AlignViewport av;
Color resBoxColour;
-
+ /**
+ * global transparency for feature
+ */
float transparency = 1.0f;
FontMetrics fm;
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)
{
}
else
+ 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].type), start, end, y1, normaliseScore(sequenceFeatures[sfindex]));
+ } else
{
renderFeature(g, seq, seq
.findIndex(sequenceFeatures[sfindex].begin) - 1, seq
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);
+ 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;
}
}
}
+ 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;
}
}
}
+ if (minmax==null)
+ {
+ minmax = new Hashtable();
+ }
for (int i = 0; i < av.alignment.getHeight(); i++)
{
SequenceFeature[] features = av.alignment.getSequenceAt(i)
{
allfeatures.addElement(features[index].getType());
}
+ if (features[index].score!=Float.NaN)
+ {
+ float[] mm = (float[]) minmax.get(features[index].getType());
+ if (mm==null)
+ {
+ mm = new float[] { features[index].score,features[index].score};
+ minmax.put(features[index].getType(), mm);
+ } else {
+ if (mm[0]>features[index].score)
+ {
+ mm[0] = features[index].score;
+ }
+ if (mm[1]<features[index].score)
+ {
+ mm[1] = features[index].score;
+ }
+ }
+ }
index++;
}
}
selectedRow = table.rowAtPoint(evt.getPoint());
if (javax.swing.SwingUtilities.isRightMouseButton(evt))
{
- popupSort((String)table.getValueAt(selectedRow, 0), evt.getX(), evt.getY());
+ popupSort((String) table.getValueAt(selectedRow, 0), fr.minmax,
+ evt.getX(), evt.getY());
}
}
});
{
fs.handlingUpdate = true;
fs.resetTable(null); // new groups may be added with new seuqence
- // feature types only
+ // feature types only
fs.handlingUpdate = false;
}
}
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
- protected void popupSort(final String type, int x, int y)
+ protected void popupSort(final String type, final Hashtable minmax,
+ int x, int y)
{
- JPopupMenu men = new JPopupMenu();
- men.setName("Sort by "+type);
- JMenuItem scr = new JMenuItem("Score");
+ JPopupMenu men = new JPopupMenu("Settings for " + type);
+ JMenuItem scr = new JMenuItem("Sort by Score");
men.add(scr);
- final FeatureSettings me=this;
- scr.addActionListener(new ActionListener() {
+ final FeatureSettings me = this;
+ scr.addActionListener(new ActionListener()
+ {
public void actionPerformed(ActionEvent e)
{
- me.sortByScore(new String[] {type});
+ me.sortByScore(new String[]
+ { type });
}
-
+
});
- JMenuItem dens = new JMenuItem("Density");
- dens.addActionListener(new ActionListener() {
+ JMenuItem dens = new JMenuItem("Sort by Density");
+ dens.addActionListener(new ActionListener()
+ {
public void actionPerformed(ActionEvent e)
{
- me.sortByDens(new String[] { type });
+ me.sortByDens(new String[]
+ { type });
}
-
+
});
men.add(dens);
+ if (minmax != null)
+ {
+ final Object typeMinMax = minmax.get(type);
+ final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height");
+ chb.setSelected(minmax.get(type) != null);
+ chb.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ chb.setState(chb.getState());
+ if (chb.getState())
+ {
+ minmax.put(type, null);
+ }
+ else
+ {
+ minmax.put(type, typeMinMax);
+ }
+ }
+
+ });
+ men.add(chb);
+ }
men.show(table, x, y);
}
{
if (!handlingUpdate)
fr.findAllFeatures(groupChanged != null); // prod to update
- // colourschemes. but don't
- // affect display
+ // colourschemes. but don't
+ // affect display
// 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--)
if (awidth[0] > 0)
{
width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
- // weight - but have to make per
- // sequence, too (awidth[2])
+ // weight - but have to make per
+ // sequence, too (awidth[2])
// if (width[i]==1) // hack to distinguish single width sequences.
num++;
}
JButton cancelDAS = new JButton();
JButton optimizeOrder = new JButton();
+
JButton sortByScore = new JButton();
+
JButton sortByDens = new JButton();
JPanel transbuttons = new JPanel(new BorderLayout());
{
sortByDens(null);
}
- }); cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ });
+ cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
cancel.setText("Cancel");
cancel.addActionListener(new ActionListener()
{
{
sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
}
- protected void sortBy(String[] typ, String methodText, final String method) {
- if (typ==null)
+
+ protected void sortBy(String[] typ, String methodText, final String method)
+ {
+ if (typ == null)
{
typ = getDisplayedFeatureTypes();
}
- String gps[]=null;
+ String gps[] = null;
gps = getDisplayedFeatureGroups();
- if (typ!=null)
+ if (typ != null)
{
- for (int i=0;i<typ.length; i++)
+ for (int i = 0; i < typ.length; i++)
{
- System.err.println("Sorting on Types:"+typ[i]);
+ System.err.println("Sorting on Types:" + typ[i]);
}
}
- if (gps!=null)
+ if (gps != null)
{
-
- for (int i=0;i<gps.length; i++)
+
+ for (int i = 0; i < gps.length; i++)
{
- System.err.println("Sorting on groups:"+gps[i]);
+ System.err.println("Sorting on groups:" + gps[i]);
}
}
AlignmentPanel alignPanel = af.alignPanel;
AlignmentI al = alignPanel.av.getAlignment();
- int start,stop;
+ int start, stop;
SequenceGroup sg = alignPanel.av.getSelectionGroup();
- if (sg!=null)
+ if (sg != null)
{
start = sg.getStartRes();
stop = sg.getEndRes();
- } else {
+ }
+ else
+ {
start = 0;
stop = al.getWidth();
}
SequenceI[] oldOrder = al.getSequencesArray();
- AlignmentSorter.sortByFeature(typ, gps, start, stop,
- al, method);
- af.addHistoryItem(new OrderCommand(methodText, oldOrder,
- alignPanel.av.getAlignment()));
+ AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
+ af.addHistoryItem(new OrderCommand(methodText, oldOrder, alignPanel.av
+ .getAlignment()));
alignPanel.paintAlignment(true);
-
+
}
protected void sortByScore(String[] typ)
private String[] getDisplayedFeatureTypes()
{
- String[] typ=null;
- if (fr!=null)
+ String[] typ = null;
+ if (fr != null)
{
- synchronized (fr.renderOrder) {
+ synchronized (fr.renderOrder)
+ {
typ = new String[fr.renderOrder.length];
System.arraycopy(fr.renderOrder, 0, typ, 0, typ.length);
- for (int i=0;i<typ.length;i++)
+ for (int i = 0; i < typ.length; i++)
{
- if (af.viewport.featuresDisplayed.get(typ[i])==null)
+ if (af.viewport.featuresDisplayed.get(typ[i]) == null)
{
typ[i] = null;
}
private String[] getDisplayedFeatureGroups()
{
- String[] gps=null;
- if (fr!=null)
+ String[] gps = null;
+ if (fr != null)
{
-
- if (fr.featureGroups!=null)
+
+ if (fr.featureGroups != null)
{
Enumeration en = fr.featureGroups.keys();
gps = new String[fr.featureColours.size()];
- int g=0;
- boolean valid=false;
+ int g = 0;
+ boolean valid = false;
while (en.hasMoreElements())
{
String gp = (String) en.nextElement();
- Boolean on = (Boolean )fr.featureGroups.get(gp);
- if (on!=null && on.booleanValue())
+ Boolean on = (Boolean) fr.featureGroups.get(gp);
+ if (on != null && on.booleanValue())
{
valid = true;
gps[g++] = gp;
}
}
- while (g<gps.length)
+ while (g < gps.length)
{
gps[g++] = null;
}
{
dassourceBrowser.initDasSources();
}
+
/**
- * examine the current list of das sources and return any matching the given nicknames in sources
- * @param sources Vector of Strings to resolve to DAS source nicknames.
+ * examine the current list of das sources and return any matching the given
+ * nicknames in sources
+ *
+ * @param sources
+ * Vector of Strings to resolve to DAS source nicknames.
* @return sources that are present in source list.
*/
public Vector resolveSourceNicknames(Vector sources)
{
return dassourceBrowser.resolveSourceNicknames(sources);
}
+
/**
- * get currently selected das sources. ensure you have called initDasSources before calling this.
+ * get currently selected das sources. ensure you have called initDasSources
+ * before calling this.
+ *
* @return vector of selected das source nicknames
*/
public Vector getSelectedSources()
{
return dassourceBrowser.getSelectedSources();
}
+
/**
* properly initialise DAS fetcher and then initiate a new thread to fetch
* features from the named sources (rather than any turned on by default)
git://source.jalview.org / jalview.git / commitdiff