X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=d4fcf979ac994dbae1117357d34420d2e11c134a;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=15b590e6d2e5c15468b2aa1ae08543cff84d247d;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index 15b590e..d4fcf97 100755 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -21,6 +21,10 @@ import java.util.*; import java.awt.*; import java.awt.event.*; +import java.awt.font.LineMetrics; +import java.awt.geom.AffineTransform; + +import jalview.analysis.AAFrequency; import jalview.datamodel.*; import jalview.schemes.ColourSchemeI; @@ -76,7 +80,8 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, this.ap = ap; av = ap.av; setLayout(null); - adjustPanelHeight(); + int height = adjustPanelHeight(); + ap.apvscroll.setValues(0, getSize().height, 0, height); addMouseMotionListener(this); @@ -92,7 +97,6 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, public void adjustmentValueChanged(AdjustmentEvent evt) { - ap.alabels.setScrollOffset(-evt.getValue()); } /** @@ -104,6 +108,10 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, public void actionPerformed(ActionEvent evt) { AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + if (aa == null) + { + return; + } Annotation[] anot = aa[activeRow].annotations; if (anot.length < av.getColumnSelection().getMax()) @@ -252,7 +260,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, return; } - int height = 0; + int height = -scrollOffset; activeRow = -1; for (int i = 0; i < aa.length; i++) @@ -322,6 +330,11 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, graphStretch = -1; graphStretchY = -1; mouseDragging = false; + if (needValidating) + { + ap.validate(); + needValidating = false; + } ap.scalePanel.mouseReleased(evt); } @@ -329,6 +342,8 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, { } + boolean needValidating = false; + public void mouseDragged(MouseEvent evt) { if (graphStretch > -1) @@ -340,7 +355,8 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0; } graphStretchY = evt.getY(); - adjustPanelHeight(); + calcPanelHeight(); + needValidating = true; ap.paintAlignment(true); } else @@ -358,7 +374,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, } int row = -1; - int height = 0; + int height = -scrollOffset; for (int i = 0; i < aa.length; i++) { @@ -405,6 +421,26 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, public int adjustPanelHeight() { + return adjustPanelHeight(true); + } + + public int adjustPanelHeight(boolean repaint) + { + int height = calcPanelHeight(); + this.setSize(new Dimension(getSize().width, height)); + if (repaint) + { + repaint(); + } + return height; + } + /** + * calculate the height for visible annotation, revalidating bounds where necessary + * ABSTRACT GUI METHOD + * @return total height of annotation + */ + public int calcPanelHeight() + { // setHeight of panels AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); int height = 0; @@ -443,15 +479,11 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, height += aa[i].height; } } - else + if (height == 0) { height = 20; } - this.setSize(getSize().width, height); - - repaint(); - return height; } @@ -493,13 +525,16 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, public void paint(Graphics g) { - - imgWidth = getSize().width; + Dimension d = getSize(); + imgWidth = d.width; // (av.endRes - av.startRes + 1) * av.charWidth; - - if (image == null || imgWidth != image.getWidth(this)) + if (imgWidth<1 || d.height<1) + { + return; + } + if (image == null || imgWidth != image.getWidth(this) || d.height != image.getHeight(this)) { - image = createImage(imgWidth, ap.annotationPanel.getSize().height); + image = createImage(imgWidth, d.height); gg = image.getGraphics(); gg.setFont(av.getFont()); fm = gg.getFontMetrics(); @@ -591,7 +626,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, } AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - + g.translate(0, -scrollOffset); int x = 0; int y = 0; int column = 0; @@ -689,9 +724,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, if (v == column) { - g - .fillRect(x * av.charWidth, y, av.charWidth, - av.charHeight); + g.fillRect(x * av.charWidth, y, av.charWidth, av.charHeight); } } } @@ -869,9 +902,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, if (sCol == 0 || row.annotations[sCol - 1] == null || row.annotations[sCol - 1].secondaryStructure != 'H') { - g - .fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, - 90, 180); + g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180); x1 += av.charWidth / 2; } @@ -982,6 +1013,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, y += aa[i].height; } } + g.translate(0, +scrollOffset); } public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, @@ -1101,15 +1133,20 @@ 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(); } - * } - */ + 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; @@ -1149,22 +1186,37 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, } } // 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); } - **/ + 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 && c < profl[0];) + { + dc[0] = (char) profl[c++]; + wdth = av.charWidth; + wdth /= (float) fm.charsWidth(dc, 0, 1); + + if (c > 2) + { + 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++; } @@ -1176,20 +1228,26 @@ 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; } - */ + 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, @@ -1218,4 +1276,12 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, x += av.charWidth; } } + + int scrollOffset = 0; + + public void setScrollOffset(int value) + { + scrollOffset = value; + repaint(); + } }