[] { sequence }, + features.toArray(new SequenceFeature[features.size()]), + false, ap); seqCanvas.highlightSearchResults(null); } @@ -1552,10 +1598,11 @@ public class SeqPanel extends JPanel implements MouseListener, if (javax.swing.SwingUtilities.isRightMouseButton(evt)) { - List allFeatures = ap.getFeatureRenderer().findFeaturesAtRes( - sequence.getDatasetSequence(), sequence.findPosition(res)); + List allFeatures = ap.getFeatureRenderer() + .findFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(res)); Vector links = new Vector(); - for (SequenceFeature sf:allFeatures) + for (SequenceFeature sf : allFeatures) { if (sf.links != null) { @@ -1871,8 +1918,7 @@ 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. - boolean iSentTheSelection = (av == source - || (source instanceof AlignViewport && ((AlignmentViewport) source) + boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source) .getSequenceSetId().equals(av.getSequenceSetId()))); if (iSentTheSelection || !av.followSelection) { @@ -1988,11 +2034,13 @@ public class SeqPanel extends JPanel implements MouseListener, 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; }