-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class FeatureRenderer
-{
- AlignViewport av;
-
- Hashtable featureColours = new Hashtable();
-
- // A higher level for grouping features of a
- // particular type
- Hashtable featureGroups = null;
-
- // Holds web links for feature groups and feature types
- // in the form label|link
- Hashtable featureLinks = null;
-
- // This is actually an Integer held in the hashtable,
- // Retrieved using the key feature type
- Object currentColour;
-
- String[] renderOrder;
-
- FontMetrics fm;
- int charOffset;
-
- float transparency = 1f;
-
- TransparencySetter transparencySetter = null;
-
- /**
- * Creates a new FeatureRenderer object.
- *
- * @param av DOCUMENT ME!
- */
- public FeatureRenderer(AlignViewport av)
- {
- this.av = av;
-
- if (!System.getProperty("java.version").startsWith("1.1"))
- {
- transparencySetter = new TransparencySetter();
- }
- }
-
- public void transferSettings(FeatureRenderer fr)
- {
- renderOrder = fr.renderOrder;
- featureGroups = fr.featureGroups;
- featureColours = fr.featureColours;
- transparency = fr.transparency;
- }
-
- public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
- {
- overview = true;
- if (!av.showSequenceFeatures)
- {
- return initialCol;
- }
-
- lastSequence = seq;
- sequenceFeatures = lastSequence.getSequenceFeatures();
- if (sequenceFeatures == null)
- {
- return initialCol;
- }
-
- sfSize = sequenceFeatures.length;
-
- if (jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))
- {
- return Color.white;
- }
-
- currentColour = null;
-
- drawSequence(null, lastSequence, lastSequence.findPosition(i), -1, -1);
-
- if (currentColour == null)
- {
- return initialCol;
- }
-
- 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();
- public int findFeatureColour(int initialCol, int seqIndex, int column)
- {
- if (!av.showSequenceFeatures)
- {
- return initialCol;
- }
-
- if (seqIndex != lastSequenceIndex)
- {
- lastSequence = av.alignment.getSequenceAt(seqIndex);
- lastSequenceIndex = seqIndex;
- sequenceFeatures = lastSequence.getSequenceFeatures();
- if (sequenceFeatures == null)
- {
- return initialCol;
- }
-
- sfSize = sequenceFeatures.length;
- }
-
- if (jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
- {
- return Color.white.getRGB();
- }
-
- currentColour = null;
-
- drawSequence(null, lastSequence, lastSequence.findPosition(column), -1, -1);
-
- if (currentColour == null)
- {
- return initialCol;
- }
-
- return ( (Integer) currentColour).intValue();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param seq DOCUMENT ME!
- * @param sg DOCUMENT ME!
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- * @param x1 DOCUMENT ME!
- * @param y1 DOCUMENT ME!
- * @param width DOCUMENT ME!
- * @param height DOCUMENT ME!
- */
- // String type;
- // SequenceFeature sf;
- int lastSequenceIndex = -1;
- SequenceI lastSequence;
- SequenceFeature[] sequenceFeatures;
- int sfSize, sfindex, spos, epos;
-
- public void drawSequence(Graphics g, SequenceI seq,
- int start, int end, int y1)
- {
- if (seq.getSequenceFeatures() == null
- || seq.getSequenceFeatures().length == 0)
- {
- return;
- }
-
- if (transparencySetter != null && g != null)
- {
- transparencySetter.setTransparency(g, transparency);
- }
-
- if (lastSequence == null || seq != lastSequence || sequenceFeatures!=seq.getSequenceFeatures())
- {
- lastSequence = seq;
- sequenceFeatures = seq.getSequenceFeatures();
- sfSize = sequenceFeatures.length;
- }
-
- if (av.featuresDisplayed == null || renderOrder == null)
- {
- findAllFeatures();
- if (av.featuresDisplayed.size() < 1)
- {
- return;
- }
-
- sequenceFeatures = seq.getSequenceFeatures();
- sfSize = sequenceFeatures.length;
- }
- if (!overview)
- {
- spos = lastSequence.findPosition(start);
- epos = lastSequence.findPosition(end);
- if (g != null)
- {
- fm = g.getFontMetrics();
- }
- }
- String type;
- for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
- {
- type = renderOrder[renderIndex];
- if (!av.featuresDisplayed.containsKey(type))
- {
- continue;
- }
-
- // loop through all features in sequence to find
- // current feature to render
- for (sfindex = 0; sfindex < sfSize; sfindex++)
- {
- if (!sequenceFeatures[sfindex].type.equals(type))
- {
- continue;
- }
-
- if (featureGroups != null
- && sequenceFeatures[sfindex].featureGroup != null
- &&
- featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
- &&
- ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
- featureGroup)).
- booleanValue())
- {
- continue;
- }
-
- if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
- || sequenceFeatures[sfindex].getEnd() < spos))
- {
- continue;
- }
-
- if (overview)
- {
- if (sequenceFeatures[sfindex].begin <= start &&
- sequenceFeatures[sfindex].end >= start)
- {
- currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
- type);
- }
-
- }
- else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
- {
-
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- new Color( ( (Integer) av.featuresDisplayed.get(
- sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- new Color( ( (Integer) av.featuresDisplayed.get(
- sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
-
- }
- else
- {
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex].type),
- start, end, y1);
- }
-
- }
- }
-
- if (transparencySetter != null && g != null)
- {
- transparencySetter.setTransparency(g, 1.0f);
- }
- }
-
- char s;
- int i;
- void renderFeature(Graphics g, SequenceI seq,
- int fstart, int fend, Color featureColour, int start,
- int end, int y1)
- {
-
- if ( ( (fstart <= end) && (fend >= start)))
- {
- if (fstart < start)
- { // fix for if the feature we have starts before the sequence start,
- fstart = start; // but the feature end is still valid!!
- }
-
- if (fend >= end)
- {
- fend = end;
- }
-
- for (i = fstart; i <= fend; i++)
- {
- s = seq.getCharAt(i);
-
- if (jalview.util.Comparison.isGap(s))
- {
- continue;
- }
-
- g.setColor(featureColour);
-
- g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
-
- if (!av.validCharWidth)
- {
- continue;
- }
-
- g.setColor(Color.white);
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s),
- charOffset + (av.charWidth * (i - start)),
- (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
-
- }
- }
- }
-
- void findAllFeatures()
- {
- jalview.schemes.UserColourScheme ucs = new
- jalview.schemes.UserColourScheme();
-
- av.featuresDisplayed = new Hashtable();
- Vector allfeatures = new Vector();
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- SequenceFeature[] features = av.alignment.getSequenceAt(i).
- getSequenceFeatures();
-
- if (features == null)
- {
- continue;
- }
-
- int index = 0;
- while (index < features.length)
- {
- if (!av.featuresDisplayed.containsKey(features[index].getType()))
- {
- if (getColour(features[index].getType()) == null)
- {
- featureColours.put(features[index].getType(),
- ucs.createColourFromName(features[index].
- getType()));
- }
-
- av.featuresDisplayed.put(features[index].getType(),
- new Integer(getColour(features[index].
- getType()).getRGB()));
- allfeatures.addElement(features[index].getType());
- }
- index++;
- }
- }
-
- renderOrder = new String[allfeatures.size()];
- Enumeration en = allfeatures.elements();
- int i = allfeatures.size() - 1;
- while (en.hasMoreElements())
- {
- renderOrder[i] = en.nextElement().toString();
- i--;
- }
- }
-
- public Color getColour(String featureType)
- {
- return (Color) featureColours.get(featureType);
- }
-
- public void addNewFeature(String name, Color col)
- {
-
- setColour(name, col);
- if (av.featuresDisplayed == null)
- {
- av.featuresDisplayed = new Hashtable();
- }
-
- av.featuresDisplayed.put(name, "NOGROUP");
- }
-
- public void setColour(String featureType, Color col)
- {
- featureColours.put(featureType, col);
- }
-
- public void setFeaturePriority(Object[][] data)
- {
- // The feature table will display high priority
- // features at the top, but theses are the ones
- // we need to render last, so invert the data
- if (av.featuresDisplayed != null)
- {
- av.featuresDisplayed.clear();
- }
-
- renderOrder = new String[data.length];
-
- if (data.length > 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;
- }
- }
- }
-
- public void featuresAdded()
- {
- findAllFeatures();
- }
-}
-
-class TransparencySetter
-{
- void setTransparency(Graphics g, float value)
- {
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(
- AlphaComposite.getInstance(
- AlphaComposite.SRC_OVER, value));
- }
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+package jalview.appletgui;\r
+\r
+import java.util.*;\r
+\r
+import java.awt.*;\r
+\r
+import java.awt.event.*;\r
+\r
+\r
+import jalview.datamodel.*;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class FeatureRenderer\r
+{\r
+ AlignViewport av;\r
+\r
+ Hashtable featureColours = new Hashtable();\r
+\r
+ // A higher level for grouping features of a\r
+ // particular type\r
+ Hashtable featureGroups = null;\r
+\r
+ // Holds web links for feature groups and feature types\r
+ // in the form label|link\r
+ Hashtable featureLinks = null;\r
+\r
+ // This is actually an Integer held in the hashtable,\r
+ // Retrieved using the key feature type\r
+ Object currentColour;\r
+\r
+ String[] renderOrder;\r
+\r
+ FontMetrics fm;\r
+ int charOffset;\r
+\r
+ float transparency = 1f;\r
+\r
+ TransparencySetter transparencySetter = null;\r
+\r
+ /**\r
+ * Creates a new FeatureRenderer object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ */\r
+ public FeatureRenderer(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+\r
+ if (!System.getProperty("java.version").startsWith("1.1"))\r
+ {\r
+ transparencySetter = new TransparencySetter();\r
+ }\r
+ }\r
+\r
+ public void transferSettings(FeatureRenderer fr)\r
+ {\r
+ renderOrder = fr.renderOrder;\r
+ featureGroups = fr.featureGroups;\r
+ featureColours = fr.featureColours;\r
+ transparency = fr.transparency;\r
+ }\r
+\r
+\r
+ static String lastFeatureAdded;\r
+ static String lastFeatureGroupAdded;\r
+ static String lastDescriptionAdded;\r
+\r
+ public boolean createNewFeatures(SequenceI[] sequences,\r
+ SequenceFeature[] features,\r
+ AlignmentPanel ap)\r
+ {\r
+ return amendFeatures(sequences, features, true, ap);\r
+ }\r
+\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
+ 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
+ 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
+\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
+ 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
+ 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 (lastFeatureGroupAdded == null)\r
+ {\r
+ if (features[0].featureGroup != null)\r
+ {\r
+ lastFeatureGroupAdded = features[0].featureGroup;\r
+ }\r
+ else\r
+ {\r
+ lastFeatureAdded = "Jalview";\r
+ }\r
+ }\r
+\r
+\r
+ String title = newFeatures ? "Create New Sequence Feature(s)" :\r
+ "Amend/Delete Features for "\r
+ + sequences[0].getName();\r
+\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
+ 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
+ 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.show();\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
+\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
+ return true;\r
+ }\r
+ else\r
+ {\r
+ return false;\r
+ }\r
+ }\r
+\r
+ findAllFeatures();\r
+\r
+ return true;\r
+ }\r
+\r
+\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
+ lastSeq = seq;\r
+ sequenceFeatures = lastSeq.getSequenceFeatures();\r
+ if (sequenceFeatures == null)\r
+ {\r
+ return initialCol;\r
+ }\r
+\r
+ sfSize = sequenceFeatures.length;\r
+\r
+ if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i)))\r
+ {\r
+ return Color.white;\r
+ }\r
+\r
+ currentColour = null;\r
+\r
+ drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1);\r
+\r
+ if (currentColour == null)\r
+ {\r
+ return initialCol;\r
+ }\r
+\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
+ * @param seq DOCUMENT ME!\r
+ * @param sg DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ * @param x1 DOCUMENT ME!\r
+ * @param y1 DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param height DOCUMENT ME!\r
+ */\r
+ // String type;\r
+ // SequenceFeature sf;\r
+\r
+ SequenceI lastSeq;\r
+ SequenceFeature[] sequenceFeatures;\r
+ int sfSize, sfindex, spos, epos;\r
+\r
+ public void drawSequence(Graphics g, SequenceI seq,\r
+ int start, int end, int y1)\r
+ {\r
+ if (seq.getSequenceFeatures() == null\r
+ || seq.getSequenceFeatures().length == 0)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (transparencySetter != null && g != null)\r
+ {\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
+ if (av.featuresDisplayed.size() < 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ sequenceFeatures = seq.getSequenceFeatures();\r
+ sfSize = sequenceFeatures.length;\r
+ }\r
+ if (!overview)\r
+ {\r
+ spos = lastSeq.findPosition(start);\r
+ epos = lastSeq.findPosition(end);\r
+ if (g != null)\r
+ {\r
+ fm = g.getFontMetrics();\r
+ }\r
+ }\r
+ String type;\r
+ for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)\r
+ {\r
+ type = renderOrder[renderIndex];\r
+ if (!av.featuresDisplayed.containsKey(type))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ // loop through all features in sequence to find\r
+ // current feature to render\r
+ for (sfindex = 0; sfindex < sfSize; sfindex++)\r
+ {\r
+ if (!sequenceFeatures[sfindex].type.equals(type))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (featureGroups != null\r
+ && sequenceFeatures[sfindex].featureGroup != null\r
+ &&\r
+ featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
+ &&\r
+ ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].\r
+ featureGroup)).\r
+ booleanValue())\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (!overview && (sequenceFeatures[sfindex].getBegin() > epos\r
+ || sequenceFeatures[sfindex].getEnd() < spos))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (overview)\r
+ {\r
+ if (sequenceFeatures[sfindex].begin <= start &&\r
+ sequenceFeatures[sfindex].end >= start)\r
+ {\r
+ currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
+ type);\r
+ }\r
+\r
+ }\r
+ else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
+ {\r
+\r
+ renderFeature(g, seq,\r
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
+ new Color( ( (Integer) av.featuresDisplayed.get(\r
+ sequenceFeatures[sfindex].type)).intValue()),\r
+ start, end, y1);\r
+ renderFeature(g, seq,\r
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
+ new Color( ( (Integer) av.featuresDisplayed.get(\r
+ sequenceFeatures[sfindex].type)).intValue()),\r
+ start, end, y1);\r
+\r
+ }\r
+ else\r
+ {\r
+ renderFeature(g, seq,\r
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
+ getColour(sequenceFeatures[sfindex].type),\r
+ start, end, y1);\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ if (transparencySetter != null && g != null)\r
+ {\r
+ transparencySetter.setTransparency(g, 1.0f);\r
+ }\r
+ }\r
+\r
+ char s;\r
+ int i;\r
+ void renderFeature(Graphics g, SequenceI seq,\r
+ int fstart, int fend, Color featureColour, int start,\r
+ int end, int y1)\r
+ {\r
+\r
+ if ( ( (fstart <= end) && (fend >= start)))\r
+ {\r
+ if (fstart < start)\r
+ { // fix for if the feature we have starts before the sequence start,\r
+ fstart = start; // but the feature end is still valid!!\r
+ }\r
+\r
+ if (fend >= end)\r
+ {\r
+ fend = end;\r
+ }\r
+\r
+ for (i = fstart; i <= fend; i++)\r
+ {\r
+ s = seq.getCharAt(i);\r
+\r
+ if (jalview.util.Comparison.isGap(s))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ g.setColor(featureColour);\r
+\r
+ g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);\r
+\r
+ if (!av.validCharWidth)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ g.setColor(Color.white);\r
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
+ g.drawString(String.valueOf(s),\r
+ charOffset + (av.charWidth * (i - start)),\r
+ (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;\r
+\r
+ }\r
+ }\r
+ }\r
+\r
+ void findAllFeatures()\r
+ {\r
+ jalview.schemes.UserColourScheme ucs = new\r
+ jalview.schemes.UserColourScheme();\r
+\r
+ av.featuresDisplayed = new Hashtable();\r
+ Vector allfeatures = new Vector();\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ SequenceFeature[] features = av.alignment.getSequenceAt(i).\r
+ getSequenceFeatures();\r
+\r
+ if (features == null)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ int index = 0;\r
+ while (index < features.length)\r
+ {\r
+ if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
+ {\r
+ if (getColour(features[index].getType()) == null)\r
+ {\r
+ featureColours.put(features[index].getType(),\r
+ ucs.createColourFromName(features[index].\r
+ getType()));\r
+ }\r
+\r
+ av.featuresDisplayed.put(features[index].getType(),\r
+ new Integer(getColour(features[index].\r
+ getType()).getRGB()));\r
+ allfeatures.addElement(features[index].getType());\r
+ }\r
+ index++;\r
+ }\r
+ }\r
+\r
+ renderOrder = new String[allfeatures.size()];\r
+ Enumeration en = allfeatures.elements();\r
+ int i = allfeatures.size() - 1;\r
+ while (en.hasMoreElements())\r
+ {\r
+ renderOrder[i] = en.nextElement().toString();\r
+ i--;\r
+ }\r
+ }\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
+ {\r
+ av.featuresDisplayed = new Hashtable();\r
+ }\r
+\r
+ av.featuresDisplayed.put(name, "NOGROUP");\r
+ }\r
+\r
+ public void setColour(String featureType, Color col)\r
+ {\r
+ featureColours.put(featureType, col);\r
+ }\r
+\r
+ public void setFeaturePriority(Object[][] data)\r
+ {\r
+ // The feature table will display high priority\r
+ // features at the top, but theses are the ones\r
+ // we need to render last, so invert the data\r
+ if (av.featuresDisplayed != null)\r
+ {\r
+ av.featuresDisplayed.clear();\r
+ }\r
+\r
+ renderOrder = new String[data.length];\r
+\r
+ if (data.length > 0)\r
+ {\r
+ for (int i = 0; i < data.length; i++)\r
+ {\r
+ String type = data[i][0].toString();\r
+ setColour(type, (Color) data[i][1]);\r
+ if ( ( (Boolean) data[i][2]).booleanValue())\r
+ {\r
+ av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
+ }\r
+\r
+ renderOrder[data.length - i - 1] = type;\r
+ }\r
+ }\r
+ }\r
+}\r
+\r
+class TransparencySetter\r
+{\r
+ void setTransparency(Graphics g, float value)\r
+ {\r
+ Graphics2D g2 = (Graphics2D) g;\r
+ g2.setComposite(\r
+ AlphaComposite.getInstance(\r
+ AlphaComposite.SRC_OVER, value));\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff