X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=d4fcf979ac994dbae1117357d34420d2e11c134a;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=cb638dda875a1e6ef53157f53921785fb50051e2;hpb=be8ed26b63eec2546c415d23e58fce77d3e14f2c;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index cb638dd..d4fcf97 100755 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -1,682 +1,1287 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 - */ - -package jalview.appletgui; - -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; - -public class AnnotationPanel - extends Panel implements AdjustmentListener -{ - 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; - - public static int GRAPH_HEIGHT = 40; - - public AnnotationPanel(AlignmentPanel ap) - { - this.ap = ap; - av = ap.av; - this.setLayout(null); - adjustPanelHeight(); - - addMouseMotionListener(new MouseMotionAdapter() - { - public void mouseMoved(MouseEvent evt) - { - doMouseMoved(evt); - } - }); - - // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this ); - } - - - public AnnotationPanel(AlignViewport av) - { - this.av = av; - } - - - public void adjustmentValueChanged(AdjustmentEvent evt) - { - ap.alabels.setScrollOffset( -evt.getValue()); - } - - public int adjustPanelHeight() - { - // setHeight of panels - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - - - int height = 0; - if (aa != null) - { - for (int i = 0; i < aa.length; i++) - { - if (!aa[i].visible) - { - continue; - } - - aa[i].height = 0; - - if (aa[i].hasText) - { - aa[i].height += av.charHeight; - } - if (aa[i].hasIcons) - { - aa[i].height += 16; - } - - if (aa[i].graph>0) - { - aa[i].height += GRAPH_HEIGHT; - } - - if (aa[i].height == 0) - { - aa[i].height = 20; - } - height += aa[i].height; - } - } - else - { - height = 20; - } - - this.setSize(getSize().width, height); - if(ap!=null) - ap.annotationScroller.setSize(getSize().width, height); - - - repaint(); - - return height; - - } - - public void addEditableColumn(int i) - { - if (activeRow == -1) - { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - if(aa ==null) - return; - - for (int j = 0; j < aa.length; j++) - { - if (aa[j].editable) - { - activeRow = j; - break; - } - } - } - - if (activeRes == null) - { - activeRes = new Vector(); - activeRes.addElement(String.valueOf(i)); - return; - } - - activeRes.addElement(String.valueOf(i)); - } - - public void doMouseMoved(MouseEvent evt) - { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - if (aa == null) - { - return; - } - - int row = -1; - int height = 0; - for (int i = 0; i < aa.length; i++) - { - - if (aa[i].visible) - { - height += aa[i].height; - } - - if (evt.getY() < height) - { - row = i; - break; - } - } - - int res = evt.getX() / av.getCharWidth() + av.getStartRes(); - if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null) - { - StringBuffer text = new StringBuffer("Sequence position " + (res + 1) + - " " + - aa[row].annotations[res].description); - ap.alignFrame.statusBar.setText(text.toString()); - } - } - - public void update(Graphics g) - { - paint(g); - } - - public void paint(Graphics g) - { - imgWidth = (av.endRes - av.startRes + 1) * av.charWidth; - - if (image == null || imgWidth != image.getWidth(this)) - { - image = createImage(imgWidth, ap.annotationPanel.getSize().height); - gg = image.getGraphics(); - gg.setFont(av.getFont()); - fm = gg.getFontMetrics(); - fastPaint = false; - } - - if (fastPaint) - { - g.drawImage(image, 0, 0, this); - fastPaint = false; - return; - } - - drawComponent(gg, av.startRes, av.endRes + 1); - g.drawImage(image, 0, 0, this); - } - - public void fastPaint(int horizontal) - { - 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); - int sr = av.startRes, er = av.endRes + 1, transX = 0; - - if (horizontal > 0) // scrollbar pulled right, image to the left - { - transX = (er - sr - horizontal) * av.charWidth; - sr = er - horizontal; - } - else if (horizontal < 0) - { - er = sr - horizontal; - } - - gg.translate(transX, 0); - - drawComponent(gg, sr, er); - - gg.translate( -transX, 0); - - fastPaint = true; - repaint(); - } - - /** - * 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()); - - if (fm == null) - fm = g.getFontMetrics(); - - - g.setColor(Color.white); - g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height); - - if ((av.alignment.getAlignmentAnnotation() == null) || - (av.alignment.getAlignmentAnnotation().length < 1)) - { - g.setColor(Color.white); - g.fillRect(0, 0, getSize().width, getSize().height); - g.setColor(Color.black); - g.drawString("Alignment has no annotations", 20, 15); - - return; - } - - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - - int j; - int x = 0; - int y = 0; - char[] lastSS = new char[aa.length]; - int[] lastSSX = new int[aa.length]; - int iconOffset = av.charHeight / 2; - boolean validRes = false; - - boolean [] graphGroupDrawn = new boolean[aa.length]; - - - //\u03B2 \u03B1 - for (int i = 0; i < aa.length; i++) - { - AlignmentAnnotation row = aa[i]; - - if (!row.visible) - { - continue; - } - - - - if (row.graph>0) - { - if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] ) - continue; - - // this is so that we draw the characters below the graph - y += row.height; - - if (row.hasText) - { - y -= av.charHeight; - } - } - - if (row.hasText) - { - iconOffset = av.charHeight / 2; - } - else - { - iconOffset = 0; - } - - for (j = startRes; j < endRes; j++) - { - if ((row.annotations.length <= j) || - (row.annotations[j] == null)) - { - validRes = false; - } - else - { - validRes = true; - } - - x = (j - startRes) * av.charWidth; - - if (activeRow == i) - { - g.setColor(Color.red); - - if (activeRes != null) - { - for (int n = 0; n < activeRes.size(); n++) - { - int v = Integer.parseInt(activeRes.elementAt(n).toString()); - - if (v == j) - { - g.fillRect((j - startRes) * av.charWidth, y, - av.charWidth, row.height); - } - } - } - } - - if (validRes && - (row.annotations[j].displayCharacter.length() > 0)) - { - - int charOffset = (av.charWidth - - fm.charWidth(row.annotations[j].displayCharacter.charAt( - 0))) / 2; - g.setColor(row.annotations[j].colour); - - if (j == 0 || row.graph>0) - { - g.drawString(row.annotations[j].displayCharacter, x+charOffset, - y + iconOffset + 3); - } - else if (((row.annotations[j - 1] == null) || - (!row.annotations[j].displayCharacter.equals( - row.annotations[j - 1].displayCharacter)))) - { - g.drawString(row.annotations[j].displayCharacter, x+charOffset, - y + iconOffset + 3); - } - } - - if (row.hasIcons) - { - if (!validRes || - (row.annotations[j].secondaryStructure != lastSS[i])) - { - switch (lastSS[i]) - { - case 'H': - g.setColor(HELIX_COLOUR); - g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i], 7, 8, 8); - - break; - - case 'E': - g.setColor(SHEET_COLOUR); - g.fillRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i] - 4, 7); - g.fillPolygon(new int[] { x - 4, x - 4, x }, - new int[] - { - y + iconOffset, y + 14 + iconOffset, - y + 8 + iconOffset - }, 3); - - break; - - - default: - g.setColor(Color.gray); - g.fillRect(lastSSX[i], y + 6 + iconOffset, - x - lastSSX[i], 2); - - break; - } - - if (validRes) - { - lastSS[i] = row.annotations[j].secondaryStructure; - } - else - { - lastSS[i] = ' '; - } - - lastSSX[i] = x; - } - } - } - - x += av.charWidth; - - if (row.hasIcons) - { - switch (lastSS[i]) - { - case 'H': - g.setColor(HELIX_COLOUR); - g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i], 7, 8, 8); - - break; - - case 'E': - g.setColor(SHEET_COLOUR); - - if (row.annotations.length > endRes - && row.annotations[endRes].secondaryStructure != 'E') - { - g.fillRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i] - 4, 7); - g.fillPolygon(new int[] - {x - 4, x - 4, x}, - new int[] - { - y + iconOffset, y + 14 + iconOffset, - y + 7 + iconOffset - }, 3); - } - else - g.fillRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i], 7); - - break; - - case 'C': - break; - - default: - g.setColor(Color.gray); - g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2); - - break; - } - } - - if (row.graph>0) - { - if(row.graph == AlignmentAnnotation.LINE_GRAPH ) - { - if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup]) - { - float groupmax=-999999, groupmin=9999999; - for(int gg=0; gggroupmax) - groupmax = aa[gg].graphMax; - if(aa[gg].graphMin0 && row.hasText) - { - y += av.charHeight; - } - - if (row.graph==0) - { - y += aa[i].height; - } - } - } - - public void drawLineGraph(Graphics g, AlignmentAnnotation aa, - int sRes, int eRes, - int y, - float min, float max, - int graphHeight) - { - if(sRes>aa.annotations.length) - return; - - - eRes = Math.min(eRes, aa.annotations.length); - - int x = 0; - - //Adjustment for fastpaint to left - if(eResaa.annotations.length) - return; - - - eRes = Math.min(eRes, aa.annotations.length); - - int x=0, y1, y2; - - float range = max - min; - - y1 = y2 = y; - - if(min<0) - y2 = (int)(y - (0-min / (range))*aa.graphHeight); - - g.setColor(Color.gray); - - g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2); - - for (int j = sRes; j < eRes; j++) - { - - if (aa.annotations[j] == null) - { - x += av.charWidth; - continue; - } - - g.setColor(aa.annotations[j].colour); - y1 = y - (int) (((aa.annotations[j].value-min) / (range)) * aa.graphHeight); - - if(y1-y2>0) - g.fillRect(x, y2, av.charWidth, y1-y2 ); - else - g.fillRect(x, y1, av.charWidth, y2-y1 ); - - x += av.charWidth; - } - - - if(aa.threshold!=null) - { - g.setColor(aa.threshold.colour); - y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight); - g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2); - } - - - } - - // used by overview window - public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes) - { - g.setColor(Color.white); - g.fillRect(0, 0, width, y); - g.setColor(new Color(0, 0, 180)); - - int x = 0, height; - - for (int j = sRes; j < eRes; j++) - { - g.setColor(aa.annotations[j].colour); - - height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT); - if(height>y) - height = y; - g.fillRect(x, y - height, av.charWidth, height); - x += av.charWidth; - } - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 +{ + 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; + + public AnnotationPanel(AlignmentPanel ap) + { + MAC = new jalview.util.Platform().isAMac(); + this.ap = ap; + av = ap.av; + setLayout(null); + int height = adjustPanelHeight(); + ap.apvscroll.setValues(0, getSize().height, 0, height); + + addMouseMotionListener(this); + + addMouseListener(this); + + // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this ); + } + + public AnnotationPanel(AlignViewport av) + { + this.av = av; + } + + public void adjustmentValueChanged(AdjustmentEvent 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()) + { + Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2]; + System.arraycopy(anot, 0, temp, 0, anot.length); + anot = temp; + aa[activeRow].annotations = anot; + } + + String label = ""; + if (av.colSel != null && av.colSel.size() > 0 + && 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++) + { + anot[av.getColumnSelection().columnAt(i)] = null; + } + } + else if (evt.getActionCommand().equals(LABEL)) + { + label = enterLabel(label, "Enter Label"); + + if (label == null) + { + return; + } + + if ((label.length() > 0) && !aa[activeRow].hasText) + { + aa[activeRow].hasText = true; + } + + for (int i = 0; i < av.getColumnSelection().size(); i++) + { + int index = av.getColumnSelection().columnAt(i); + + if (!av.colSel.isVisible(index)) + continue; + + if (anot[index] == null) + { + anot[index] = new Annotation(label, "", ' ', 0); + } + + anot[index].displayCharacter = label; + } + } + else if (evt.getActionCommand().equals(COLOUR)) + { + UserDefinedColours udc = new UserDefinedColours(this, Color.black, + ap.alignFrame); + + Color col = udc.getColor(); + + for (int i = 0; i < av.getColumnSelection().size(); i++) + { + int index = av.getColumnSelection().columnAt(i); + + if (!av.colSel.isVisible(index)) + continue; + + if (anot[index] == null) + { + anot[index] = new Annotation("", "", ' ', 0); + } + + anot[index].colour = col; + } + } + else + // HELIX OR SHEET + { + char type = 0; + String symbol = "\u03B1"; + + if (evt.getActionCommand().equals(HELIX)) + { + type = 'H'; + } + else if (evt.getActionCommand().equals(SHEET)) + { + type = 'E'; + symbol = "\u03B2"; + } + + if (!aa[activeRow].hasIcons) + { + aa[activeRow].hasIcons = true; + } + + label = enterLabel(symbol, "Enter Label"); + + if (label == null) + { + return; + } + + if ((label.length() > 0) && !aa[activeRow].hasText) + { + aa[activeRow].hasText = true; + } + + for (int i = 0; i < av.getColumnSelection().size(); i++) + { + int index = av.getColumnSelection().columnAt(i); + + if (!av.colSel.isVisible(index)) + continue; + + if (anot[index] == null) + { + anot[index] = new Annotation(label, "", type, 0); + } + + anot[index].secondaryStructure = type; + anot[index].displayCharacter = label; + } + } + + adjustPanelHeight(); + repaint(); + + return; + } + + String enterLabel(String text, String label) + { + EditNameDialog dialog = new EditNameDialog(text, null, label, null, + ap.alignFrame, "Enter Label", 400, 200, true); + + if (dialog.accept) + return dialog.getName(); + else + return null; + } + + public void mousePressed(MouseEvent evt) + { + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + if (aa == null) + { + return; + } + + int height = -scrollOffset; + activeRow = -1; + + for (int i = 0; i < aa.length; i++) + { + if (aa[i].visible) + { + height += aa[i].height; + } + + if (evt.getY() < height) + { + if (aa[i].editable) + { + activeRow = i; + } + else if (aa[i].graph > 0) + { + // Stretch Graph + graphStretch = i; + graphStretchY = evt.getY(); + } + + break; + } + } + + if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK + && activeRow != -1) + { + if (av.getColumnSelection() == null) + { + return; + } + + 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) + { + 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) + { + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + if (aa == null) + { + return; + } + + int row = -1; + int height = -scrollOffset; + for (int i = 0; i < aa.length; i++) + { + + if (aa[i].visible) + { + height += aa[i].height; + } + + if (evt.getY() < height) + { + row = i; + break; + } + } + + int res = evt.getX() / av.getCharWidth() + av.getStartRes(); + + if (av.hasHiddenColumns) + { + res = av.getColumnSelection().adjustForHiddenColumns(res); + } + + 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) + { + text.append(" " + aa[row].annotations[res].description); + } + 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; + + if (aa != null) + { + for (int i = 0; i < aa.length; i++) + { + if (!aa[i].visible) + { + continue; + } + + aa[i].height = 0; + + if (aa[i].hasText) + { + aa[i].height += av.charHeight; + } + + if (aa[i].hasIcons) + { + aa[i].height += 16; + } + + if (aa[i].graph > 0) + { + aa[i].height += aa[i].graphHeight; + } + + if (aa[i].height == 0) + { + aa[i].height = 20; + } + + height += aa[i].height; + } + } + if (height == 0) + { + height = 20; + } + + return height; + + } + + public void addEditableColumn(int i) + { + if (activeRow == -1) + { + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + if (aa == null) + { + return; + } + + for (int j = 0; j < aa.length; j++) + { + if (aa[j].editable) + { + activeRow = j; + break; + } + } + } + + if (activeRes == null) + { + activeRes = new Vector(); + activeRes.addElement(String.valueOf(i)); + return; + } + + activeRes.addElement(String.valueOf(i)); + } + + public void update(Graphics g) + { + paint(g); + } + + public void paint(Graphics g) + { + Dimension d = getSize(); + imgWidth = d.width; + // (av.endRes - av.startRes + 1) * av.charWidth; + if (imgWidth<1 || d.height<1) + { + 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(); + fastPaint = false; + } + + if (fastPaint) + { + g.drawImage(image, 0, 0, this); + fastPaint = false; + return; + } + + gg.setColor(Color.white); + gg.fillRect(0, 0, getSize().width, getSize().height); + drawComponent(gg, av.startRes, av.endRes + 1); + + g.drawImage(image, 0, 0, this); + } + + public void fastPaint(int horizontal) + { + 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); + int sr = av.startRes, er = av.endRes + 1, transX = 0; + + if (horizontal > 0) // scrollbar pulled right, image to the left + { + transX = (er - sr - horizontal) * av.charWidth; + sr = er - horizontal; + } + else if (horizontal < 0) + { + er = sr - horizontal; + } + + gg.translate(transX, 0); + + drawComponent(gg, sr, er); + + gg.translate(-transX, 0); + + fastPaint = true; + repaint(); + } + + /** + * DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + * @param startRes + * DOCUMENT ME! + * @param endRes + * DOCUMENT ME! + */ + public void drawComponent(Graphics g, int startRes, int endRes) + { + Font ofont = av.getFont(); + g.setFont(ofont); + + g.setColor(Color.white); + g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height); + + if (fm == null) + { + fm = g.getFontMetrics(); + } + + if ((av.alignment.getAlignmentAnnotation() == null) + || (av.alignment.getAlignmentAnnotation().length < 1)) + { + g.setColor(Color.white); + g.fillRect(0, 0, getSize().width, getSize().height); + g.setColor(Color.black); + if (av.validCharWidth) + { + g.drawString("Alignment has no annotations", 20, 15); + } + + return; + } + + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + g.translate(0, -scrollOffset); + int x = 0; + int y = 0; + int column = 0; + char lastSS; + 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]; + 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]; + + if (!row.visible) + { + continue; + } + centreColLabels = row.centreColLabels || centreColLabelsDef; + labelAllCols = row.showAllColLabels; + scaleColLabel = row.scaleColLabel; + lastSS = ' '; + lastSSX = 0; + + if (row.graph > 0) + { + if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup]) + { + continue; + } + + // this is so that we draw the characters below the graph + y += row.height; + + if (row.hasText) + { + iconOffset = av.charHeight - fm.getDescent(); + y -= av.charHeight; + } + } + // TODO: else is the logic used in application, applet had no 'else' + else if (row.hasText) + { + iconOffset = av.charHeight - fm.getDescent(); + + } + else + { + iconOffset = 0; + } + + x = 0; + while (x < endRes - startRes) + { + if (av.hasHiddenColumns) + { + column = av.getColumnSelection().adjustForHiddenColumns( + startRes + x); + if (column > row.annotations.length - 1) + { + break; + } + } + else + { + column = startRes + x; + } + + if ((row.annotations.length <= column) + || (row.annotations[column] == null)) + { + validRes = false; + } + else + { + validRes = true; + } + + if (activeRow == i) + { + g.setColor(Color.red); + + if (av.getColumnSelection() != null) + { + for (int n = 0; n < av.getColumnSelection().size(); n++) + { + int v = av.getColumnSelection().columnAt(n); + + if (v == column) + { + 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 (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); + else + g.setColor(row.annotations[column].colour); + + if (column == 0 || row.graph > 0) + { + g.drawString(row.annotations[column].displayCharacter, + (x * av.charWidth) + charOffset, y + iconOffset + 3); // + + // 3? + } + 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); // +3? + } + g.setFont(ofont); + } + + if (row.hasIcons) + { + 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 (!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; + } + + 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) + { + lastSS = row.annotations[column].secondaryStructure; + } + else + { + lastSS = ' '; + } + + lastSSX = (x * av.charWidth); + } + } + + column++; + x++; + } + + if (column >= row.annotations.length) + { + column = row.annotations.length - 1; + validEnd = false; + } + else + { + validEnd = true; + } + + // 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; + } + + 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); + + break; + + case 'E': + g.setColor(SHEET_COLOUR); + + 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); + } + + break; + } + } + + if (row.graph > 0 && row.graphHeight > 0) + { + if (row.graph == AlignmentAnnotation.LINE_GRAPH) + { + if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup]) + { + float groupmax = -999999, groupmin = 9999999; + for (int gg = 0; gg < aa.length; gg++) + { + if (aa[gg].graphGroup != row.graphGroup) + { + continue; + } + + if (aa[gg] != row) + { + aa[gg].visible = false; + } + + if (aa[gg].graphMax > groupmax) + { + groupmax = aa[gg].graphMax; + } + if (aa[gg].graphMin < groupmin) + { + groupmin = aa[gg].graphMin; + } + } + + for (int gg = 0; gg < aa.length; gg++) + { + if (aa[gg].graphGroup == row.graphGroup) + { + drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin, + groupmax, row.graphHeight); + } + } + + graphGroupDrawn[row.graphGroup] = true; + } + else + { + 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); + } + } + + if (row.graph > 0 && row.hasText) + { + y += av.charHeight; + } + + if (row.graph == 0) + { + 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) + { + if (sRes > aa.annotations.length) + { + return; + } + + int x = 0; + + // Adjustment for fastpaint to left + if (eRes < av.endRes) + { + eRes++; + } + + eRes = Math.min(eRes, aa.annotations.length); + + int y1 = y, y2 = y; + float range = max - min; + + // //Draw origin + if (min < 0) + { + y2 = y - (int) ((0 - min / range) * graphHeight); + } + + g.setColor(Color.gray); + g.drawLine(x - av.charWidth, y2, (eRes - sRes) * av.charWidth, y2); + + eRes = Math.min(eRes, aa.annotations.length); + + int column; + int aaMax = aa.annotations.length - 1; + + while (x < eRes - sRes) + { + column = sRes + x; + if (av.hasHiddenColumns) + { + column = av.getColumnSelection().adjustForHiddenColumns(column); + } + + if (column > aaMax) + { + break; + } + + if (aa.annotations[column] == null) // || coaa.annotations[column - 1] == + // null) + { + x++; + continue; + } + + if (aa.annotations[column].colour == null) + g.setColor(Color.black); + else + g.setColor(aa.annotations[column].colour); + 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 - 1].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); + x++; + } + + if (aa.threshold != null) + { + g.setColor(aa.threshold.colour); + + 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) + { + 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; + + float range = max - min; + + if (min < 0) + { + y2 = y - (int) ((0 - min / (range)) * aa.graphHeight); + } + + g.setColor(Color.gray); + + g.drawLine(x, y2, (eRes - sRes) * av.charWidth, y2); + + 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) + { + column = sRes + x; + if (av.hasHiddenColumns) + { + column = av.getColumnSelection().adjustForHiddenColumns(column); + } + + if (column > aaMax) + { + break; + } + + if (aa.annotations[column] == null) + { + x++; + continue; + } + + if (aa.annotations[column].colour == null) + g.setColor(Color.black); + else + g.setColor(aa.annotations[column].colour); + + y1 = y + - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight); + + if (renderHistogram) + { + 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 + 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++; + + } + if (aa.threshold != null) + { + g.setColor(aa.threshold.colour); + 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) + { + eRes = Math.min(eRes, aa.annotations.length); + g.setColor(Color.white); + g.fillRect(0, 0, width, y); + g.setColor(new Color(0, 0, 180)); + + int x = 0, height; + + for (int j = sRes; j < eRes; j++) + { + if (aa.annotations[j].colour == null) + g.setColor(Color.black); + else + g.setColor(aa.annotations[j].colour); + + height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT); + if (height > y) + { + height = y; + } + g.fillRect(x, y - height, av.charWidth, height); + x += av.charWidth; + } + } + + int scrollOffset = 0; + + public void setScrollOffset(int value) + { + scrollOffset = value; + repaint(); + } +}