X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=982d3ecab6e5911cdb904e9b04a73679f8c83672;hb=a4a4122f1a7b0c615d6780197456c811db6b8a2f;hp=38e033185f04ce180ded9682b20ac1bfefc751d7;hpb=77ee0174127cb2fd3d817b010b5a36278dd37c45;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index 38e0331..982d3ec 100755 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1) + * 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.appletgui; @@ -22,8 +21,8 @@ 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 @@ -59,13 +58,14 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, int imgWidth = 0; boolean fastPaint = false; - //Used For mouse Dragging and resizing graphs + + // Used For mouse Dragging and resizing graphs int graphStretch = -1; int graphStretchY = -1; - - boolean mouseDragging=false; - + + boolean mouseDragging = false; + public static int GRAPH_HEIGHT = 40; boolean MAC = false; @@ -99,11 +99,15 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, * 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()) @@ -268,13 +272,12 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, { activeRow = i; } - else if (aa[i].graph > 0) + else if (aa[i].graph > 0) { // Stretch Graph graphStretch = i; graphStretchY = evt.getY(); } - break; } @@ -323,13 +326,18 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, graphStretch = -1; graphStretchY = -1; mouseDragging = false; + if (needValidating) + { + ap.validate(); + needValidating=false; + } ap.scalePanel.mouseReleased(evt); } public void mouseClicked(MouseEvent evt) { } - + boolean needValidating=false; public void mouseDragged(MouseEvent evt) { if (graphStretch > -1) @@ -342,6 +350,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, } graphStretchY = evt.getY(); adjustPanelHeight(); + needValidating=true; ap.paintAlignment(true); } else @@ -444,13 +453,11 @@ 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; @@ -558,15 +565,16 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, * 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) { - 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 +608,14 @@ 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 +625,9 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, { continue; } - + centreColLabels = row.centreColLabels || centreColLabelsDef; + labelAllCols = row.showAllColLabels; + scaleColLabel = row.scaleColLabel; lastSS = ' '; lastSSX = 0; @@ -627,13 +643,15 @@ 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 { @@ -692,13 +710,36 @@ 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); @@ -708,16 +749,19 @@ 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 - .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 + 3); + (x * av.charWidth) + charOffset, y + iconOffset + 3); // +3? } + g.setFont(ofont); } if (row.hasIcons) @@ -883,7 +927,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, } } - if (row.graph > 0 && row.graphHeight> 0) + if (row.graph > 0 && row.graphHeight > 0) { if (row.graph == AlignmentAnnotation.LINE_GRAPH) { @@ -997,7 +1041,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, } if (aa.annotations[column] == null) // || coaa.annotations[column - 1] == - // null) + // null) { x++; continue; @@ -1037,11 +1081,16 @@ 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 +1108,16 @@ 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; @@ -1087,15 +1145,34 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, 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); - } - else - { - g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1); + 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); + } } - + // 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 +1184,21 @@ 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)