From be9cbda993c0cb66255c0eb8274ee2bfa9199220 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Thu, 16 Mar 2006 15:13:43 +0000 Subject: [PATCH] Feature rendering in groups --- src/jalview/appletgui/FeatureRenderer.java | 62 ++++---- src/jalview/appletgui/FeatureSettings.java | 229 ++++++++++++++++++++-------- 2 files changed, 202 insertions(+), 89 deletions(-) diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index 21c401a..0b504be 100755 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -45,7 +45,6 @@ public class FeatureRenderer String [] renderOrder; - boolean drawText = true; FontMetrics fm; int charOffset; @@ -85,11 +84,11 @@ public class FeatureRenderer return new Color( ((Integer)currentColour).intValue() ); } + /** * This is used by the Molecule Viewer to get the accurate colour * of the rendered sequence */ - boolean overview = false; int white = Color.white.getRGB(); @@ -152,12 +151,12 @@ public class FeatureRenderer return; - if(g!=null) - fm = g.getFontMetrics(); - if (av.featuresDisplayed == null || renderOrder==null) { findAllFeatures(); + if(av.featuresDisplayed.size()<1) + return; + sequenceFeatures = seq.getSequenceFeatures(); sfSize = sequenceFeatures.length; } @@ -171,11 +170,15 @@ public class FeatureRenderer { spos = lastSequence.findPosition(start); epos = lastSequence.findPosition(end); + if(g!=null) + fm = g.getFontMetrics(); } String type; for(int renderIndex=0; renderIndex0) - for(int i=0; i 0) + for (int i = 0; i < data.length; i++) + { + String type = data[i][0].toString(); + setColour(type, (Color) data[i][1]); + if ( ( (Boolean) data[i][2]).booleanValue()) + { + av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB())); + } + renderOrder[data.length - i - 1] = type; + } } Hashtable featureColours = new Hashtable(); diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index 20e4a4d..6710ed4 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -27,13 +27,14 @@ import java.awt.event.*; public class FeatureSettings extends Panel implements ItemListener, MouseListener, MouseMotionListener { - final FeatureRenderer fr; - final AlignmentPanel ap; - final AlignViewport av; - final Frame frame; + FeatureRenderer fr; + AlignmentPanel ap; + AlignViewport av; + Frame frame; Panel groupPanel; Panel featurePanel = new Panel(); ScrollPane scrollPane; + boolean alignmentHasFeatures = false; public FeatureSettings(AlignViewport av, final AlignmentPanel ap) { @@ -46,91 +47,106 @@ public class FeatureSettings extends Panel implements ItemListener, this.setLayout(new BorderLayout()); scrollPane = new ScrollPane(); scrollPane.add(featurePanel); - add(scrollPane, BorderLayout.CENTER); + if (alignmentHasFeatures) + add(scrollPane, BorderLayout.CENTER); + if(groupPanel!=null) { groupPanel.setLayout( - new GridLayout(groupPanel.getComponentCount() / 4, 4)); + new GridLayout( fr.featureGroups.size() / 4 + 1, 4)); groupPanel.validate(); add(groupPanel, BorderLayout.NORTH); } frame = new Frame(); frame.add(this); - int height = featurePanel.getComponentCount()*50 ; - if (height>400) - height = 400; + int height = featurePanel.getComponentCount()*50 +30; + + height = Math.max(100, height); + height = Math.min(400, height); - jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 250, + jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 280, height); } + public void paint(Graphics g) + { + g.setColor(Color.black); + g.drawString("No Features added to this alignment!!", 10, 20); + } + void setTableData() { + alignmentHasFeatures = false; + if(fr.featureGroups==null) fr.featureGroups = new Hashtable(); - else - fr.featureGroups.clear(); Vector allFeatures = new Vector(); + Vector allGroups = new Vector(); SequenceFeature[] tmpfeatures; + String group; + for (int i = 0; i < av.alignment.getHeight(); i++) { if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null) continue; + alignmentHasFeatures = true; + tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures(); int index = 0; while (index < tmpfeatures.length) { - if(tmpfeatures[index].getFeatureGroup()!=null - && tmpfeatures[index].getFeatureGroup().length()>0 - && !fr.featureGroups.containsKey(tmpfeatures[index].getFeatureGroup())) + if(tmpfeatures[index].getFeatureGroup()!=null) { - fr.featureGroups.put(tmpfeatures[index].getFeatureGroup(), new Boolean(true)); - if(groupPanel==null) - { - groupPanel = new Panel(); - } - - Checkbox check = new Checkbox(tmpfeatures[index].getFeatureGroup(), true); - check.setFont(new Font("Serif", Font.BOLD, 12)); - check.addItemListener(this); - groupPanel.add(check); + group = tmpfeatures[index].featureGroup; + if(!allGroups.contains(group)) + { + allGroups.addElement(group); + + boolean visible = true; + if (fr.featureGroups.containsKey(group)) + { + visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue(); + } + + fr.featureGroups.put(group, new Boolean(visible)); + + if (groupPanel == null) + { + groupPanel = new Panel(); + } + + Checkbox check = new Checkbox(group, visible); + check.setFont(new Font("Serif", Font.BOLD, 12)); + check.addItemListener(this); + groupPanel.add(check); + } } if (!allFeatures.contains(tmpfeatures[index].getType())) { allFeatures.addElement(tmpfeatures[index].getType()); } - - - index ++; + index ++; } } - resetTable(); - featurePanel.setLayout(new GridLayout(allFeatures.size(), 2, 10,5)); - featurePanel.validate(); + resetTable(false); } - void resetTable() + //This routine adds and removes checkboxes depending on + //Group selection states + void resetTable(boolean groupsChanged) { - featurePanel.removeAll(); - Enumeration groups = fr.featureGroups.keys(); SequenceFeature [] tmpfeatures; - String group, type; - Vector checksAdded = new Vector(); - - while(groups.hasMoreElements()) - { - group = groups.nextElement().toString(); - if ( !( (Boolean) fr.featureGroups.get(group)).booleanValue()) - continue; + String group=null, type; + Vector visibleChecks = new Vector(); for (int i = 0; i < av.alignment.getHeight(); i++) - { + { if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null) continue; @@ -138,28 +154,105 @@ public class FeatureSettings extends Panel implements ItemListener, int index = 0; while (index < tmpfeatures.length) { - if (tmpfeatures[index].getFeatureGroup() != null && - tmpfeatures[index].getFeatureGroup().equals(group)) + group = tmpfeatures[index].featureGroup; + + if (group==null || fr.featureGroups.get(group)==null || + ((Boolean) fr.featureGroups.get(group)).booleanValue()) { type = tmpfeatures[index].getType(); - if(!checksAdded.contains(type)) + if(!visibleChecks.contains(type) ) { - checksAdded.addElement(type); - Checkbox check = new Checkbox(type, true); - check.addMouseListener(this); - check.addMouseMotionListener(this); - check.setBackground(fr.getColour(type)); - check.addItemListener(this); - featurePanel.add(check); + visibleChecks.addElement(type); } } index++; } } - } + + Component[] comps; + int cSize = featurePanel.getComponentCount(); + Checkbox check; + //This will remove any checkboxes which shouldn't be + //visible + for (int i = 0; i < cSize; i++) + { + comps = featurePanel.getComponents(); + check = (Checkbox) comps[i]; + if (!visibleChecks.contains(check.getLabel())) + { + featurePanel.remove(i); + cSize --; + i--; + } + } + + if(fr.renderOrder!=null) + { + //First add the checks in the previous render order, + //in case the window has been closed and reopened + for(int ro=fr.renderOrder.length-1; ro>-1; ro--) + { + String item = fr.renderOrder[ro]; + + if(!visibleChecks.contains(item)) + continue; + + visibleChecks.removeElement(item); + + addCheck(false, item); + } + } + + // now add checkboxes which should be visible, + // if they have not already been added + Enumeration en = visibleChecks.elements(); + while(en.hasMoreElements()) + { + addCheck(groupsChanged, en.nextElement().toString()); + } + + + featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1, 10,5)); featurePanel.validate(); + + if(scrollPane!=null) scrollPane.validate(); + + itemStateChanged(null); + } + + void addCheck(boolean groupsChanged, String type) + { + boolean addCheck; + Component [] comps = featurePanel.getComponents(); + Checkbox check; + addCheck = true; + for (int i = 0; i < featurePanel.getComponentCount(); i++) + { + check = (Checkbox) comps[i]; + if (check.getLabel().equals(type)) + { + addCheck = false; + break; + } + } + + if (addCheck) + { + boolean selected = false; + if (groupsChanged || av.featuresDisplayed.containsKey(type)) + { + selected = true; + } + + check = new Checkbox(type, selected); + check.addMouseListener(this); + check.addMouseMotionListener(this); + check.setBackground(fr.getColour(type)); + check.addItemListener(this); + featurePanel.add(check); + } } public void itemStateChanged(ItemEvent evt) @@ -175,7 +268,7 @@ public class FeatureSettings extends Panel implements ItemListener, if (ap.overviewPanel != null) ap.overviewPanel.updateOverviewImage(); - resetTable(); + resetTable(true); return; } } @@ -188,9 +281,6 @@ public class FeatureSettings extends Panel implements ItemListener, for (int i = 0; i < cSize; i++) { Checkbox check = (Checkbox) comps[i]; - if(!check.getState()) - continue; - tmp[tmpSize][0] = check.getLabel(); tmp[tmpSize][1] = fr.getColour(check.getLabel()); tmp[tmpSize][2] = new Boolean(check.getState()); @@ -226,7 +316,6 @@ public class FeatureSettings extends Panel implements ItemListener, int height = evt.getY()+evt.getComponent().getLocation().y; - if(height > this.getSize().height) { comp = featurePanel.getComponent(featurePanel.getComponentCount()-1); @@ -245,7 +334,9 @@ public class FeatureSettings extends Panel implements ItemListener, if(comp!=null && comp instanceof Checkbox) target = (Checkbox)comp; - if (selectedCheck != null && target != null && selectedCheck != target) + if ( selectedCheck != null + && target != null + && selectedCheck != target) { int targetIndex = -1; for(int i=0; i1) + { + new UserDefinedColours(this, check.getLabel(), + fr.getColour(check.getLabel())); + } + } public void mouseMoved(MouseEvent evt){} } -- 1.7.10.2