\r
import java.awt.*;\r
\r
+import java.awt.event.*;\r
+\r
+\r
import jalview.datamodel.*;\r
\r
/**\r
transparency = fr.transparency;\r
}\r
\r
- public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
+\r
+ static String lastFeatureAdded;\r
+ static String lastFeatureGroupAdded;\r
+ static String lastDescriptionAdded;\r
+\r
+ int featureIndex = 0;\r
+ boolean deleteFeature = false;\r
+ Panel colourPanel;\r
+ boolean amendFeatures(final SequenceI[] sequences,\r
+ final SequenceFeature[] features,\r
+ boolean newFeatures,\r
+ final AlignmentPanel ap)\r
{\r
- overview = true;\r
- if (!av.showSequenceFeatures)\r
+ Panel bigPanel = new Panel(new BorderLayout());\r
+ final TextField name = new TextField(16);\r
+ final TextField source = new TextField(16);\r
+ final TextArea description = new TextArea(3, 35);\r
+ final TextField start = new TextField(8);\r
+ final TextField end = new TextField(8);\r
+ final Choice overlaps;\r
+ Button deleteButton = new Button("Delete");\r
+ deleteFeature = false;\r
+\r
+ colourPanel = new Panel(null);\r
+ colourPanel.setSize(110,15);\r
+ final FeatureRenderer fr = this;\r
+\r
+ Panel panel = new Panel(new GridLayout(3, 1));\r
+\r
+ Panel tmp;\r
+\r
+ ///////////////////////////////////////\r
+ ///MULTIPLE FEATURES AT SELECTED RESIDUE\r
+ if(!newFeatures && features.length>1)\r
{\r
- return initialCol;\r
+ panel = new Panel(new GridLayout(4, 1));\r
+ tmp = new Panel();\r
+ tmp.add(new Label("Select Feature: "));\r
+ overlaps = new Choice();\r
+ for(int i=0; i<features.length; i++)\r
+ {\r
+ String item = features[i].getType()\r
+ +"/"+features[i].getBegin()+"-"+features[i].getEnd();\r
+\r
+ if(features[i].getFeatureGroup()!=null)\r
+ item += " ("+features[i].getFeatureGroup()+")";\r
+\r
+ overlaps.addItem(item);\r
+ }\r
+\r
+ tmp.add(overlaps);\r
+\r
+ overlaps.addItemListener(new java.awt.event.ItemListener()\r
+ {\r
+ public void itemStateChanged(java.awt.event.ItemEvent e)\r
+ {\r
+ int index = overlaps.getSelectedIndex();\r
+ if (index != -1)\r
+ {\r
+ featureIndex = index;\r
+ name.setText(features[index].getType());\r
+ description.setText(features[index].getDescription());\r
+ source.setText(features[index].getFeatureGroup());\r
+ start.setText(features[index].getBegin()+"");\r
+ end.setText(features[index].getEnd()+"");\r
+\r
+ SearchResults highlight = new SearchResults();\r
+ highlight.addResult(sequences[0],\r
+ features[index].getBegin(),\r
+ features[index].getEnd());\r
+\r
+ ap.seqPanel.seqCanvas.highlightSearchResults(highlight);\r
+\r
+ }\r
+ Color col = getColour(name.getText());\r
+ if (col == null)\r
+ {\r
+ col = new\r
+ jalview.schemes.UserColourScheme()\r
+ .createColourFromName(name.getText());\r
+ }\r
+\r
+ colourPanel.setBackground(col);\r
+ }\r
+ });\r
+\r
+\r
+ panel.add(tmp);\r
}\r
+ //////////\r
+ //////////////////////////////////////\r
\r
- lastSequence = seq;\r
- sequenceFeatures = lastSequence.getSequenceFeatures();\r
- if (sequenceFeatures == null)\r
+\r
+ tmp = new Panel();\r
+ panel.add(tmp);\r
+ tmp.add(new Label("Name: ", Label.RIGHT));\r
+ tmp.add(name);\r
+\r
+ tmp = new Panel();\r
+ panel.add(tmp);\r
+ tmp.add(new Label("Group: ",Label.RIGHT));\r
+ tmp.add(source);\r
+\r
+ tmp = new Panel();\r
+ panel.add(tmp);\r
+ tmp.add(new Label("Colour: ", Label.RIGHT));\r
+ tmp.add(colourPanel);\r
+\r
+ bigPanel.add(panel, BorderLayout.NORTH);\r
+\r
+ panel = new Panel();\r
+ panel.add(new Label("Description: ", Label.RIGHT));\r
+ panel.add(new ScrollPane().add(description));\r
+\r
+ if (!newFeatures)\r
{\r
- return initialCol;\r
+ bigPanel.add(panel, BorderLayout.SOUTH);\r
+\r
+ panel = new Panel();\r
+ panel.add(new Label(" Start:", Label.RIGHT));\r
+ panel.add(start);\r
+ panel.add(new Label(" End:", Label.RIGHT));\r
+ panel.add(end);\r
+ bigPanel.add(panel, BorderLayout.CENTER);\r
+ }\r
+ else\r
+ {\r
+ bigPanel.add(panel, BorderLayout.CENTER);\r
}\r
\r
- sfSize = sequenceFeatures.length;\r
+ if (lastFeatureAdded == null)\r
+ {\r
+ if (features[0].type != null)\r
+ {\r
+ lastFeatureAdded = features[0].type;\r
+ }\r
+ else\r
+ {\r
+ lastFeatureAdded = "feature_1";\r
+ }\r
+ }\r
\r
- if (jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))\r
+ if (lastFeatureGroupAdded == null)\r
{\r
- return Color.white;\r
+ if (features[0].featureGroup != null)\r
+ {\r
+ lastFeatureGroupAdded = features[0].featureGroup;\r
+ }\r
+ else\r
+ {\r
+ lastFeatureAdded = "Jalview";\r
+ }\r
}\r
\r
- currentColour = null;\r
\r
- drawSequence(null, lastSequence, lastSequence.findPosition(i), -1, -1);\r
+ String title = newFeatures ? "Create New Sequence Feature(s)" :\r
+ "Amend/Delete Features for "\r
+ + sequences[0].getName();\r
\r
- if (currentColour == null)\r
+ final JVDialog dialog = new JVDialog(ap.alignFrame,\r
+ title,\r
+ true,\r
+ 385,240);\r
+\r
+ dialog.setMainPanel(bigPanel);\r
+\r
+ if(newFeatures)\r
{\r
- return initialCol;\r
+ name.setText(lastFeatureAdded);\r
+ source.setText(lastFeatureGroupAdded);\r
+ }\r
+ else\r
+ {\r
+ dialog.ok.setLabel("Amend");\r
+ dialog.buttonPanel.add(deleteButton, 1);\r
+ deleteButton.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ deleteFeature = true;\r
+ dialog.setVisible(false);\r
+ }\r
+ });\r
+ name.setText(features[0].getType());\r
+ source.setText(features[0].getFeatureGroup());\r
}\r
\r
- return new Color( ( (Integer) currentColour).intValue());\r
+ start.setText(features[0].getBegin()+"");\r
+ end.setText(features[0].getEnd()+"");\r
+ description.setText(features[0].getDescription());\r
+\r
+ Color col = getColour(name.getText());\r
+ if (col == null)\r
+ {\r
+ col = new\r
+ jalview.schemes.UserColourScheme()\r
+ .createColourFromName(name.getText());\r
+ }\r
+\r
+ colourPanel.setBackground(col);\r
+\r
+ dialog.setResizable(true);\r
+\r
+\r
+ colourPanel.addMouseListener(new java.awt.event.MouseAdapter()\r
+ {\r
+ public void mousePressed(java.awt.event.MouseEvent evt)\r
+ {\r
+ new UserDefinedColours(fr, ap.alignFrame);\r
+ }\r
+ });\r
+\r
+ dialog.setVisible(true);\r
+\r
+ jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();\r
+\r
+ if (dialog.accept)\r
+ {\r
+ //This ensures that the last sequence\r
+ //is refreshed and new features are rendered\r
+ lastSeq = null;\r
+ lastFeatureAdded = name.getText().trim();\r
+ lastFeatureGroupAdded = source.getText().trim();\r
+ lastDescriptionAdded = description.getText().replace('\n', ' ');\r
+ }\r
+\r
+ if(lastFeatureGroupAdded !=null && lastFeatureGroupAdded.length()<1)\r
+ lastFeatureGroupAdded = null;\r
+\r
+\r
+ if (!newFeatures)\r
+ {\r
+ SequenceFeature sf = features[featureIndex];\r
+\r
+ if (dialog.accept)\r
+ {\r
+ sf.type = lastFeatureAdded;\r
+ sf.featureGroup = lastFeatureGroupAdded;\r
+ sf.description = lastDescriptionAdded;\r
+ setColour(sf.type, colourPanel.getBackground());\r
+ try\r
+ {\r
+ sf.begin = Integer.parseInt(start.getText());\r
+ sf.end = Integer.parseInt(end.getText());\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {}\r
+\r
+ ffile.parseDescriptionHTML(sf, false);\r
+ }\r
+ if (deleteFeature)\r
+ {\r
+ sequences[0].deleteFeature(sf);\r
+ }\r
+\r
+ }\r
+ else\r
+ {\r
+ if (dialog.accept && name.getText().length()>0)\r
+ {\r
+ for (int i = 0; i < sequences.length; i++)\r
+ {\r
+ features[i].type = lastFeatureAdded;\r
+ features[i].featureGroup = lastFeatureGroupAdded;\r
+ features[i].description = lastDescriptionAdded;\r
+ sequences[i].addSequenceFeature(features[i]);\r
+ ffile.parseDescriptionHTML(features[i], false);\r
+ }\r
+\r
+ if (av.featuresDisplayed == null)\r
+ {\r
+ av.featuresDisplayed = new Hashtable();\r
+ }\r
+\r
+ if (featureGroups == null)\r
+ {\r
+ featureGroups = new Hashtable();\r
+ }\r
+\r
+ col = colourPanel.getBackground();\r
+ setColour(lastFeatureAdded, col);\r
+\r
+ if(lastFeatureGroupAdded!=null)\r
+ {\r
+ featureGroups.put(lastFeatureGroupAdded, new Boolean(true));\r
+ av.featuresDisplayed.put(lastFeatureGroupAdded,\r
+ new Integer(col.getRGB()));\r
+ }\r
+ findAllFeatures();\r
+\r
+ String [] tro = new String[renderOrder.length];\r
+ tro[0] = renderOrder[renderOrder.length-1];\r
+ System.arraycopy(renderOrder,0,tro,1,renderOrder.length-1);\r
+ renderOrder = tro;\r
+\r
+ ap.paintAlignment(true);\r
+\r
+ return true;\r
+ }\r
+ else\r
+ {\r
+ return false;\r
+ }\r
+ }\r
+\r
+ findAllFeatures();\r
+\r
+ ap.paintAlignment(true);\r
+\r
+ return true;\r
}\r
\r
- /**\r
- * This is used by the Molecule Viewer to get the accurate colour\r
- * of the rendered sequence\r
- */\r
- boolean overview = false;\r
\r
- int white = Color.white.getRGB();\r
- public int findFeatureColour(int initialCol, int seqIndex, int column)\r
+ public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
{\r
+ overview = true;\r
if (!av.showSequenceFeatures)\r
{\r
return initialCol;\r
}\r
\r
- if (seqIndex != lastSequenceIndex)\r
+ lastSeq = seq;\r
+ sequenceFeatures = lastSeq.getSequenceFeatures();\r
+ if (sequenceFeatures == null)\r
{\r
- lastSequence = av.alignment.getSequenceAt(seqIndex);\r
- lastSequenceIndex = seqIndex;\r
- sequenceFeatures = lastSequence.getSequenceFeatures();\r
- if (sequenceFeatures == null)\r
- {\r
- return initialCol;\r
- }\r
-\r
- sfSize = sequenceFeatures.length;\r
+ return initialCol;\r
}\r
\r
- if (jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))\r
+ sfSize = sequenceFeatures.length;\r
+\r
+ if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i)))\r
{\r
- return Color.white.getRGB();\r
+ return Color.white;\r
}\r
\r
currentColour = null;\r
\r
- drawSequence(null, lastSequence, lastSequence.findPosition(column), -1, -1);\r
+ drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1);\r
\r
if (currentColour == null)\r
{\r
return initialCol;\r
}\r
\r
- return ( (Integer) currentColour).intValue();\r
+ return new Color( ( (Integer) currentColour).intValue());\r
}\r
\r
/**\r
+ * This is used by the Molecule Viewer to get the accurate colour\r
+ * of the rendered sequence\r
+ */\r
+ boolean overview = false;\r
+\r
+\r
+ /**\r
* DOCUMENT ME!\r
*\r
* @param g DOCUMENT ME!\r
*/\r
// String type;\r
// SequenceFeature sf;\r
- int lastSequenceIndex = -1;\r
- SequenceI lastSequence;\r
+\r
+ SequenceI lastSeq;\r
SequenceFeature[] sequenceFeatures;\r
int sfSize, sfindex, spos, epos;\r
\r
- public void drawSequence(Graphics g, SequenceI seq,\r
+ synchronized public void drawSequence(Graphics g, SequenceI seq,\r
int start, int end, int y1)\r
{\r
if (seq.getSequenceFeatures() == null\r
transparencySetter.setTransparency(g, transparency);\r
}\r
\r
+ if (lastSeq == null || seq != lastSeq || sequenceFeatures!=seq.getSequenceFeatures())\r
+ {\r
+ lastSeq = seq;\r
+ sequenceFeatures = seq.getSequenceFeatures();\r
+ sfSize = sequenceFeatures.length;\r
+ }\r
+\r
if (av.featuresDisplayed == null || renderOrder == null)\r
{\r
findAllFeatures();\r
sequenceFeatures = seq.getSequenceFeatures();\r
sfSize = sequenceFeatures.length;\r
}\r
- if (lastSequence == null || seq != lastSequence)\r
- {\r
- lastSequence = seq;\r
- sequenceFeatures = seq.getSequenceFeatures();\r
- sfSize = sequenceFeatures.length;\r
- }\r
if (!overview)\r
{\r
- spos = lastSequence.findPosition(start);\r
- epos = lastSequence.findPosition(end);\r
+ spos = lastSeq.findPosition(start);\r
+ epos = lastSeq.findPosition(end);\r
if (g != null)\r
{\r
fm = g.getFontMetrics();\r
\r
public Color getColour(String featureType)\r
{\r
- return (Color) featureColours.get(featureType);\r
- }\r
-\r
- public void addNewFeature(String name, Color col)\r
- {\r
-\r
- setColour(name, col);\r
- if (av.featuresDisplayed == null)\r
+ if (!featureColours.containsKey(featureType))\r
{\r
- av.featuresDisplayed = new Hashtable();\r
+ jalview.schemes.UserColourScheme ucs = new\r
+ jalview.schemes.UserColourScheme();\r
+ Color col = ucs.createColourFromName(featureType);\r
+ featureColours.put(featureType, col);\r
+ return col;\r
}\r
-\r
- av.featuresDisplayed.put(name, "NOGROUP");\r
+ else\r
+ return (Color) featureColours.get(featureType);\r
}\r
\r
+\r
public void setColour(String featureType, Color col)\r
{\r
featureColours.put(featureType, col);\r
av.featuresDisplayed.clear();\r
}\r
\r
+ /* if (visibleNew)\r
+ {\r
+ if (av.featuresDisplayed != null)\r
+ {\r
+ av.featuresDisplayed.clear();\r
+ }\r
+ else\r
+ {\r
+ av.featuresDisplayed = new Hashtable();\r
+ }\r
+ }\r
+ if (data == null)\r
+ {\r
+ return;\r
+ }*/\r
+\r
+\r
renderOrder = new String[data.length];\r
\r
if (data.length > 0)\r
{\r
void setTransparency(Graphics g, float value)\r
{\r
- /* Graphics2D g2 = (Graphics2D) g;\r
+ Graphics2D g2 = (Graphics2D) g;\r
g2.setComposite(\r
AlphaComposite.getInstance(\r
- AlphaComposite.SRC_OVER, value));*/\r
+ AlphaComposite.SRC_OVER, value));\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff