X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=fb7bce5dca5e8fa9189932305890e208317da826;hb=98637eee5027a7d57c71a38a3d4062220bb94f9c;hp=fdd727f749d8b006258e3da453c7b36164f97c25;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index fdd727f..fb7bce5 100755 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -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()); } /** @@ -104,7 +108,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, public void actionPerformed(ActionEvent evt) { AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - if (aa==null) + if (aa == null) { return; } @@ -256,7 +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++) @@ -329,7 +333,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, if (needValidating) { ap.validate(); - needValidating=false; + needValidating = false; } ap.scalePanel.mouseReleased(evt); } @@ -337,7 +341,9 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, public void mouseClicked(MouseEvent evt) { } - boolean needValidating=false; + + boolean needValidating = false; + public void mouseDragged(MouseEvent evt) { if (graphStretch > -1) @@ -350,7 +356,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, } graphStretchY = evt.getY(); adjustPanelHeight(); - needValidating=true; + needValidating = true; ap.paintAlignment(true); } else @@ -368,7 +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++) { @@ -415,6 +421,12 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, public int adjustPanelHeight() { + return adjustPanelHeight(true); + } + + public int adjustPanelHeight(boolean repaint) + { + // setHeight of panels AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); int height = 0; @@ -453,12 +465,15 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, height += aa[i].height; } } - if (height==0) + if (height == 0) { height = 20; } - this.setSize(getSize().width, height); - repaint(); + this.setSize(new Dimension(getSize().width, height)); + if (repaint) + { + repaint(); + } return height; @@ -599,7 +614,7 @@ 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; @@ -697,9 +712,7 @@ 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); } } } @@ -877,9 +890,7 @@ 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; } @@ -990,6 +1001,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, y += aa[i].height; } } + g.translate(0, +scrollOffset); } public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, @@ -1109,15 +1121,20 @@ 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; @@ -1157,22 +1174,37 @@ 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++; } @@ -1184,20 +1216,26 @@ 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, @@ -1226,4 +1264,12 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, x += av.charWidth; } } + + int scrollOffset = 0; + + public void setScrollOffset(int value) + { + scrollOffset = value; + repaint(); + } }