/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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
import java.awt.*;
import java.awt.event.*;
+import java.awt.font.LineMetrics;
+import java.awt.geom.AffineTransform;
import java.awt.image.*;
+import java.util.Hashtable;
+
import javax.swing.*;
+import jalview.analysis.AAFrequency;
import jalview.datamodel.*;
+import jalview.schemes.ColourSchemeI;
/**
* DOCUMENT ME!
}
/**
- * DOCUMENT ME!
+ * Calculates the height of the annotation displayed in the annotation panel.
+ * Callers should normally call the ap.adjustAnnotationHeight method to ensure all
+ * annotation associated components are updated correctly.
+ *
*/
public int adjustPanelHeight()
{
}
this.setPreferredSize(new Dimension(1, height));
+ ap.alabels.validate();
return height;
}
|| label2.equals(LABEL))
{
tlabel = anot[index].description;
- if (tlabel == null)
+ if (tlabel == null || tlabel.length()<1)
{
if (label2.equals(HELIX) || label2.equals(SHEET))
{
int iconOffset = 0;
boolean validRes = false;
boolean validEnd = false;
+ boolean labelAllCols = false;
+ boolean centreColLabels,centreColLabelsDef = av.getCentreColumnLabels();
+ boolean scaleColLabel=false;
boolean[] graphGroupDrawn = new boolean[aa.length];
-
+ int charOffset = 0; // offset for a label
+ float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a column.
+ Font ofont = g.getFont();
// \u03B2 \u03B1
for (int i = 0; i < aa.length; i++)
{
{
continue;
}
-
+ centreColLabels = row.centreColLabels || centreColLabelsDef;
+ labelAllCols = row.showAllColLabels;
+ scaleColLabel = row.scaleColLabel;
lastSS = ' ';
lastSSX = 0;
&& row.annotations[column].displayCharacter != null
&& (row.annotations[column].displayCharacter.length() > 0))
{
-
- int charOffset = (av.getCentreColumnLabels()) ? ((av.charWidth - fm
- .charsWidth(row.annotations[column].displayCharacter
- .toCharArray(), 0,
- row.annotations[column].displayCharacter.length())) / 2)
- : (av.charWidth - fm
- .charWidth(row.annotations[column].displayCharacter
- .charAt(0))) / 2;
-
+
+ if (centreColLabels || scaleColLabel)
+ {
+ fmWidth = (float) fm
+ .charsWidth(row.annotations[column].displayCharacter
+ .toCharArray(), 0,
+ row.annotations[column].displayCharacter.length());
+
+ if ( scaleColLabel ) {
+ // justify the label and scale to fit in column
+ if (fmWidth > av.charWidth) {
+ // scale only if the current font isn't already small enough
+ fmScaling = av.charWidth;
+ fmScaling /= fmWidth;
+ g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(fmScaling, 1.0)));
+ // and update the label's width to reflect the scaling.
+ fmWidth = av.charWidth;
+ }
+ }
+ } else {
+ fmWidth = (float) fm
+ .charWidth(row.annotations[column].displayCharacter.charAt(0));
+ }
+ charOffset = (int) ((av.charWidth - fmWidth) / 2f);
+
if (row.annotations[column].colour == null)
g.setColor(Color.black);
else
(x * av.charWidth) + charOffset, y + iconOffset);
}
else if (row.annotations[column - 1] == null
- || (!row.annotations[column].displayCharacter
+ || (labelAllCols||!row.annotations[column].displayCharacter
.equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter
.length() < 2 && row.annotations[column].secondaryStructure == ' ')))
{
g.drawString(row.annotations[column].displayCharacter, x
* av.charWidth + charOffset, y + iconOffset);
}
+ g.setFont(ofont);
}
if (row.hasIcons)
x1 += av.charWidth / 2;
}
- if (row.annotations[column] == null
+ if (!validRes || row.annotations[column] == null
|| row.annotations[column].secondaryStructure != 'H')
{
g.fillArc((x * av.charWidth) - av.charWidth, y + 4
public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
int eRes, float min, float max, int y)
{
+ ColourSchemeI profcolour = av.getGlobalColourScheme();
+ if (profcolour==null)
+ {
+ profcolour = new jalview.schemes.ZappoColourScheme();
+ }
if (sRes > aa.annotations.length)
{
return;
}
-
+ Font ofont = g.getFont();
eRes = Math.min(eRes, aa.annotations.length);
int x = 0, y1 = y, y2 = y;
{
g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);
}
-
+ // draw profile if available
+ if (aa.annotations[column].value!=0)
+ {
+ int profl[] = getProfileFor(aa,column);
+ int ht = y1,htn=y2-y1;//aa.graphHeight;
+ float wdth;
+ double ht2=0;
+ char[] dc = new char[1];
+ LineMetrics lm;
+ for (int c=1;profl!=null && c<profl[0];)
+ {
+ dc[0] = (char) profl[c++];
+ wdth = av.charWidth;
+ wdth/=(float) fm
+ .charsWidth(dc,0,1);
+
+ if (c>2)
+ {
+ ht+=(int)ht2;
+ }
+ {
+ //if (aa.annotations[column].value==0) {
+ // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, (ht2=(aa.graphHeight*0.1/av.charHeight)))));
+ // ht = y2-(int)ht2;
+ //} else {
+ g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, (ht2=(htn*((double)profl[c++])/100.0))/av.charHeight)));
+ lm = g.getFontMetrics().getLineMetrics(dc,0,1, g);
+ //htn -=ht2;
+ //}
+ g.setColor(profcolour.findColour(dc[0])); // (av.globalColourScheme!=null) ? );// try to get a colourscheme for the group(aa.groupRef.cs==null) ? av.textColour2 : cs.findColour(dc));
+ g.drawChars(dc,0,1,x*av.charWidth, (int) (ht+lm.getHeight()));
+ // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent();
+ }
+ }
+ g.setFont(ofont);
+ }
x++;
-
}
if (aa.threshold != null)
{
}
}
+ private int[] getProfileFor(AlignmentAnnotation aa, int column)
+ {
+ if (aa.groupRef!=null && aa.groupRef.consensusData!=null) {
+ return AAFrequency.extractProfile(aa.groupRef.consensusData[column],aa.groupRef.getIgnoreGapsConsensus());
+ }
+ // TODO extend annotation row to enable dynamic and static profile data to be stored
+ if (aa.autoCalculated && aa.groupRef==null && aa.sequenceRef==null && aa.label.equals("Consensus"))
+ {
+ return AAFrequency.extractProfile(av.hconsensus[column],av.getIgnoreGapsConsensus());
+ }
+ return null;
+ }
+
// used by overview window
public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
int y, int sRes, int eRes)
git://source.jalview.org / jalview.git / blobdiff