X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=e32c5cfdf246cc14ef53fba7c6224ecf45e9e1c8;hb=743075ad19dc11ae8456491c51a0c8808b996dc1;hp=bdfcef466942d8965fa6b621416cf999f9745c77;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index bdfcef4..e32c5cf 100755 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -22,6 +22,7 @@ import java.util.*; import java.awt.*; import java.awt.event.*; + import javax.swing.*; import jalview.commands.*; @@ -36,7 +37,8 @@ import jalview.structure.*; * @version $Revision$ */ public class SeqPanel extends JPanel implements MouseListener, - MouseMotionListener, MouseWheelListener, SequenceListener + MouseMotionListener, MouseWheelListener, SequenceListener, + SelectionListener { /** DOCUMENT ME!! */ @@ -98,9 +100,9 @@ public class SeqPanel extends JPanel implements MouseListener, * Creates a new SeqPanel object. * * @param avp - * DOCUMENT ME! + * DOCUMENT ME! * @param p - * DOCUMENT ME! + * DOCUMENT ME! */ public SeqPanel(AlignViewport av, AlignmentPanel ap) { @@ -124,6 +126,7 @@ public class SeqPanel extends JPanel implements MouseListener, addMouseWheelListener(this); ssm = StructureSelectionManager.getStructureSelectionManager(); ssm.addStructureViewerListener(this); + ssm.addSelectionListener(this); } } @@ -455,6 +458,7 @@ public class SeqPanel extends JPanel implements MouseListener, } ap.paintAlignment(false); + av.sendSelection(); } void insertGapAtCursor(boolean group) @@ -520,7 +524,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseReleased(MouseEvent evt) { @@ -540,7 +544,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mousePressed(MouseEvent evt) { @@ -605,6 +609,10 @@ public class SeqPanel extends JPanel implements MouseListener, public void highlightSequence(SearchResults results) { + if (av.followHighlight) + { + ap.scrollToPosition(results, false); + } seqCanvas.highlightSearchResults(results); } @@ -618,7 +626,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseMoved(MouseEvent evt) { @@ -679,42 +687,111 @@ public class SeqPanel extends JPanel implements MouseListener, // use aa to see if the mouse pointer is on a if (av.showSequenceFeatures) { + int rpos; SequenceFeature[] features = findFeaturesAtRes(sequence - .getDatasetSequence(), sequence.findPosition(res)); + .getDatasetSequence(), rpos = sequence.findPosition(res)); + appendFeatures(tooltipText, linkImageURL.toString(), rpos, features,this.ap.seqPanel.seqCanvas.fr.minmax); + } + if (tooltipText.length() == 6) // + { + setToolTipText(null); + lastTooltip = null; + } + else + { + tooltipText.append(""); + if (lastTooltip == null + || !lastTooltip.equals(tooltipText.toString())) + { + setToolTipText(tooltipText.toString()); + lastTooltip = tooltipText.toString(); + } + + } + + } + private Point lastp=null; + /* + * (non-Javadoc) + * + * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent) + */ + public Point getToolTipLocation(MouseEvent event) + { + int x = event.getX(), w = getWidth(); + int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too + // close to edge + Point p = lastp; + if (!event.isShiftDown() || p==null) { + p = (tooltipText != null && tooltipText.length() > 6) ? new Point( + event.getX() + wdth, event.getY() - 20) + : null; + } + /* + * TODO: try to modify position region is not obcured by tooltip + */ + return lastp=p; + } - if (features != null) + /** + * appends the features at rpos to the given stringbuffer ready for display in + * a tooltip + * + * @param tooltipText2 + * @param linkImageURL + * @param rpos + * @param features + * TODO refactor to Jalview 'utilities' somehow. + */ + public void appendFeatures(StringBuffer tooltipText2, + String linkImageURL, int rpos, SequenceFeature[] features) + { + appendFeatures(tooltipText2,linkImageURL,rpos,features,null); + } + public void appendFeatures(StringBuffer tooltipText2, String string, + int rpos, SequenceFeature[] features, Hashtable minmax) + { + String tmpString; + if (features != null) + { + for (int i = 0; i < features.length; i++) { - for (int i = 0; i < features.length; i++) + if (features[i].getType().equals("disulfide bond")) { - if (features[i].getType().equals("disulfide bond")) + if (features[i].getBegin() == rpos + || features[i].getEnd() == rpos) { - if (features[i].getBegin() == sequence.findPosition(res) - || features[i].getEnd() == sequence.findPosition(res)) + if (tooltipText2.length() > 6) { - if (tooltipText.length() > 6) - { - tooltipText.append("
"); - } - tooltipText.append("disulfide bond " + features[i].getBegin() - + ":" + features[i].getEnd()); - if (features[i].links != null) - { - tooltipText.append(" "); - } + tooltipText2.append("
"); + } + tooltipText2.append("disulfide bond " + features[i].getBegin() + + ":" + features[i].getEnd()); + if (features[i].links != null) + { + tooltipText2.append(" "); } } - else + } + else + { + if (tooltipText2.length() > 6) { - if (tooltipText.length() > 6) + tooltipText2.append("
"); + } + // TODO: remove this hack to display link only features + boolean linkOnly = features[i].getValue("linkonly") != null; + if (!linkOnly) + { + tooltipText2.append(features[i].getType() + " "); + if (rpos != 0) { - tooltipText.append("
"); + // we are marking a positional feature + tooltipText2.append(features[i].begin); } - - tooltipText.append(features[i].getType() + " " - + features[i].begin); if (features[i].begin != features[i].end) { - tooltipText.append(" " + features[i].end); + tooltipText2.append(" " + features[i].end); } if (features[i].getDescription() != null @@ -740,7 +817,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (startTag > -1) { - tooltipText.append("; " + tmpString); + tooltipText2.append("; " + tmpString); } else { @@ -752,50 +829,41 @@ public class SeqPanel extends JPanel implements MouseListener, tmpString = tmpString.replaceAll("<", "<"); tmpString = tmpString.replaceAll(">", ">"); - tooltipText.append("; "); - tooltipText.append(tmpString); + tooltipText2.append("; "); + tooltipText2.append(tmpString); } else { - tooltipText.append("; " + tmpString); + tooltipText2.append("; " + tmpString); } } } + // check score should be shown + if (features[i].getScore() != Float.NaN) { + float[][] rng=(minmax==null) ? null : ((float[][])minmax.get(features[i].getType())); + if (rng!=null && rng[0]!=null && rng[0][0]!=rng[0][1]) { + tooltipText2.append(" Score=" + features[i].getScore()); + } + } if (features[i].getValue("status") != null) { String status = features[i].getValue("status").toString(); if (status.length() > 0) { - tooltipText.append("; (" + features[i].getValue("status") + tooltipText2.append("; (" + features[i].getValue("status") + ")"); } } - - if (features[i].links != null) - { - tooltipText.append(" "); - } - } + if (features[i].links != null) + { + tooltipText2.append(" "); + } + } } } - - if (tooltipText.length() == 6) // - { - setToolTipText(null); - } - else - { - tooltipText.append(""); - if (lastTooltip == null - || !lastTooltip.equals(tooltipText.toString())) - setToolTipText(tooltipText.toString()); - - lastTooltip = tooltipText.toString(); - } - } String lastTooltip; @@ -804,11 +872,11 @@ public class SeqPanel extends JPanel implements MouseListener, * Set status message in alignment panel * * @param sequence - * aligned sequence object + * aligned sequence object * @param res - * alignment column + * alignment column * @param seq - * index of sequence in alignment + * index of sequence in alignment * @return position of res in sequence */ int setStatusMessage(SequenceI sequence, int res, int seq) @@ -852,7 +920,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseDragged(MouseEvent evt) { @@ -1320,7 +1388,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseEntered(MouseEvent e) { @@ -1340,7 +1408,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseExited(MouseEvent e) { @@ -1398,13 +1466,14 @@ public class SeqPanel extends JPanel implements MouseListener, { ap.scrollUp(true); } + // TODO Update tooltip for new position. } /** * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void doMousePressedDefineMode(MouseEvent evt) { @@ -1514,6 +1583,7 @@ public class SeqPanel extends JPanel implements MouseListener, sg.setEndRes(res); sg.addSequence(sequence, false); av.setSelectionGroup(sg); + stretchGroup = sg; if (av.getConservationSelected()) @@ -1548,7 +1618,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void doMouseReleasedDefineMode(MouseEvent evt) { @@ -1591,14 +1661,14 @@ public class SeqPanel extends JPanel implements MouseListener, changeEndRes = false; changeStartRes = false; stretchGroup = null; - + av.sendSelection(); } /** * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void doMouseDraggedDefineMode(MouseEvent evt) { @@ -1791,4 +1861,79 @@ public class SeqPanel extends JPanel implements MouseListener, } } } + + /** + * modify current selection according to a received message. + */ + public void selection(SequenceGroup seqsel, ColumnSelection colsel, + SelectionSource source) + { + // TODO: fix this hack - source of messages is align viewport, but SeqPanel + // handles selection messages... + if (av == source) + { + return; + } + // do we want to thread this ? (contention with seqsel and colsel locks, I + // suspect) + boolean repaint = false; + if (av.followSelection) + { + if (av.selectionGroup == null || !av.isSelectionGroupChanged()) + { + SequenceGroup sgroup = null; + if (seqsel != null) + { + if (av.alignment==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.alignment, + (av.hasHiddenRows) ? av.hiddenRepSequences : null); + } + if (sgroup != null && sgroup.getSize() > 0) + { + av.setSelectionGroup(sgroup); + } + else + { + av.setSelectionGroup(null); + } + repaint = av.isSelectionGroupChanged(); + } + if (av.colSel == null || !av.isColSelChanged()) + { + // the current selection is unset or from a previous message + // so import the new colsel. + if (colsel == null || colsel.size() == 0) + { + if (av.colSel!=null) + { + av.colSel.clear(); + } + } + else + { + if (av.colSel == null) + { + av.colSel = new ColumnSelection(colsel); + } else { + av.colSel.setElementsFrom(colsel); + } + } + repaint |= av.isColSelChanged(); + } + } + if (av.hasHiddenColumns && (av.colSel==null || av.colSel.getHiddenColumns()==null)) + { + System.err.println("Bad things"); + } + if (repaint) + { + // probably finessing with multiple redraws here + PaintRefresher.Refresh(this, av.getSequenceSetId()); + // ap.paintAlignment(false); + } + } }