/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
-import java.util.*;
-import java.util.concurrent.ConcurrentHashMap;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyChangeSupport;
-
-import javax.swing.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
import jalview.schemes.GraduatedColor;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSpinner;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer implements jalview.api.FeatureRenderer
+public class FeatureRenderer extends
+ jalview.renderer.seqfeatures.FeatureRenderer implements
+ jalview.api.FeatureRenderer
{
- AlignmentPanel ap;
-
- AlignViewport av;
-
Color resBoxColour;
- /**
- * global transparency for feature
- */
- float transparency = 1.0f;
-
- FontMetrics fm;
-
- int charOffset;
-
- Map featureColours = new ConcurrentHashMap();
-
- // A higher level for grouping features of a
- // particular type
- Map featureGroups = new ConcurrentHashMap();
-
- // This is actually an Integer held in the hashtable,
- // Retrieved using the key feature type
- Object currentColour;
-
- String[] renderOrder;
-
- PropertyChangeSupport changeSupport = new PropertyChangeSupport(this);
-
- Vector allfeatures;
+ AlignmentPanel ap;
/**
* Creates a new FeatureRenderer object.
*/
public FeatureRenderer(AlignmentPanel ap)
{
+ super();
this.ap = ap;
this.av = ap.av;
- if (ap != null && ap.getSeqPanel() != null && ap.getSeqPanel().seqCanvas != null
+ if (ap != null && ap.getSeqPanel() != null
+ && ap.getSeqPanel().seqCanvas != null
&& ap.getSeqPanel().seqCanvas.fr != null)
{
transferSettings(ap.getSeqPanel().seqCanvas.fr);
}
}
- public class FeatureRendererSettings implements Cloneable
- {
- String[] renderOrder;
-
- Map featureGroups;
-
- Map featureColours;
-
- float transparency;
-
- Map featureOrder;
-
- public FeatureRendererSettings(String[] renderOrder,
- Hashtable featureGroups, Hashtable featureColours,
- float transparency, Hashtable featureOrder)
- {
- super();
- this.renderOrder = renderOrder;
- this.featureGroups = featureGroups;
- this.featureColours = featureColours;
- this.transparency = transparency;
- this.featureOrder = featureOrder;
- }
-
- /**
- * create an independent instance of the feature renderer settings
- *
- * @param fr
- */
- public FeatureRendererSettings(FeatureRenderer fr)
- {
- renderOrder = null;
- featureGroups = new ConcurrentHashMap();
- featureColours = new ConcurrentHashMap();
- featureOrder = new ConcurrentHashMap();
- if (fr.renderOrder != null)
- {
- this.renderOrder = new String[fr.renderOrder.length];
- System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
- fr.renderOrder.length);
- }
- if (fr.featureGroups != null)
- {
- this.featureGroups = new ConcurrentHashMap(fr.featureGroups);
- }
- if (fr.featureColours != null)
- {
- this.featureColours = new ConcurrentHashMap(fr.featureColours);
- }
- Iterator en = fr.featureColours.keySet().iterator();
- while (en.hasNext())
- {
- Object next = en.next();
- Object val = featureColours.get(next);
- if (val instanceof GraduatedColor)
- {
- featureColours
- .put(next, new GraduatedColor((GraduatedColor) val));
- }
- }
- this.transparency = fr.transparency;
- if (fr.featureOrder != null)
- {
- this.featureOrder = new ConcurrentHashMap(fr.featureOrder);
- }
- }
- }
-
- public FeatureRendererSettings getSettings()
- {
- return new FeatureRendererSettings(this);
- }
-
- public void transferSettings(FeatureRendererSettings fr)
- {
- this.renderOrder = fr.renderOrder;
- this.featureGroups = fr.featureGroups;
- this.featureColours = fr.featureColours;
- this.transparency = fr.transparency;
- this.featureOrder = fr.featureOrder;
- }
-
- /**
- * update from another feature renderer
- *
- * @param fr
- * settings to copy
- */
- public void transferSettings(FeatureRenderer fr)
- {
- FeatureRendererSettings frs = new FeatureRendererSettings(fr);
- this.renderOrder = frs.renderOrder;
- this.featureGroups = frs.featureGroups;
- this.featureColours = frs.featureColours;
- this.transparency = frs.transparency;
- this.featureOrder = frs.featureOrder;
- if (av != null && av != fr.av)
- {
- // copy over the displayed feature settings
- if (fr.av != null)
- {
- if (fr.av.featuresDisplayed != null)
- {
- // update display settings
- if (av.featuresDisplayed == null)
- {
- av.featuresDisplayed = new Hashtable(fr.av.featuresDisplayed);
- }
- else
- {
- av.featuresDisplayed.clear();
- Enumeration en = fr.av.featuresDisplayed.keys();
- while (en.hasMoreElements())
- {
- av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
- }
-
- }
- }
- }
- }
- }
-
- BufferedImage offscreenImage;
-
- boolean offscreenRender = false;
-
- public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
- {
- return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
- }
-
- /**
- * This is used by the Molecule Viewer and Overview to get the accurate
- * colourof the rendered sequence
- */
- public synchronized int findFeatureColour(int initialCol, SequenceI seq,
- int column)
- {
- if (!av.showSequenceFeatures)
- {
- return initialCol;
- }
-
- if (seq != lastSeq)
- {
- lastSeq = seq;
- sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
- if (sequenceFeatures != null)
- {
- sfSize = sequenceFeatures.length;
- }
- }
-
- if (sequenceFeatures != lastSeq.getDatasetSequence()
- .getSequenceFeatures())
- {
- sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
- if (sequenceFeatures != null)
- {
- sfSize = sequenceFeatures.length;
- }
- }
-
- if (sequenceFeatures == null || sfSize == 0)
- {
- return initialCol;
- }
-
- if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
- {
- return Color.white.getRGB();
- }
-
- // Only bother making an offscreen image if transparency is applied
- if (transparency != 1.0f && offscreenImage == null)
- {
- offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
- }
-
- currentColour = null;
- // TODO: non-threadsafe - each rendering thread needs its own instance of
- // the feature renderer - or this should be synchronized.
- offscreenRender = true;
-
- if (offscreenImage != null)
- {
- offscreenImage.setRGB(0, 0, initialCol);
- drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0);
-
- return offscreenImage.getRGB(0, 0);
- }
- else
- {
- drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1);
-
- if (currentColour == null)
- {
- return initialCol;
- }
- else
- {
- 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;
- SequenceI lastSeq;
-
- SequenceFeature[] sequenceFeatures;
-
- int sfSize, sfindex, spos, epos;
-
- /**
- * show scores as heights
- */
- protected boolean varyHeight = false;
-
- synchronized public void drawSequence(Graphics g, SequenceI seq,
- int start, int end, int y1)
- {
-
- if (seq.getDatasetSequence().getSequenceFeatures() == null
- || seq.getDatasetSequence().getSequenceFeatures().length == 0)
- {
- return;
- }
-
- if (g != null)
- {
- fm = g.getFontMetrics();
- }
-
- if (av.featuresDisplayed == null || renderOrder == null
- || newFeatureAdded)
- {
- findAllFeatures();
- if (av.featuresDisplayed.size() < 1)
- {
- return;
- }
-
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- }
-
- if (lastSeq == null
- || seq != lastSeq
- || seq.getDatasetSequence().getSequenceFeatures() != sequenceFeatures)
- {
- lastSeq = seq;
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- }
-
- if (transparency != 1 && g != null)
- {
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
- transparency));
- }
-
- if (!offscreenRender)
- {
- spos = lastSeq.findPosition(start);
- epos = lastSeq.findPosition(end);
- }
-
- sfSize = sequenceFeatures.length;
- String type;
- for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
- {
- type = renderOrder[renderIndex];
-
- if (type == null || !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
- && sequenceFeatures[sfindex].featureGroup.length() != 0
- && featureGroups
- .containsKey(sequenceFeatures[sfindex].featureGroup)
- && !((Boolean) featureGroups
- .get(sequenceFeatures[sfindex].featureGroup))
- .booleanValue())
- {
- continue;
- }
-
- if (!offscreenRender
- && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
- .getEnd() < spos))
- {
- continue;
- }
-
- if (offscreenRender && offscreenImage == null)
- {
- if (sequenceFeatures[sfindex].begin <= start
- && sequenceFeatures[sfindex].end >= start)
- {
- // this is passed out to the overview and other sequence renderers
- // (e.g. molecule viewer) to get displayed colour for rendered
- // sequence
- currentColour = new Integer(
- getColour(sequenceFeatures[sfindex]).getRGB());
- // used to be retreived from av.featuresDisplayed
- // 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,
- getColour(sequenceFeatures[sfindex])
- // 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,
- getColour(sequenceFeatures[sfindex])
- // new Color(((Integer) av.featuresDisplayed
- // .get(sequenceFeatures[sfindex].type)).intValue())
- , start, end, y1);
-
- }
- else if (showFeature(sequenceFeatures[sfindex]))
- {
- if (av.showSeqFeaturesHeight
- && sequenceFeatures[sfindex].score != Float.NaN)
- {
- renderScoreFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex]), start, end, y1,
- normaliseScore(sequenceFeatures[sfindex]));
- }
- else
- {
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex]), start, end, y1);
- }
- }
-
- }
-
- }
-
- if (transparency != 1.0f && g != null)
- {
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
- 1.0f));
- }
- }
-
- Hashtable minmax = new Hashtable();
-
- /**
- * normalise a score against the max/min bounds for the feature type.
- *
- * @param sequenceFeature
- * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
- * (0-255) value.
- */
- private final byte[] normaliseScore(SequenceFeature sequenceFeature)
- {
- float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
- final byte[] r = new byte[]
- { 0, (byte) 255 };
- if (mm != null)
- {
- if (r[0] != 0 || mm[0] < 0.0)
- {
- r[0] = 1;
- r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
- }
- else
- {
- r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
- }
- }
- return r;
- }
-
- 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;
- }
- int pady = (y1 + av.charHeight) - av.charHeight / 5;
- 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 (offscreenRender || !av.validCharWidth)
- {
- continue;
- }
-
- g.setColor(Color.white);
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s), charOffset
- + (av.charWidth * (i - start)), pady);
-
- }
- }
- }
-
- void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend,
- Color featureColour, int start, int end, int y1, byte[] bs)
- {
-
- 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;
- }
- int pady = (y1 + av.charHeight) - av.charHeight / 5;
- int ystrt = 0, yend = av.charHeight;
- if (bs[0] != 0)
- {
- // signed - zero is always middle of residue line.
- if (bs[1] < 128)
- {
- yend = av.charHeight * (128 - bs[1]) / 512;
- ystrt = av.charHeight - yend / 2;
- }
- else
- {
- ystrt = av.charHeight / 2;
- yend = av.charHeight * (bs[1] - 128) / 512;
- }
- }
- else
- {
- yend = av.charHeight * bs[1] / 255;
- ystrt = av.charHeight - yend;
-
- }
- for (i = fstart; i <= fend; i++)
- {
- s = seq.getCharAt(i);
-
- if (jalview.util.Comparison.isGap(s))
- {
- continue;
- }
-
- g.setColor(featureColour);
- int x = (i - start) * av.charWidth;
- g.drawRect(x, y1, av.charWidth, av.charHeight);
- g.fillRect(x, y1 + ystrt, av.charWidth, yend);
-
- if (offscreenRender || !av.validCharWidth)
- {
- continue;
- }
-
- g.setColor(Color.black);
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s), charOffset
- + (av.charWidth * (i - start)), pady);
-
- }
- }
- }
-
- boolean newFeatureAdded = false;
-
- /**
- * Called when alignment in associated view has new/modified features to
- * discover and display.
- *
- */
- public void featuresAdded()
- {
- lastSeq = null;
- findAllFeatures();
- }
-
- boolean findingFeatures = false;
-
- /**
- * search the alignment for all new features, give them a colour and display
- * them. Then fires a PropertyChangeEvent on the changeSupport object.
- *
- */
- void findAllFeatures()
- {
- synchronized (firing)
- {
- if (firing.equals(Boolean.FALSE))
- {
- firing = Boolean.TRUE;
- findAllFeatures(true); // add all new features as visible
- changeSupport.firePropertyChange("changeSupport", null, null);
- firing = Boolean.FALSE;
- }
- }
- }
-
- /**
- * Searches alignment for all features and updates colours
- *
- * @param newMadeVisible
- * if true newly added feature types will be rendered immediatly
- */
- synchronized void findAllFeatures(boolean newMadeVisible)
- {
- newFeatureAdded = false;
-
- if (findingFeatures)
- {
- newFeatureAdded = true;
- return;
- }
-
- findingFeatures = true;
-
- if (av.featuresDisplayed == null)
- {
- av.featuresDisplayed = new Hashtable();
- }
-
- allfeatures = new Vector();
- Vector oldfeatures = new Vector();
- if (renderOrder != null)
- {
- for (int i = 0; i < renderOrder.length; i++)
- {
- if (renderOrder[i] != null)
- {
- oldfeatures.addElement(renderOrder[i]);
- }
- }
- }
- if (minmax == null)
- {
- minmax = new Hashtable();
- }
- AlignmentI alignment = av.getAlignment();
- for (int i = 0; i < alignment.getHeight(); i++)
- {
- SequenceFeature[] features = alignment.getSequenceAt(i)
- .getDatasetSequence().getSequenceFeatures();
-
- if (features == null)
- {
- continue;
- }
-
- int index = 0;
- while (index < features.length)
- {
- if (!av.featuresDisplayed.containsKey(features[index].getType()))
- {
-
- if (featureGroups.containsKey(features[index].getType()))
- {
- boolean visible = ((Boolean) featureGroups
- .get(features[index].featureGroup)).booleanValue();
-
- if (!visible)
- {
- index++;
- continue;
- }
- }
-
- if (!(features[index].begin == 0 && features[index].end == 0))
- {
- // If beginning and end are 0, the feature is for the whole sequence
- // and we don't want to render the feature in the normal way
-
- if (newMadeVisible
- && !oldfeatures.contains(features[index].getType()))
- {
- // this is a new feature type on the alignment. Mark it for
- // display.
- av.featuresDisplayed.put(features[index].getType(),
- new Integer(getColour(features[index].getType())
- .getRGB()));
- setOrder(features[index].getType(), 0);
- }
- }
- }
- if (!allfeatures.contains(features[index].getType()))
- {
- allfeatures.addElement(features[index].getType());
- }
- if (features[index].score != Float.NaN)
- {
- int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
- float[][] mm = (float[][]) minmax.get(features[index].getType());
- if (mm == null)
- {
- mm = new float[][]
- { null, null };
- minmax.put(features[index].getType(), mm);
- }
- if (mm[nonpos] == null)
- {
- mm[nonpos] = new float[]
- { features[index].score, features[index].score };
-
- }
- else
- {
- if (mm[nonpos][0] > features[index].score)
- {
- mm[nonpos][0] = features[index].score;
- }
- if (mm[nonpos][1] < features[index].score)
- {
- mm[nonpos][1] = features[index].score;
- }
- }
- }
- index++;
- }
- }
- updateRenderOrder(allfeatures);
- findingFeatures = false;
- }
-
- protected Boolean firing = Boolean.FALSE;
-
- /**
- * replaces the current renderOrder with the unordered features in
- * allfeatures. The ordering of any types in both renderOrder and allfeatures
- * is preserved, and all new feature types are rendered on top of the existing
- * types, in the order given by getOrder or the order given in allFeatures.
- * Note. this operates directly on the featureOrder hash for efficiency. TODO:
- * eliminate the float storage for computing/recalling the persistent ordering
- * New Cability: updates min/max for colourscheme range if its dynamic
- *
- * @param allFeatures
- */
- private void updateRenderOrder(Vector allFeatures)
- {
- Vector allfeatures = new Vector(allFeatures);
- String[] oldRender = renderOrder;
- renderOrder = new String[allfeatures.size()];
- Object mmrange, fc = null;
- boolean initOrders = (featureOrder == null);
- int opos = 0;
- if (oldRender != null && oldRender.length > 0)
- {
- for (int j = 0; j < oldRender.length; j++)
- {
- if (oldRender[j] != null)
- {
- if (initOrders)
- {
- setOrder(oldRender[j], (1 - (1 + (float) j)
- / (float) oldRender.length));
- }
- if (allfeatures.contains(oldRender[j]))
- {
- renderOrder[opos++] = oldRender[j]; // existing features always
- // appear below new features
- allfeatures.removeElement(oldRender[j]);
- if (minmax != null)
- {
- mmrange = minmax.get(oldRender[j]);
- if (mmrange != null)
- {
- fc = featureColours.get(oldRender[j]);
- if (fc != null && fc instanceof GraduatedColor
- && ((GraduatedColor) fc).isAutoScale())
- {
- ((GraduatedColor) fc).updateBounds(
- ((float[][]) mmrange)[0][0],
- ((float[][]) mmrange)[0][1]);
- }
- }
- }
- }
- }
- }
- }
- if (allfeatures.size() == 0)
- {
- // no new features - leave order unchanged.
- return;
- }
- int i = allfeatures.size() - 1;
- int iSize = i;
- boolean sort = false;
- String[] newf = new String[allfeatures.size()];
- float[] sortOrder = new float[allfeatures.size()];
- Enumeration en = allfeatures.elements();
- // sort remaining elements
- while (en.hasMoreElements())
- {
- newf[i] = en.nextElement().toString();
- if (minmax != null)
- {
- // update from new features minmax if necessary
- mmrange = minmax.get(newf[i]);
- if (mmrange != null)
- {
- fc = featureColours.get(newf[i]);
- if (fc != null && fc instanceof GraduatedColor
- && ((GraduatedColor) fc).isAutoScale())
- {
- ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0],
- ((float[][]) mmrange)[0][1]);
- }
- }
- }
- if (initOrders || !featureOrder.containsKey(newf[i]))
- {
- int denom = initOrders ? allfeatures.size() : featureOrder.size();
- // new unordered feature - compute persistent ordering at head of
- // existing features.
- setOrder(newf[i], i / (float) denom);
- }
- // set order from newly found feature from persisted ordering.
- sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue();
- if (i < iSize)
- {
- // only sort if we need to
- sort = sort || sortOrder[i] > sortOrder[i + 1];
- }
- i--;
- }
- if (iSize > 1 && sort)
- {
- jalview.util.QuickSort.sort(sortOrder, newf);
- }
- sortOrder = null;
- System.arraycopy(newf, 0, renderOrder, opos, newf.length);
- }
-
- /**
- * get a feature style object for the given type string. Creates a
- * java.awt.Color for a featureType with no existing colourscheme. TODO:
- * replace return type with object implementing standard abstract colour/style
- * interface
- *
- * @param featureType
- * @return java.awt.Color or GraduatedColor
- */
- public Object getFeatureStyle(String featureType)
- {
- Object fc = featureColours.get(featureType);
- if (fc == null)
- {
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
- Color col = ucs.createColourFromName(featureType);
- featureColours.put(featureType, fc = col);
- }
- return fc;
- }
-
- /**
- * return a nominal colour for this feature
- *
- * @param featureType
- * @return standard color, or maximum colour for graduated colourscheme
- */
- public Color getColour(String featureType)
- {
- Object fc = getFeatureStyle(featureType);
-
- if (fc instanceof Color)
- {
- return (Color) fc;
- }
- else
- {
- if (fc instanceof GraduatedColor)
- {
- return ((GraduatedColor) fc).getMaxColor();
- }
- }
- throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().toString(),featureType}));
- }
-
- /**
- * calculate the render colour for a specific feature using current feature
- * settings.
- *
- * @param feature
- * @return render colour for the given feature
- */
- public Color getColour(SequenceFeature feature)
- {
- Object fc = getFeatureStyle(feature.getType());
- if (fc instanceof Color)
- {
- return (Color) fc;
- }
- else
- {
- if (fc instanceof GraduatedColor)
- {
- return ((GraduatedColor) fc).findColor(feature);
- }
- }
- throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().toString(),feature.getType()}));
- }
-
- private boolean showFeature(SequenceFeature sequenceFeature)
- {
- Object fc = getFeatureStyle(sequenceFeature.type);
- if (fc instanceof GraduatedColor)
- {
- return ((GraduatedColor) fc).isColored(sequenceFeature);
- }
- else
- {
- return true;
- }
- }
-
// // /////////////
// // Feature Editing Dialog
// // Will be refactored in next release.
if (fcol instanceof Color)
{
Color col = JColorChooser.showDialog(Desktop.desktop,
- MessageManager.getString("label.select_feature_colour"), ((Color) fcol));
+ MessageManager.getString("label.select_feature_colour"),
+ ((Color) fcol));
if (col != null)
{
fcol = col;
Object[] options;
if (!newFeatures)
{
- options = new Object[]
- { "Amend", "Delete", "Cancel" };
+ options = new Object[] { "Amend", "Delete", "Cancel" };
}
else
{
- options = new Object[]
- { "OK", "Cancel" };
+ options = new Object[] { "OK", "Cancel" };
}
- String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
- : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
+ String title = newFeatures ? MessageManager
+ .getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features",
+ new String[] { sequences[0].getName() });
int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok"));
+ JOptionPane.QUESTION_MESSAGE, null, options,
+ MessageManager.getString("action.ok"));
jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
lastDescriptionAdded = description.getText().replaceAll("\n", " ");
// TODO: determine if the null feature group is valid
if (lastFeatureGroupAdded.length() < 1)
+ {
lastFeatureGroupAdded = null;
+ }
}
if (!newFeatures)
sf.description = lastDescriptionAdded;
setColour(sf.type, fcol);
- av.featuresDisplayed.put(sf.type, getColour(sf.type));
+ getFeaturesDisplayed().setVisible(sf.type);
try
{
for (int i = 0; i < sequences.length; i++)
{
features[i].type = lastFeatureAdded;
- if (lastFeatureGroupAdded != null)
- features[i].featureGroup = lastFeatureGroupAdded;
+ // fix for JAL-1538 - always set feature group here
+ features[i].featureGroup = lastFeatureGroupAdded;
features[i].description = lastDescriptionAdded;
sequences[i].addSequenceFeature(features[i]);
ffile.parseDescriptionHTML(features[i], false);
}
- if (av.featuresDisplayed == null)
- {
- av.featuresDisplayed = new Hashtable();
- }
-
if (lastFeatureGroupAdded != null)
{
- if (featureGroups == null)
- featureGroups = new Hashtable();
- featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
+ setGroupVisibility(lastFeatureGroupAdded, true);
}
setColour(lastFeatureAdded, fcol);
- av.featuresDisplayed.put(lastFeatureAdded,
- getColour(lastFeatureAdded));
+ setVisible(lastFeatureAdded);
findAllFeatures(false);
// colour.setForeground(colour.getBackground());
}
}
-
- public void setColour(String featureType, Object col)
- {
- // overwrite
- // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
- // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
- // Object c = featureColours.get(featureType);
- // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
- // !((GraduatedColor)c).getMaxColor().equals(_col)))
- {
- featureColours.put(featureType, col);
- }
- }
-
- public void setTransparency(float value)
- {
- transparency = value;
- }
-
- public float getTransparency()
- {
- return transparency;
- }
-
- /**
- * Replace current ordering with new ordering
- *
- * @param data
- * { String(Type), Colour(Type), Boolean(Displayed) }
- */
- public void setFeaturePriority(Object[][] data)
- {
- setFeaturePriority(data, true);
- }
-
- /**
- *
- * @param data
- * { String(Type), Colour(Type), Boolean(Displayed) }
- * @param visibleNew
- * when true current featureDisplay list will be cleared
- */
- public void setFeaturePriority(Object[][] data, boolean visibleNew)
- {
- if (visibleNew)
- {
- if (av.featuresDisplayed != null)
- {
- av.featuresDisplayed.clear();
- }
- else
- {
- av.featuresDisplayed = new Hashtable();
- }
- }
- if (data == null)
- {
- return;
- }
-
- // 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
- 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, data[i][1]); // todo : typesafety - feature color
- // interface object
- if (((Boolean) data[i][2]).booleanValue())
- {
- av.featuresDisplayed.put(type, new Integer(getColour(type)
- .getRGB()));
- }
-
- renderOrder[data.length - i - 1] = type;
- }
- }
-
- }
-
- Map featureOrder = null;
-
- /**
- * analogous to colour - store a normalized ordering for all feature types in
- * this rendering context.
- *
- * @param type
- * Feature type string
- * @param position
- * normalized priority - 0 means always appears on top, 1 means
- * always last.
- */
- public float setOrder(String type, float position)
- {
- if (featureOrder == null)
- {
- featureOrder = new Hashtable();
- }
- featureOrder.put(type, new Float(position));
- return position;
- }
-
- /**
- * get the global priority (0 (top) to 1 (bottom))
- *
- * @param type
- * @return [0,1] or -1 for a type without a priority
- */
- public float getOrder(String type)
- {
- if (featureOrder != null)
- {
- if (featureOrder.containsKey(type))
- {
- return ((Float) featureOrder.get(type)).floatValue();
- }
- }
- return -1;
- }
-
- /**
- * @param listener
- * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
- */
- public void addPropertyChangeListener(PropertyChangeListener listener)
- {
- changeSupport.addPropertyChangeListener(listener);
- }
-
- /**
- * @param listener
- * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
- */
- public void removePropertyChangeListener(PropertyChangeListener listener)
- {
- changeSupport.removePropertyChangeListener(listener);
- }
}
git://source.jalview.org / jalview.git / blobdiff