From 0b1ca393b3e936f798048c8c92d52a31b3498fb0 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 23 Apr 2010 10:56:28 +0000 Subject: [PATCH] ported logo rendering and label fit to column width - but disabled due to 1.1 incompatibility. --- src/jalview/appletgui/AnnotationPanel.java | 137 ++++++++++++++++++++++++---- 1 file changed, 117 insertions(+), 20 deletions(-) diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index 38e0331..c5da18b 100755 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -22,8 +22,8 @@ import java.util.*; import java.awt.*; import java.awt.event.*; - import jalview.datamodel.*; +import jalview.schemes.ColourSchemeI; public class AnnotationPanel extends Panel implements AdjustmentListener, ActionListener, MouseListener, MouseMotionListener @@ -566,7 +566,8 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, */ public void drawComponent(Graphics g, int startRes, int endRes) { - g.setFont(av.getFont()); + Font ofont = av.getFont(); + g.setFont(ofont); g.setColor(Color.white); g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height); @@ -600,8 +601,12 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, int iconOffset = av.charHeight / 2; 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. // \u03B2 \u03B1 for (int i = 0; i < aa.length; i++) { @@ -611,7 +616,9 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, { continue; } - + centreColLabels = row.centreColLabels || centreColLabelsDef; + labelAllCols = row.showAllColLabels; + scaleColLabel = row.scaleColLabel; lastSS = ' '; lastSSX = 0; @@ -627,13 +634,15 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, if (row.hasText) { + iconOffset = av.charHeight - fm.getDescent(); y -= av.charHeight; } } - - if (row.hasText) + //TODO: else is the logic used in application, applet had no 'else' + else if (row.hasText) { - iconOffset = av.charHeight / 2; + iconOffset = av.charHeight - fm.getDescent(); + } else { @@ -692,14 +701,31 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, && (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; + // not 1.1 // g.setFont(new Font(ofont,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 @@ -708,16 +734,17 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, if (column == 0 || row.graph > 0) { g.drawString(row.annotations[column].displayCharacter, - (x * av.charWidth) + charOffset, y + iconOffset + 3); + (x * av.charWidth) + charOffset, y + iconOffset + 3); // + 3? } 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 + 3); + (x * av.charWidth) + charOffset, y + iconOffset + 3); // +3? } + g.setFont(ofont); } if (row.hasIcons) @@ -1037,11 +1064,16 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, 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; @@ -1059,7 +1091,19 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, int column; int aaMax = aa.annotations.length - 1; - + boolean renderHistogram = true, renderProfile = false; + /* Logos are disabled for 2.5 release : Bug # 0060064 + * if (aa.autoCalculated && aa.label.startsWith("Consensus")) { + // TODO: generalise this to have render styles for consensus/profile data + if (aa.groupRef!=null) + { + renderHistogram = aa.groupRef.isShowConsensusHistogram(); + renderProfile = aa.groupRef.isShowSequenceLogo(); + } else { + renderHistogram = av.isShowConsensusHistogram(); + renderProfile = av.isShowSequenceLogo(); + } + }*/ while (x < eRes - sRes) { column = sRes + x; @@ -1087,6 +1131,8 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, y1 = y - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight); + if (renderHistogram) + { if (y1 - y2 > 0) { g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2); @@ -1095,7 +1141,40 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, { g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1); } + } + // draw profile if available + // Disabled for 2.5 release: see bug #0060064 + /** + if (aa.annotations[column].value!=0 && renderProfile) + { + 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 && c2) + { + ht+=(int)ht2; + } + { + // not java 1.1 compatible: Bug # 0060064 + g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, (ht2=(htn*((double)profl[c++])/100.0))/av.charHeight))); + lm = g.getFontMetrics().getLineMetrics(dc,0,1, g); + g.setColor(profcolour.findColour(dc[0])); + g.drawChars(dc,0,1,x*av.charWidth, (int) (ht+lm.getHeight())); + } + } + g.setFont(ofont); + } + **/ x++; } @@ -1107,6 +1186,24 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, } } + /* + * Disabled for 2.5 release - see bug #0060064 + private int[] getProfileFor(AlignmentAnnotation aa, int column) + { +// if (aa.autoCalculated && aa.label.startsWith("Consensus")) { + if (aa.groupRef!=null && aa.groupRef.consensusData!=null) { // && aa.groupRef.isShowSequenceLogo()) { + 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.groupRef==null && aa.sequenceRef==null) // && av.isShowSequenceLogo()) + { + 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) -- 1.7.10.2