X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=695ecedf86c5aa8d3ab45eb9dfb1c8be5cf681c6;hb=1660a4fe03b8dda74b008ae4de2d804f8044a463;hp=743e1fa827f59774f19d29bd685b289b34f2176e;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 743e1fa..695eced 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -20,10 +20,16 @@ package jalview.gui; 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! @@ -120,7 +126,10 @@ public class AnnotationPanel extends JPanel implements MouseListener, } /** - * 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() { @@ -132,6 +141,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, { for (int i = 0; i < aa.length; i++) { + if (aa[i]==null) + { + System.err.println("Null annotation row: ignoring."); + continue; + } if (!aa[i].visible) { continue; @@ -168,6 +182,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, } this.setPreferredSize(new Dimension(1, height)); + if (ap!=null) + { + // revalidate only when the alignment panel is fully constructed + ap.validate(); + } return height; } @@ -329,7 +348,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, || label2.equals(LABEL)) { tlabel = anot[index].description; - if (tlabel == null) + if (tlabel == null || tlabel.length()<1) { if (label2.equals(HELIX) || label2.equals(SHEET)) { @@ -765,8 +784,13 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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++) { @@ -776,7 +800,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, { continue; } - + centreColLabels = row.centreColLabels || centreColLabelsDef; + labelAllCols = row.showAllColLabels; + scaleColLabel = row.scaleColLabel; lastSS = ' '; lastSSX = 0; @@ -893,15 +919,31 @@ public class AnnotationPanel extends JPanel implements MouseListener, && 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 @@ -913,13 +955,14 @@ public class AnnotationPanel extends JPanel implements MouseListener, (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) @@ -953,7 +996,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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 @@ -1239,11 +1282,16 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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; @@ -1261,7 +1309,18 @@ public class AnnotationPanel extends JPanel implements MouseListener, int column; int aaMax = aa.annotations.length - 1; - + boolean renderHistogram = true, renderProfile = true; + 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; @@ -1280,7 +1339,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, x++; continue; } - if (aa.annotations[column].colour == null) g.setColor(Color.black); else @@ -1289,7 +1347,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, y1 = y - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight); - if (y1 - y2 > 0) + if (renderHistogram) + { + if (y1 - y2 > 0) { g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2); } @@ -1297,9 +1357,44 @@ public class AnnotationPanel extends JPanel implements MouseListener, { g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1); } - + } + // draw profile if available + 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; + } + { + //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) { @@ -1315,6 +1410,21 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } + 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)