From 55442cd37d5587dacdb8b642a3349debdffc4188 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Wed, 7 Jun 2006 12:58:21 +0000 Subject: [PATCH] ignore begin==0 and end==0 for the moment --- src/jalview/gui/FeatureSettings.java | 19 ++++- src/jalview/gui/SeqPanel.java | 132 +++++++++++++++++++++++++--------- 2 files changed, 114 insertions(+), 37 deletions(-) diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 5565292..7917efa 100755 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -169,9 +169,16 @@ public class FeatureSettings extends JPanel alignmentHasFeatures = true; tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures(); + int index = 0; while (index < tmpfeatures.length) { + if(tmpfeatures[index].begin == 0 && tmpfeatures[index].end ==0) + { + index++; + continue; + } + if(tmpfeatures[index].getFeatureGroup()!=null) { group = tmpfeatures[index].featureGroup; @@ -257,6 +264,12 @@ public class FeatureSettings extends JPanel { group = tmpfeatures[index].featureGroup; + if(tmpfeatures[index].begin==0 && tmpfeatures[index].end==0) + { + index ++; + continue; + } + if (group==null || fr.featureGroups.get(group)==null || ((Boolean) fr.featureGroups.get(group)).booleanValue()) { @@ -300,6 +313,10 @@ public class FeatureSettings extends JPanel //which was just selected type = visibleChecks.elementAt(i).toString(); data[dataIndex][0] = type; + + if(fr.getColour(type)==null) + fr.createRandomColour(type); + data[dataIndex][1] = fr.getColour(type); data[dataIndex][2] = new Boolean(true); dataIndex++; @@ -429,8 +446,6 @@ public class FeatureSettings extends JPanel Enumeration e = fr.featureColours.keys(); while(e.hasMoreElements()) { - - jalview.binding.Colour col = new jalview.binding.Colour(); col.setName(e.nextElement().toString()); col.setRGB(jalview.util.Format.getHexString( diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 126d755..19ee273 100755 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -27,6 +27,8 @@ import java.awt.event.*; import javax.swing.*; +import java.util.Vector; + /** * DOCUMENT ME! @@ -70,6 +72,8 @@ public class SeqPanel extends JPanel implements MouseListener, StringBuffer keyboardNo1; StringBuffer keyboardNo2; + java.net.URL linkImageURL; + /** * Creates a new SeqPanel object. * @@ -78,6 +82,7 @@ public class SeqPanel extends JPanel implements MouseListener, */ public SeqPanel(AlignViewport avp, AlignmentPanel p) { + linkImageURL = getClass().getResource("/images/link.gif"); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -167,6 +172,29 @@ public class SeqPanel extends JPanel implements MouseListener, return seq; } + Vector getAllFeaturesAtRes(SequenceI seq, int res) + { + Vector allFeatures = new Vector(); + int index = 0; + if(seq.getSequenceFeatures()!=null) + { + while (index < seq.getSequenceFeatures().length) + { + SequenceFeature sf = seq.getSequenceFeatures()[index]; + if (sf.getBegin() <= res && + sf.getEnd() >= res) + { + if (av.featuresDisplayed.containsKey(sf.getType())) + { + allFeatures.addElement(sf); + } + } + index++; + } + } + return allFeatures; + } + void endEditing() { startseq = -1; @@ -501,6 +529,7 @@ public class SeqPanel extends JPanel implements MouseListener, if(features!=null) { StringBuffer sbuffer = new StringBuffer(""); + StringBuffer seqSpecific = new StringBuffer(); for (int i = 0; i < features.length; i++) { @@ -522,16 +551,19 @@ public class SeqPanel extends JPanel implements MouseListener, sbuffer.append("
"); sbuffer.append("disulfide bond " + features[i].getBegin() + ":" + features[i].getEnd()); + if (features[i].links != null) + sbuffer.append(""); } } else { if (sbuffer.length() > 6) sbuffer.append("
"); - if(features[i].featureGroup!=null) - sbuffer.append(features[i].featureGroup+";"); - sbuffer.append(features[i].getType()); + sbuffer.append(features[i].getType() + " " + + features[i].begin); + if (features[i].begin != features[i].end) + sbuffer.append(" " + features[i].end); if (features[i].getDescription() != null && !features[i].description.equals(features[i].getType())) @@ -541,11 +573,24 @@ public class SeqPanel extends JPanel implements MouseListener, { sbuffer.append("; (" + features[i].getStatus() + ")"); } + if (features[i].links != null) + sbuffer.append(""); + } } + else if(features[i].begin==0 && features[i].end==0) + { + // seqSpecific.append(features[i].featureGroup+": " + // + features[i].getType()+" " + // +features[i].getDescription()+"
"); + } } + if(seqSpecific.length()>0) + seqSpecific.setLength(seqSpecific.length()-4); + + sbuffer.append(seqSpecific); sbuffer.append(""); if(sbuffer.length()==13) // setToolTipText(""); @@ -1145,7 +1190,7 @@ public class SeqPanel extends JPanel implements MouseListener, "Cannot edit annotations in wrapped view.", "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE); - return; + return; } if(seq<0 || res<0) @@ -1190,12 +1235,13 @@ public class SeqPanel extends JPanel implements MouseListener, (allGroups[i].getEndRes() >= res)) { stretchGroup = allGroups[i]; - av.setSelectionGroup(stretchGroup); - break; } } } + + av.setSelectionGroup(stretchGroup); + } if (av.cursorMode) @@ -1207,49 +1253,65 @@ public class SeqPanel extends JPanel implements MouseListener, } - if (stretchGroup == null) + if (javax.swing.SwingUtilities.isRightMouseButton(evt)) { - // define a new group here - SequenceGroup sg = new SequenceGroup(); - sg.setStartRes(res); - sg.setEndRes(res); - sg.addSequence(sequence, false); - av.setSelectionGroup(sg); - stretchGroup = sg; - - if (av.getConservationSelected()) + Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(res)); + Vector links = new Vector();; + for (int i = 0; i < allFeatures.size(); i++) { - SliderPanel.setConservationSlider(ap, - av.getGlobalColourScheme(), "Background"); + SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i); + if (sf.links != null) + { + for (int j = 0; j < sf.links.size(); j++) + { + links.addElement(sf.links.elementAt(j)); + } + } } - if (av.getAbovePIDThreshold()) - { - SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), - "Background"); - } + + jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links); + pop.show(this, evt.getX(), evt.getY()); } - else if (javax.swing.SwingUtilities.isRightMouseButton(evt)) + else if (stretchGroup == null) { - jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null); - pop.show(this, evt.getX(), evt.getY()); + //Only if left mouse button do we want to change group sizes - // edit the properties of existing group - } + // define a new group here + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(res); + sg.setEndRes(res); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + stretchGroup = sg; - if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) - { + if (av.getConservationSelected()) + { + SliderPanel.setConservationSlider(ap, + av.getGlobalColourScheme(), + "Background"); + } + + if (av.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), + "Background"); + } + if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res)) + { // Edit end res position of selected group changeEndRes = true; - } - else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res)) - { + } + else if ( (stretchGroup != null) && + (stretchGroup.getStartRes() == res)) + { // Edit end res position of selected group changeStartRes = true; + } + stretchGroup.getWidth(); } - stretchGroup.getWidth(); - seqCanvas.repaint(); } -- 1.7.10.2