X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=7d1333bff4796e55ac3e36a8b2eaeb684f3d587f;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=ec5fbd8e84176b18362e5673d76668744b61eaa8;hpb=e7139af89390be3dc16db40cfba05dca066507fb;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index ec5fbd8..7d1333b 100755 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -1,54 +1,75 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, 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 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. - * - * 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 - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * 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. + * + * 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; 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; -public class AnnotationPanel - extends Panel - implements AdjustmentListener, ActionListener, MouseListener, MouseMotionListener +public class AnnotationPanel extends Panel implements AdjustmentListener, + ActionListener, MouseListener, MouseMotionListener { AlignViewport av; + AlignmentPanel ap; + int activeRow = -1; Vector activeRes; + static String HELIX = "Helix"; + static String SHEET = "Sheet"; + static String LABEL = "Label"; + static String REMOVE = "Remove Annotation"; + static String COLOUR = "Colour"; + static Color HELIX_COLOUR = Color.red.darker(); + static Color SHEET_COLOUR = Color.green.darker().darker(); - + Image image; + Graphics gg; + FontMetrics fm; + int imgWidth = 0; boolean fastPaint = false; + + // Used For mouse Dragging and resizing graphs + int graphStretch = -1; + + int graphStretchY = -1; + + boolean mouseDragging = false; + public static int GRAPH_HEIGHT = 40; boolean MAC = false; @@ -59,13 +80,13 @@ public class AnnotationPanel this.ap = ap; av = ap.av; setLayout(null); - adjustPanelHeight(); + int height = adjustPanelHeight(); + ap.apvscroll.setValues(0, getSize().height, 0, height); addMouseMotionListener(this); addMouseListener(this); - // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this ); } @@ -76,17 +97,21 @@ public class AnnotationPanel public void adjustmentValueChanged(AdjustmentEvent evt) { - ap.alabels.setScrollOffset( -evt.getValue()); } /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * 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()) @@ -99,10 +124,9 @@ public class AnnotationPanel String label = ""; if (av.colSel != null && av.colSel.size() > 0 - && anot[av.colSel.getMin()] != null) + && anot[av.colSel.getMin()] != null) label = anot[av.getColumnSelection().getMin()].displayCharacter; - if (evt.getActionCommand().equals(REMOVE)) { for (int i = 0; i < av.getColumnSelection().size(); i++) @@ -119,7 +143,7 @@ public class AnnotationPanel return; } - if ( (label.length() > 0) && !aa[activeRow].hasText) + if ((label.length() > 0) && !aa[activeRow].hasText) { aa[activeRow].hasText = true; } @@ -128,7 +152,7 @@ public class AnnotationPanel { int index = av.getColumnSelection().columnAt(i); - if(!av.colSel.isVisible(index)) + if (!av.colSel.isVisible(index)) continue; if (anot[index] == null) @@ -141,9 +165,8 @@ public class AnnotationPanel } else if (evt.getActionCommand().equals(COLOUR)) { - UserDefinedColours udc = new UserDefinedColours( - this, - Color.black, ap.alignFrame); + UserDefinedColours udc = new UserDefinedColours(this, Color.black, + ap.alignFrame); Color col = udc.getColor(); @@ -151,7 +174,7 @@ public class AnnotationPanel { int index = av.getColumnSelection().columnAt(i); - if(!av.colSel.isVisible(index)) + if (!av.colSel.isVisible(index)) continue; if (anot[index] == null) @@ -162,7 +185,8 @@ public class AnnotationPanel anot[index].colour = col; } } - else // HELIX OR SHEET + else + // HELIX OR SHEET { char type = 0; String symbol = "\u03B1"; @@ -189,7 +213,7 @@ public class AnnotationPanel return; } - if ( (label.length() > 0) && !aa[activeRow].hasText) + if ((label.length() > 0) && !aa[activeRow].hasText) { aa[activeRow].hasText = true; } @@ -198,7 +222,7 @@ public class AnnotationPanel { int index = av.getColumnSelection().columnAt(i); - if(!av.colSel.isVisible(index)) + if (!av.colSel.isVisible(index)) continue; if (anot[index] == null) @@ -219,10 +243,10 @@ public class AnnotationPanel String enterLabel(String text, String label) { - EditNameDialog dialog = new EditNameDialog(text,null,label,null, - ap.alignFrame,"Enter Label", 400,200, true); + EditNameDialog dialog = new EditNameDialog(text, null, label, null, + ap.alignFrame, "Enter Label", 400, 200, true); - if(dialog.accept) + if (dialog.accept) return dialog.getName(); else return null; @@ -230,83 +254,115 @@ public class AnnotationPanel public void mousePressed(MouseEvent evt) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - if (aa == null) - { - return; - } - - int height = 0; - activeRow = -1; + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + if (aa == null) + { + return; + } + int height = -scrollOffset; + activeRow = -1; - for (int i = 0; i < aa.length; i++) + for (int i = 0; i < aa.length; i++) + { + if (aa[i].visible) { - if (aa[i].visible) - { - height += aa[i].height; - } - - if (evt.getY() < height) - { - if (aa[i].editable) - { - activeRow = i; - } - - break; - } + height += aa[i].height; } - if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) == - InputEvent.BUTTON3_MASK && activeRow != -1) + if (evt.getY() < height) { - if (av.getColumnSelection() == null) + if (aa[i].editable) { - return; + activeRow = i; + } + else if (aa[i].graph > 0) + { + // Stretch Graph + graphStretch = i; + graphStretchY = evt.getY(); } - PopupMenu pop = new PopupMenu("Structure type"); - MenuItem item = new MenuItem(HELIX); - item.addActionListener(this); - pop.add(item); - item = new MenuItem(SHEET); - item.addActionListener(this); - pop.add(item); - item = new MenuItem(LABEL); - item.addActionListener(this); - pop.add(item); - item = new MenuItem(COLOUR); - item.addActionListener(this); - pop.add(item); - item = new MenuItem(REMOVE); - item.addActionListener(this); - pop.add(item); - ap.alignFrame.add(pop); - pop.show(this, evt.getX(), evt.getY()); - - return; + break; } + } - if (aa == null) + if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK + && activeRow != -1) + { + if (av.getColumnSelection() == null) { return; } - ap.scalePanel.mousePressed(evt); + PopupMenu pop = new PopupMenu("Structure type"); + MenuItem item = new MenuItem(HELIX); + item.addActionListener(this); + pop.add(item); + item = new MenuItem(SHEET); + item.addActionListener(this); + pop.add(item); + item = new MenuItem(LABEL); + item.addActionListener(this); + pop.add(item); + item = new MenuItem(COLOUR); + item.addActionListener(this); + pop.add(item); + item = new MenuItem(REMOVE); + item.addActionListener(this); + pop.add(item); + ap.alignFrame.add(pop); + pop.show(this, evt.getX(), evt.getY()); + + return; + } + + if (aa == null) + { + return; + } + + ap.scalePanel.mousePressed(evt); } public void mouseReleased(MouseEvent evt) { + 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) { - ap.scalePanel.mouseDragged(evt); + if (graphStretch > -1) + { + av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY + - evt.getY(); + if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0) + { + av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0; + } + graphStretchY = evt.getY(); + calcPanelHeight(); + needValidating = true; + ap.paintAlignment(true); + } + else + { + ap.scalePanel.mouseDragged(evt); + } } public void mouseMoved(MouseEvent evt) @@ -318,7 +374,7 @@ public class AnnotationPanel } int row = -1; - int height = 0; + int height = -scrollOffset; for (int i = 0; i < aa.length; i++) { @@ -341,7 +397,8 @@ public class AnnotationPanel res = av.getColumnSelection().adjustForHiddenColumns(res); } - if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null) + if (row > -1 && res < aa[row].annotations.length + && aa[row].annotations[res] != null) { StringBuffer text = new StringBuffer("Sequence position " + (res + 1)); if (aa[row].annotations[res].description != null) @@ -351,18 +408,39 @@ public class AnnotationPanel ap.alignFrame.statusBar.setText(text.toString()); } } + public void mouseEntered(MouseEvent evt) { ap.scalePanel.mouseEntered(evt); } + public void mouseExited(MouseEvent evt) { ap.scalePanel.mouseExited(evt); } - 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; @@ -401,15 +479,11 @@ public class AnnotationPanel height += aa[i].height; } } - else + if (height == 0) { height = 20; } - this.setSize(getSize().width, height); - - repaint(); - return height; } @@ -444,7 +518,6 @@ public class AnnotationPanel activeRes.addElement(String.valueOf(i)); } - public void update(Graphics g) { paint(g); @@ -452,13 +525,16 @@ public class AnnotationPanel public void paint(Graphics g) { - - imgWidth = getSize().width; - //(av.endRes - av.startRes + 1) * av.charWidth; - - if (image == null || imgWidth != image.getWidth(this)) + Dimension d = getSize(); + imgWidth = d.width; + // (av.endRes - av.startRes + 1) * av.charWidth; + if (imgWidth<1 || d.height<1) { - image = createImage(imgWidth, ap.annotationPanel.getSize().height); + return; + } + if (image == null || imgWidth != image.getWidth(this) || d.height != image.getHeight(this)) + { + image = createImage(imgWidth, d.height); gg = image.getGraphics(); gg.setFont(av.getFont()); fm = gg.getFontMetrics(); @@ -481,16 +557,15 @@ public class AnnotationPanel public void fastPaint(int horizontal) { - if (horizontal == 0 - || av.alignment.getAlignmentAnnotation() == null - || av.alignment.getAlignmentAnnotation().length < 1 - ) + if (horizontal == 0 || av.alignment.getAlignmentAnnotation() == null + || av.alignment.getAlignmentAnnotation().length < 1) { repaint(); return; } - gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal * av.charWidth, 0); + gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal + * av.charWidth, 0); int sr = av.startRes, er = av.endRes + 1, transX = 0; if (horizontal > 0) // scrollbar pulled right, image to the left @@ -507,7 +582,7 @@ public class AnnotationPanel drawComponent(gg, sr, er); - gg.translate( -transX, 0); + gg.translate(-transX, 0); fastPaint = true; repaint(); @@ -515,14 +590,18 @@ public class AnnotationPanel /** * DOCUMENT ME! - * - * @param g DOCUMENT ME! - * @param startRes DOCUMENT ME! - * @param endRes DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + * @param startRes + * DOCUMENT ME! + * @param endRes + * 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); @@ -532,8 +611,8 @@ public class AnnotationPanel fm = g.getFontMetrics(); } - if ( (av.alignment.getAlignmentAnnotation() == null) || - (av.alignment.getAlignmentAnnotation().length < 1)) + if ((av.alignment.getAlignmentAnnotation() == null) + || (av.alignment.getAlignmentAnnotation().length < 1)) { g.setColor(Color.white); g.fillRect(0, 0, getSize().width, getSize().height); @@ -547,7 +626,7 @@ public class AnnotationPanel } AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - + g.translate(0, -scrollOffset); int x = 0; int y = 0; int column = 0; @@ -555,10 +634,16 @@ public class AnnotationPanel int lastSSX; 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]; - - //\u03B2 \u03B1 + 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++) { AlignmentAnnotation row = aa[i]; @@ -567,7 +652,9 @@ public class AnnotationPanel { continue; } - + centreColLabels = row.centreColLabels || centreColLabelsDef; + labelAllCols = row.showAllColLabels; + scaleColLabel = row.scaleColLabel; lastSS = ' '; lastSSX = 0; @@ -583,13 +670,15 @@ public class AnnotationPanel 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 { @@ -601,7 +690,8 @@ public class AnnotationPanel { if (av.hasHiddenColumns) { - column = av.getColumnSelection().adjustForHiddenColumns(startRes + x); + column = av.getColumnSelection().adjustForHiddenColumns( + startRes + x); if (column > row.annotations.length - 1) { break; @@ -612,8 +702,8 @@ public class AnnotationPanel column = startRes + x; } - if ( (row.annotations.length <= column) || - (row.annotations[column] == null)) + if ((row.annotations.length <= column) + || (row.annotations[column] == null)) { validRes = false; } @@ -634,25 +724,47 @@ public class AnnotationPanel if (v == column) { - g.fillRect(x * av.charWidth, y, - av.charWidth, av.charHeight); + g.fillRect(x * av.charWidth, y, av.charWidth, av.charHeight); } } } } + if (av.validCharWidth + && validRes + && (row.annotations[column].displayCharacter != null && row.annotations[column].displayCharacter + .length() > 0)) + { + if (centreColLabels || scaleColLabel) + { + fmWidth = (float) fm.charsWidth( + row.annotations[column].displayCharacter.toCharArray(), + 0, row.annotations[column].displayCharacter.length()); - if (av.validCharWidth && validRes && - (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 (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); @@ -662,87 +774,81 @@ public class AnnotationPanel 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.length() < 2 && - row.annotations[column].secondaryStructure == ' '))) + else if (row.annotations[column - 1] == null + || (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) { - if (!validRes || - (row.annotations[column].secondaryStructure != lastSS)) + if (!validRes + || (row.annotations[column].secondaryStructure != lastSS)) { switch (lastSS) { - case 'H': - g.setColor(HELIX_COLOUR); - if (MAC) - { - //Off by 1 offset when drawing rects and ovals - //to offscreen image on the MAC - g.fillRoundRect(lastSSX, y + 4 + iconOffset, - (x * av.charWidth) - lastSSX, 7, 8, 8); - break; - } - - int sCol = (lastSSX / av.charWidth) + startRes; - int x1 = lastSSX; - int x2 = (x * av.charWidth); - - 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); - x1 += av.charWidth / 2; - } - - if (row.annotations[column] == null || - row.annotations[column].secondaryStructure != 'H') - { - g.fillArc( (x * av.charWidth) - av.charWidth, - y + 4 + iconOffset, av.charWidth, 8, 270, 180); - x2 -= av.charWidth / 2; - } - - g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); + case 'H': + g.setColor(HELIX_COLOUR); + if (MAC) + { + // Off by 1 offset when drawing rects and ovals + // to offscreen image on the MAC + g.fillRoundRect(lastSSX, y + 4 + iconOffset, + (x * av.charWidth) - lastSSX, 7, 8, 8); break; + } - case 'E': - g.setColor(SHEET_COLOUR); - g.fillRect(lastSSX, y + 4 + iconOffset, - (x * av.charWidth) - lastSSX - 4, 7); - g.fillPolygon(new int[] - { (x * av.charWidth) - 4, - (x * av.charWidth) - 4, - (x * av.charWidth)}, - new int[] - { - y + iconOffset, y + 14 + iconOffset, - y + 8 + iconOffset - }, 3); + int sCol = (lastSSX / av.charWidth) + startRes; + int x1 = lastSSX; + int x2 = (x * av.charWidth); - break; + 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); + x1 += av.charWidth / 2; + } - default: - g.setColor(Color.gray); - g.fillRect(lastSSX, y + 6 + iconOffset, - (x * av.charWidth) - lastSSX, 2); + if (!validRes || row.annotations[column] == null + || row.annotations[column].secondaryStructure != 'H') + { + g.fillArc((x * av.charWidth) - av.charWidth, y + 4 + + iconOffset, av.charWidth, 8, 270, 180); + x2 -= av.charWidth / 2; + } - break; + g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); + break; + + case 'E': + g.setColor(SHEET_COLOUR); + g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) + - lastSSX - 4, 7); + g.fillPolygon(new int[] + { (x * av.charWidth) - 4, (x * av.charWidth) - 4, + (x * av.charWidth) }, new int[] + { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, + 3); + + break; + + default: + g.setColor(Color.gray); + g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) + - lastSSX, 2); + + break; } if (validRes) @@ -765,88 +871,86 @@ public class AnnotationPanel if (column >= row.annotations.length) { column = row.annotations.length - 1; + validEnd = false; + } + else + { + validEnd = true; } - // x ++; + // x ++; if (row.hasIcons) { switch (lastSS) { - case 'H': - g.setColor(HELIX_COLOUR); - if (MAC) - { - //Off by 1 offset when drawing rects and ovals - //to offscreen image on the MAC - g.fillRoundRect(lastSSX, y + 4 + iconOffset, - (x * av.charWidth) - lastSSX, 7, 8, 8); - break; - } + case 'H': + g.setColor(HELIX_COLOUR); + if (MAC) + { + // Off by 1 offset when drawing rects and ovals + // to offscreen image on the MAC + g.fillRoundRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) + - lastSSX, 7, 8, 8); + break; + } - int sCol = (lastSSX / av.charWidth) + startRes; - int x1 = lastSSX; - int x2 = (x * av.charWidth); + int sCol = (lastSSX / av.charWidth) + startRes; + int x1 = lastSSX; + int x2 = (x * av.charWidth); - 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); - x1 += av.charWidth / 2; - } + 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); + x1 += av.charWidth / 2; + } - if (row.annotations[column] == null || - row.annotations[column].secondaryStructure != 'H') - { - g.fillArc( (x * av.charWidth) - av.charWidth, - y + 4 + iconOffset, av.charWidth, 8, 270, - 180); - x2 -= av.charWidth / 2; - } + if (row.annotations[column] == null + || row.annotations[column].secondaryStructure != 'H') + { + g.fillArc((x * av.charWidth) - av.charWidth, + y + 4 + iconOffset, av.charWidth, 8, 270, 180); + x2 -= av.charWidth / 2; + } - g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); + g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); - break; + break; - case 'E': - g.setColor(SHEET_COLOUR); + case 'E': + g.setColor(SHEET_COLOUR); - if (row.annotations[endRes] == null - || row.annotations[endRes].secondaryStructure != 'E') - { - g.fillRect(lastSSX, y + 4 + iconOffset, - (x * av.charWidth) - lastSSX - 4, 7); - g.fillPolygon(new int[] - { (x * av.charWidth) - 4, - (x * av.charWidth) - 4, - (x * av.charWidth)}, - new int[] - { - y + iconOffset, y + 14 + iconOffset, - y + 7 + iconOffset - }, 3); - } - else - { - g.fillRect(lastSSX, y + 4 + iconOffset, - x * av.charWidth - lastSSX, 7); - } - break; + if (!validEnd || row.annotations[endRes] == null + || row.annotations[endRes].secondaryStructure != 'E') + { + g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) + - lastSSX - 4, 7); + g.fillPolygon(new int[] + { (x * av.charWidth) - 4, (x * av.charWidth) - 4, + (x * av.charWidth) }, new int[] + { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, 3); + } + else + { + g.fillRect(lastSSX, y + 4 + iconOffset, x * av.charWidth + - lastSSX, 7); + } + break; - default: - g.setColor(Color.gray); - if (!av.wrapAlignment || endRes == av.endRes) - { - g.fillRect(lastSSX, y + 6 + iconOffset, - (x * av.charWidth) - lastSSX, 2); - } + default: + g.setColor(Color.gray); + if (!av.wrapAlignment || endRes == av.endRes) + { + g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) + - lastSSX, 2); + } - break; + break; } } - if (row.graph > 0) + if (row.graph > 0 && row.graphHeight > 0) { if (row.graph == AlignmentAnnotation.LINE_GRAPH) { @@ -879,9 +983,8 @@ public class AnnotationPanel { if (aa[gg].graphGroup == row.graphGroup) { - drawLineGraph(g, aa[gg], startRes, endRes, y, - groupmin, groupmax, - row.graphHeight); + drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin, + groupmax, row.graphHeight); } } @@ -889,14 +992,14 @@ public class AnnotationPanel } else { - drawLineGraph(g, row, startRes, endRes, - y, row.graphMin, row.graphMax, row.graphHeight); + drawLineGraph(g, row, startRes, endRes, y, row.graphMin, + row.graphMax, row.graphHeight); } } else if (row.graph == AlignmentAnnotation.BAR_GRAPH) { - drawBarGraph(g, row, startRes, endRes, - row.graphMin, row.graphMax, y); + drawBarGraph(g, row, startRes, endRes, row.graphMin, + row.graphMax, y); } } @@ -910,13 +1013,11 @@ public class AnnotationPanel y += aa[i].height; } } + g.translate(0, +scrollOffset); } - public void drawLineGraph(Graphics g, AlignmentAnnotation aa, - int sRes, int eRes, - int y, - float min, float max, - int graphHeight) + public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, + int eRes, int y, float min, float max, int graphHeight) { if (sRes > aa.annotations.length) { @@ -925,7 +1026,7 @@ public class AnnotationPanel int x = 0; - //Adjustment for fastpaint to left + // Adjustment for fastpaint to left if (eRes < av.endRes) { eRes++; @@ -936,10 +1037,10 @@ public class AnnotationPanel int y1 = y, y2 = y; float range = max - min; - ////Draw origin + // //Draw origin if (min < 0) { - y2 = y - (int) ( (0 - min / range) * graphHeight); + y2 = y - (int) ((0 - min / range) * graphHeight); } g.setColor(Color.gray); @@ -962,8 +1063,9 @@ public class AnnotationPanel { break; } - - if (aa.annotations[column] == null) // || coaa.annotations[column - 1] == null) + + if (aa.annotations[column] == null) // || coaa.annotations[column - 1] == + // null) { x++; continue; @@ -973,19 +1075,21 @@ public class AnnotationPanel g.setColor(Color.black); else g.setColor(aa.annotations[column].colour); - if (column==0 || aa.annotations[column-1]==null) + if (column == 0 || aa.annotations[column - 1] == null) + { + y1 = y + - (int) (((aa.annotations[column].value - min) / range) * graphHeight); + } + else { - y1 = y - - (int) ( ( (aa.annotations[column].value - min) / range) * graphHeight); - } else { - y1 = y - - (int) ( ( (aa.annotations[column-1].value - min) / range) * graphHeight); + y1 = y + - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight); } - y2 = y - - (int) ( ( (aa.annotations[column].value - min) / range) * graphHeight); + y2 = y + - (int) (((aa.annotations[column].value - min) / range) * graphHeight); - g.drawLine(x * av.charWidth - av.charWidth / 2, y1, - x * av.charWidth + av.charWidth / 2, y2); + g.drawLine(x * av.charWidth - av.charWidth / 2, y1, x * av.charWidth + + av.charWidth / 2, y2); x++; } @@ -993,21 +1097,24 @@ public class AnnotationPanel { g.setColor(aa.threshold.colour); - y2 = (int) (y - ( (aa.threshold.value - min) / range) * graphHeight); + y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight); g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2); } } - public void drawBarGraph(Graphics g, AlignmentAnnotation aa, - int sRes, int eRes, - float min, float max, - int y) + 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; @@ -1016,7 +1123,7 @@ public class AnnotationPanel if (min < 0) { - y2 = y - (int) ( (0 - min / (range)) * aa.graphHeight); + y2 = y - (int) ((0 - min / (range)) * aa.graphHeight); } g.setColor(Color.gray); @@ -1025,6 +1132,20 @@ public class AnnotationPanel int column; int aaMax = aa.annotations.length - 1; + boolean renderHistogram = true, renderProfile = false; + 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) { @@ -1050,16 +1171,50 @@ public class AnnotationPanel else g.setColor(aa.annotations[column].colour); - y1 = y - - (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight); + 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; + } + { // 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++; @@ -1068,14 +1223,35 @@ public class AnnotationPanel if (aa.threshold != null) { g.setColor(aa.threshold.colour); - y2 = (int) (y - ( (aa.threshold.value - min) / range) * aa.graphHeight); + y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight); g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2); } } + 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) + public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, + int y, int sRes, int eRes) { eRes = Math.min(eRes, aa.annotations.length); g.setColor(Color.white); @@ -1091,7 +1267,7 @@ public class AnnotationPanel else g.setColor(aa.annotations[j].colour); - height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT); + height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT); if (height > y) { height = y; @@ -1100,4 +1276,12 @@ public class AnnotationPanel x += av.charWidth; } } + + int scrollOffset = 0; + + public void setScrollOffset(int value) + { + scrollOffset = value; + repaint(); + } }