X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=101bddf40c56877c6c1d35588644235f65165944;hb=1f9990748644d3380bc045aad1f694c0252cc35f;hp=ec5fbc62576a272d4b6584ed570de7421977c2de;hpb=7720c1e94b0b88c9be05becae787078f152d8c5b;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index ec5fbc6..101bddf 100755 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 @@ -27,7 +27,8 @@ import java.awt.event.*; import jalview.datamodel.*; public class AnnotationPanel - extends Panel implements AdjustmentListener + extends Panel + implements AdjustmentListener, ActionListener, MouseListener, MouseMotionListener { AlignViewport av; AlignmentPanel ap; @@ -51,33 +52,325 @@ public class AnnotationPanel public static int GRAPH_HEIGHT = 40; + boolean MAC = false; + public AnnotationPanel(AlignmentPanel ap) { + if (System.getProperty("os.name").startsWith("Mac")) + { + MAC = true; + } + this.ap = ap; av = ap.av; - this.setLayout(null); + setLayout(null); adjustPanelHeight(); - addMouseMotionListener(new MouseMotionAdapter() - { - public void mouseMoved(MouseEvent evt) - { - doMouseMoved(evt); - } - }); + addMouseMotionListener(this); + + addMouseListener(this); + // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this ); } + public AnnotationPanel(AlignViewport av) + { + this.av = av; + } + public void adjustmentValueChanged(AdjustmentEvent evt) { ap.alabels.setScrollOffset( -evt.getValue()); } - public void adjustPanelHeight() + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void actionPerformed(ActionEvent evt) + { + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + 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); + + 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 = 0; + 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; + } + + 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) + { + ap.scalePanel.mouseReleased(evt); + } + + public void mouseClicked(MouseEvent evt) + {} + + public void mouseDragged(MouseEvent evt) + { + ap.scalePanel.mouseDragged(evt); + } + + public void mouseMoved(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 (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() { // setHeight of panels AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + int height = 0; if (aa != null) { @@ -99,7 +392,7 @@ public class AnnotationPanel aa[i].height += 16; } - if (aa[i].isGraph) + if (aa[i].graph > 0) { aa[i].height += GRAPH_HEIGHT; } @@ -117,12 +410,11 @@ public class AnnotationPanel } this.setSize(getSize().width, height); - ap.annotationScroller.setSize(getSize().width, height); - -// ap.annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height); repaint(); + return height; + } public void addEditableColumn(int i) @@ -130,6 +422,11 @@ public class AnnotationPanel if (activeRow == -1) { AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + if (aa == null) + { + return; + } + for (int j = 0; j < aa.length; j++) { if (aa[j].editable) @@ -150,40 +447,6 @@ public class AnnotationPanel 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) { @@ -192,9 +455,9 @@ public class AnnotationPanel public void paint(Graphics g) { - g.setColor(Color.white); - g.fillRect(0,0, getSize().width, getSize().height); - imgWidth = (av.endRes - av.startRes + 1) * av.charWidth; + + imgWidth = getSize().width; + //(av.endRes - av.startRes + 1) * av.charWidth; if (image == null || imgWidth != image.getWidth(this)) { @@ -212,9 +475,11 @@ public class AnnotationPanel 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); + g.drawImage(image, 0, 0, this); } public void fastPaint(int horizontal) @@ -251,46 +516,80 @@ public class AnnotationPanel 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()); + g.setColor(Color.white); g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height); - if (av.alignment.getAlignmentAnnotation() == null || - av.alignment.getAlignmentAnnotation().length < 1) + + 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); - g.drawString("Alignment has no annotations", 20, 15); + if (av.validCharWidth) + { + g.drawString("Alignment has no annotations", 20, 15); + } + return; } AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - int j, x = 0, y = 0; - char[] lastSS = new char[aa.length]; - int[] lastSSX = new int[aa.length]; + int x = 0; + int y = 0; + int column = 0; + char lastSS; + int lastSSX; int iconOffset = av.charHeight / 2; boolean validRes = false; - //\u03B2 \u03B1 + 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.isGraph) + 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) { y -= av.charHeight; } } + if (row.hasText) { iconOffset = av.charHeight / 2; @@ -300,9 +599,24 @@ public class AnnotationPanel iconOffset = 0; } - for (j = startRes; j < endRes; j++) + x = 0; + while (x < endRes - startRes) { - if (row.annotations.length <= j || row.annotations[j] == null) + 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; } @@ -311,191 +625,480 @@ public class AnnotationPanel validRes = true; } - x = (j - startRes) * av.charWidth; - if (activeRow == i) { - g.setColor(Color.red); - if (activeRes != null) + if (av.getColumnSelection() != null) { - for (int n = 0; n < activeRes.size(); n++) + for (int n = 0; n < av.getColumnSelection().size(); n++) { - int v = Integer.parseInt(activeRes.elementAt(n).toString()); - if (v == j) + int v = av.getColumnSelection().columnAt(n); + + if (v == column) { - g.fillRect( (j - startRes) * av.charWidth, y, av.charWidth, - row.height); + g.fillRect(x * av.charWidth, y, + av.charWidth, av.charHeight); } } } } - if (validRes && row.annotations[j].displayCharacter.length() > 0) + + + if (av.validCharWidth && validRes && + (row.annotations[column].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.isGraph) - { - if (row.annotations[0].secondaryStructure == 'H' - || row.annotations[0].secondaryStructure == 'E') - { - g.drawString(row.annotations[j].displayCharacter, x, - y + iconOffset + 3); - } - } - else if ( (row.annotations[j].secondaryStructure == 'H' - || row.annotations[j].secondaryStructure == 'E') && - (row.annotations[j - 1] == null || - row.annotations[j].secondaryStructure != - row.annotations[j - 1].secondaryStructure)) - { + fm.charWidth(row.annotations[column]. + displayCharacter.charAt( + 0))) / 2; + + if (row.annotations[column].colour == null) + g.setColor(Color.black); + else + g.setColor(row.annotations[column].colour); - g.drawString(row.annotations[j].displayCharacter, x + charOffset, + if (column == 0 || row.graph > 0) + { + g.drawString(row.annotations[column].displayCharacter, + (x * av.charWidth) + charOffset, y + iconOffset + 3); } - - if (!row.hasIcons) + 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 == ' '))) { - g.drawString(row.annotations[j].displayCharacter, x + charOffset, + g.drawString(row.annotations[column].displayCharacter, + (x * av.charWidth) + charOffset, y + iconOffset + 3); } } if (row.hasIcons) { - if (!validRes || row.annotations[j].secondaryStructure != lastSS[i]) + if (!validRes || + (row.annotations[column].secondaryStructure != lastSS)) { - switch (lastSS[i]) + switch (lastSS) { case 'H': g.setColor(HELIX_COLOUR); - g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i], - 7, 8, 8); + 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); - g.fillRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i] - 4, - 7); + g.fillRect(lastSSX, y + 4 + iconOffset, + (x * av.charWidth) - lastSSX - 4, 7); g.fillPolygon(new int[] - {x - 4, x - 4, x} - , new int[] - {y + iconOffset, y + 14 + iconOffset, - y + 8 + iconOffset}, 3); - break; - case 'C': + { (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[i], y + 6 + iconOffset, x - lastSSX[i], 2); + g.fillRect(lastSSX, y + 6 + iconOffset, + (x * av.charWidth) - lastSSX, 2); + break; } if (validRes) { - lastSS[i] = row.annotations[j].secondaryStructure; + lastSS = row.annotations[column].secondaryStructure; } else { - lastSS[i] = ' '; + lastSS = ' '; } - lastSSX[i] = x; - } - } - - if (validRes && row.isGraph) - { - g.setColor(new Color(0, 0, 180)); - int height = (int) ( (row.annotations[j].value / row.graphMax) * - GRAPH_HEIGHT); - - if (row.windowLength > 1) - { - int total = 0; - for (int i2 = j - (row.windowLength / 2); - i2 < j + (row.windowLength / 2); i2++) - { - if (i2 < 0 || i2 >= av.alignment.getWidth()) - { - continue; - } - - total += row.annotations[i2].value; - } - - total /= row.windowLength; - height = (int) ( (total / row.graphMax) * GRAPH_HEIGHT); + lastSSX = (x * av.charWidth); } - g.setColor(row.annotations[j].colour); - g.fillRect(x, y - height, av.charWidth, height); } + column++; + x++; } - x += av.charWidth; + if (column >= row.annotations.length) + { + column = row.annotations.length - 1; + } + + // x ++; if (row.hasIcons) { - switch (lastSS[i]) + switch (lastSS) { case 'H': g.setColor(HELIX_COLOUR); - g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i], 7, - 8, 8); + 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); - 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); - break; - case 'C': + + 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; + default: g.setColor(Color.gray); - g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2); + if (!av.wrapAlignment || endRes == av.endRes) + { + g.fillRect(lastSSX, y + 6 + iconOffset, + (x * av.charWidth) - lastSSX, 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; 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.isGraph && row.hasText) + if (row.graph > 0 && row.hasText) { y += av.charHeight; } - if (!row.isGraph) + + if (row.graph == 0) { y += aa[i].height; } } } - // used by overview window - public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes) + public void drawLineGraph(Graphics g, AlignmentAnnotation aa, + int sRes, int eRes, + int y, + float min, float max, + int graphHeight) { - g.setColor(Color.white); - g.fillRect(0, 0, width, y); - g.setColor(new Color(0, 0, 180)); + 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); + + if (sRes == 0) + { + sRes++; + x += av.charWidth; + } + + 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 || aa.annotations[column - 1] == 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 - 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); - int x = 0, height; + 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) + { + if (sRes > aa.annotations.length) + { + return; + } + + 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; + + 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); - for (int j = sRes; j < eRes; j++) + y1 = y - + (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight); + + if (y1 - y2 > 0) { - g.setColor(new Color(0, 0, 180)); + g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2); + } + else + { + g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1); + } + + 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); + } + } + + // 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; - 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; + 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; } + } }