X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=37c70b79b2579a3be295eddab4415f94e9f45b93;hb=ca79e93cac909fb78e5f6143906e7b635d9bdc35;hp=af1ff7a4d87d4bb2bff91b5ef1f7b662263b4926;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index af1ff7a..37c70b7 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -1,29 +1,34 @@ /* - * 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 (Version 2.5) + * Copyright (C) 2010 J Procter, AM Waterhouse, 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 - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ 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! @@ -84,7 +89,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * Creates a new AnnotationPanel object. * * @param ap - * DOCUMENT ME! + * DOCUMENT ME! */ public AnnotationPanel(AlignmentPanel ap) { @@ -112,7 +117,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void adjustmentValueChanged(AdjustmentEvent evt) { @@ -120,7 +125,10 @@ 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 +140,11 @@ 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; @@ -162,12 +175,18 @@ public class AnnotationPanel extends JPanel implements MouseListener, height += aa[i].height; } } - else + if (height==0) { + // set minimum height = 20; } this.setPreferredSize(new Dimension(1, height)); + if (ap != null) + { + // revalidate only when the alignment panel is fully constructed + ap.validate(); + } return height; } @@ -176,11 +195,15 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ 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()) @@ -224,9 +247,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (anot[index] == null) { anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that - // null exceptions - // aren't raised - // elsewhere. + // null exceptions + // aren't raised + // elsewhere. } else { @@ -329,7 +352,7 @@ 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)) { @@ -358,7 +381,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mousePressed(MouseEvent evt) { @@ -437,7 +460,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseReleased(MouseEvent evt) { @@ -451,7 +474,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseEntered(MouseEvent evt) { @@ -462,7 +485,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseExited(MouseEvent evt) { @@ -473,7 +496,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseDragged(MouseEvent evt) { @@ -499,7 +522,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseMoved(MouseEvent evt) { @@ -542,7 +565,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, res = av.getColumnSelection().adjustForHiddenColumns(res); } - if (aa[row].annotations != null && row > -1 + if (row > -1 && aa[row].annotations != null && res < (int) aa[row].annotations.length) { if (aa[row].graphGroup > -1) @@ -564,10 +587,16 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } else if (aa[row].annotations[res] != null - && aa[row].annotations[res].description != null) + && aa[row].annotations[res].description != null + && aa[row].annotations[res].description.length() > 0) { this.setToolTipText(aa[row].annotations[res].description); } + else + { + // clear the tooltip. + this.setToolTipText(null); + } if (aa[row].annotations[res] != null) { @@ -592,7 +621,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseClicked(MouseEvent evt) { @@ -602,7 +631,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! */ public void paintComponent(Graphics g) { @@ -649,7 +678,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * non-Thread safe repaint * * @param horizontal - * repaint with horizontal shift in alignment + * repaint with horizontal shift in alignment */ public void fastPaint(int horizontal) { @@ -693,11 +722,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! * @param startRes - * DOCUMENT ME! + * DOCUMENT ME! * @param endRes - * DOCUMENT ME! + * DOCUMENT ME! */ public void drawComponent(Graphics g, int startRes, int endRes) { @@ -765,8 +794,15 @@ 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 +812,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, { continue; } - + centreColLabels = row.centreColLabels || centreColLabelsDef; + labelAllCols = row.showAllColLabels; + scaleColLabel = row.scaleColLabel; lastSS = ' '; lastSSX = 0; @@ -894,13 +932,34 @@ public class AnnotationPanel extends JPanel implements MouseListener, && (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); @@ -913,13 +972,15 @@ public class AnnotationPanel extends JPanel implements MouseListener, (x * av.charWidth) + charOffset, y + iconOffset); } else if (row.annotations[column - 1] == null - || (!row.annotations[column].displayCharacter - .equals(row.annotations[column - 1].displayCharacter) || (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 +1014,7 @@ 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 +1300,16 @@ 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 +1327,21 @@ 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 +1360,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, x++; continue; } - if (aa.annotations[column].colour == null) g.setColor(Color.black); else @@ -1289,17 +1368,62 @@ public class AnnotationPanel extends JPanel implements MouseListener, y1 = y - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight); - if (y1 - y2 > 0) + if (renderHistogram) { - g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2); + if (y1 - y2 > 0) + { + g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2); + } + else + { + g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1); + } } - else + // draw profile if available + if (aa.annotations[column].value != 0 && renderProfile) { - g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1); - } + 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) { @@ -1315,6 +1439,29 @@ 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)