X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=86d5c6dacbec1fdb25a40cead49521e1ceb6d244;hb=266c4e2544701f88a8d21294b4a4f4cc42cf76cc;hp=a6c2055230f953ce3687ee212899a59abb4f0e9c;hpb=18dbe82eae761c1e96d2eb5b842747a515db116f;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index a6c2055..86d5c6d 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/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 @@ -18,8 +18,6 @@ */ package jalview.gui; -import java.util.*; - import java.awt.*; import java.awt.event.*; import java.awt.image.*; @@ -27,31 +25,57 @@ import javax.swing.*; import jalview.datamodel.*; +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ public class AnnotationPanel extends JPanel implements MouseListener, MouseMotionListener, ActionListener, AdjustmentListener { - 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(); - - public static int GRAPH_HEIGHT = 40; + final String HELIX = "Helix"; + final String SHEET = "Sheet"; + final String LABEL = "Label"; + final String REMOVE = "Remove Annotation"; + final String COLOUR = "Colour"; + final Color HELIX_COLOUR = Color.red.darker(); + final Color SHEET_COLOUR = Color.green.darker().darker(); + + /** DOCUMENT ME!! */ AlignViewport av; AlignmentPanel ap; int activeRow = -1; - Vector activeRes; BufferedImage image; + BufferedImage fadedImage; Graphics2D gg; FontMetrics fm; int imgWidth = 0; boolean fastPaint = false; + //Used For mouse Dragging and resizing graphs + int graphStretch = -1; + int graphStretchY = -1; + int min; //used by mouseDragged to see if user + int max; //used by mouseDragged to see if user + boolean mouseDragging = false; + + boolean MAC = false; + + /** + * Creates a new AnnotationPanel object. + * + * @param ap DOCUMENT ME! + */ public AnnotationPanel(AlignmentPanel ap) { + + if (System.getProperty("os.name").startsWith("Mac")) + { + MAC = true; + } + ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -63,12 +87,25 @@ public class AnnotationPanel ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this); } + public AnnotationPanel(AlignViewport av) + { + this.av = av; + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ public void adjustmentValueChanged(AdjustmentEvent evt) { ap.alabels.setScrollOffset( -evt.getValue()); } - public void adjustPanelHeight() + /** + * DOCUMENT ME! + */ + public int adjustPanelHeight() { // setHeight of panels AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); @@ -95,9 +132,9 @@ public class AnnotationPanel aa[i].height += 16; } - if (aa[i].isGraph) + if (aa[i].graph > 0) { - aa[i].height += GRAPH_HEIGHT; + aa[i].height += aa[i].graphHeight; } if (aa[i].height == 0) @@ -114,69 +151,33 @@ public class AnnotationPanel } this.setPreferredSize(new Dimension(1, height)); - } - - - public void removeEditableColumn(int col) - { - if (activeRow == -1) - { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - - for (int j = 0; j < aa.length; j++) - { - if (aa[j].editable) - { - activeRow = j; - break; - } - } - } - if (activeRes != null && activeRes.contains(String.valueOf(col))) - { - activeRes.removeElement(String.valueOf(col)); - } - repaint(); - } - - - public void addEditableColumn(int col) - { - if (activeRow == -1) - { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - - for (int j = 0; j < aa.length; j++) - { - if (aa[j].editable) - { - activeRow = j; - break; - } - } - } - - if (activeRes == null) - activeRes = new Vector(); - - if (!activeRes.contains(String.valueOf(col))) - activeRes.addElement(String.valueOf(col)); - - repaint(); + return height; } + /** + * 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; + } + if (evt.getActionCommand().equals(REMOVE)) { - for (int i = 0; i < activeRes.size(); i++) + for (int i = 0; i < av.getColumnSelection().size(); i++) { - anot[Integer.parseInt(activeRes.get(i).toString())] = null; - anot[Integer.parseInt(activeRes.get(i).toString())] = null; + anot[av.getColumnSelection().columnAt(i)] = null; } } else if (evt.getActionCommand().equals(LABEL)) @@ -186,21 +187,27 @@ public class AnnotationPanel JOptionPane.QUESTION_MESSAGE); if (label == null) + { return; + } if ( (label.length() > 0) && !aa[activeRow].hasText) { aa[activeRow].hasText = true; } - for (int i = 0; i < activeRes.size(); i++) + for (int i = 0; i < av.getColumnSelection().size(); i++) { - int index = Integer.parseInt(activeRes.get(i).toString()); + 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; } } @@ -210,9 +217,12 @@ public class AnnotationPanel "Choose foreground colour", Color.black); - for (int i = 0; i < activeRes.size(); i++) + for (int i = 0; i < av.getColumnSelection().size(); i++) { - int index = Integer.parseInt(activeRes.get(i).toString()); + int index = av.getColumnSelection().columnAt(i); + + if(!av.colSel.isVisible(index)) + continue; if (anot[index] == null) { @@ -247,16 +257,21 @@ public class AnnotationPanel symbol); if (label == null) + { return; + } if ( (label.length() > 0) && !aa[activeRow].hasText) { aa[activeRow].hasText = true; } - for (int i = 0; i < activeRes.size(); i++) + for (int i = 0; i < av.getColumnSelection().size(); i++) { - int index = Integer.parseInt(activeRes.get(i).toString()); + int index = av.getColumnSelection().columnAt(i); + + if(!av.colSel.isVisible(index)) + continue; if (anot[index] == null) { @@ -269,42 +284,59 @@ public class AnnotationPanel } adjustPanelHeight(); - activeRes = null; repaint(); return; } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ public void mousePressed(MouseEvent evt) { + + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + if (aa == null) + { + return; + } + int height = 0; activeRow = -1; - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); for (int i = 0; i < aa.length; i++) { - height += aa[i].height; + if (aa[i].visible) + { + height += aa[i].height; + } if (evt.getY() < height) { if (aa[i].editable) - activeRow = i; - else - activeRes = null; + { + activeRow = i; + } + else if (aa[i].graph > 0) + { + //Stretch Graph + graphStretch = i; + graphStretchY = evt.getY(); + } break; } } - - if (SwingUtilities.isRightMouseButton(evt)) + if (SwingUtilities.isRightMouseButton(evt) && activeRow != -1) { - if (activeRes == null) + if (av.getColumnSelection() == null) { return; } - JPopupMenu pop = new JPopupMenu("Structure type"); JMenuItem item = new JMenuItem(HELIX); item.addActionListener(this); @@ -326,75 +358,85 @@ public class AnnotationPanel return; } - if (aa == null) { return; } + ap.scalePanel.mousePressed(evt); - int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); - - if (evt.isControlDown() || evt.isAltDown()) - { - addEditableColumn(res); - } - else if (evt.isShiftDown()) - { - if (activeRes == null) - { - activeRes = new Vector(); - } - else - { - int start = Integer.parseInt(activeRes.get(activeRes.size() - - 1).toString()); - int end = res; - - if (end < start) - { - int temp = end; - end = start; - start = temp; - } - - for (int n = start; n <= end; n++) - { - addEditableColumn(n); - } - } - } - else - { - activeRes = new Vector(); - activeRes.addElement(String.valueOf(res)); - } - - repaint(); } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ public void mouseReleased(MouseEvent evt) { + graphStretch = -1; + graphStretchY = -1; + mouseDragging = false; + ap.scalePanel.mouseReleased(evt); } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ public void mouseEntered(MouseEvent evt) { + ap.scalePanel.mouseEntered(evt); } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ public void mouseExited(MouseEvent evt) { + ap.scalePanel.mouseExited(evt); } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ 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(); + adjustPanelHeight(); + ap.paintAlignment(true); + } + else + { + ap.scalePanel.mouseDragged(evt); + } } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ public void mouseMoved(MouseEvent evt) { AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); if (aa == null) { + this.setToolTipText(null); return; } @@ -416,60 +458,135 @@ public class AnnotationPanel } } + if (row == -1) + { + this.setToolTipText(null); + return; + } + int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); - if ( (row > -1) && (res < aa[row].annotations.length) && - (aa[row].annotations[res] != null)) + if (av.hasHiddenColumns) + { + res = av.getColumnSelection().adjustForHiddenColumns(res); + } + + if (aa[row].annotations != null + && row > -1 + && res < (int) aa[row].annotations.length) { - this.setToolTipText(aa[row].annotations[res].description); + if (aa[row].graphGroup > -1) + { + StringBuffer tip = new StringBuffer(""); + for (int gg = 0; gg < aa.length; gg++) + { + if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res] != null) + { + tip.append(aa[gg].label + " " + aa[gg].annotations[res].description + + "
"); + } + } + if (tip.length() != 6) + { + tip.setLength(tip.length() - 4); + this.setToolTipText(tip.toString() + ""); + } + } + else if (aa[row].annotations[res] != null + && aa[row].annotations[res].description != null) + { + this.setToolTipText(aa[row].annotations[res].description); + } + + if (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); + } - StringBuffer text = new StringBuffer("Sequence position " + - (res + 1) + " " + - aa[row].annotations[res].description); - ap.alignFrame.statusBar.setText(text.toString()); + ap.alignFrame.statusBar.setText(text.toString()); + } + } + else + { + this.setToolTipText(null); } } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ public void mouseClicked(MouseEvent evt) { } + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + */ public void paintComponent(Graphics g) { g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); - if (fastPaint) + if (image != null) { - g.drawImage(image, 0, 0, this); - fastPaint = false; - - return; + if (fastPaint + || (getVisibleRect().width != g.getClipBounds().width) + || (getVisibleRect().height != g.getClipBounds().height)) + { + g.drawImage(image, 0, 0, this); + fastPaint = false; + return; + } } - imgWidth = (av.endRes - av.startRes + 1) * av.charWidth; - image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(), - BufferedImage.TYPE_INT_RGB); - gg = (Graphics2D) image.getGraphics(); - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); + if (image == null || imgWidth != image.getWidth() + || image.getHeight(this) != getHeight()) + { + image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(), + BufferedImage.TYPE_INT_RGB); + gg = (Graphics2D) image.getGraphics(); + + if (av.antiAlias) + { + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } - gg.setFont(av.getFont()); - fm = gg.getFontMetrics(); + gg.setFont(av.getFont()); + fm = gg.getFontMetrics(); + gg.setColor(Color.white); + gg.fillRect(0, 0, imgWidth, image.getHeight()); + } drawComponent(gg, av.startRes, av.endRes + 1); g.drawImage(image, 0, 0, this); } + /** + * DOCUMENT ME! + * + * @param horizontal DOCUMENT ME! + */ public void fastPaint(int horizontal) { - if ( (horizontal == 0) || - (av.alignment.getAlignmentAnnotation() == null) || - (av.alignment.getAlignmentAnnotation().length < 1)) + if ( (horizontal == 0) + || gg == null + || av.alignment.getAlignmentAnnotation() == null + || av.alignment.getAlignmentAnnotation().length < 1 + || av.updatingConsensus + || av.updatingConservation) { repaint(); - return; } @@ -496,35 +613,89 @@ public class AnnotationPanel gg.translate( -transX, 0); fastPaint = true; + repaint(); + } - public void drawComponent(Graphics2D g, int startRes, int endRes) + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + * @param startRes DOCUMENT ME! + * @param endRes DOCUMENT ME! + */ + public void drawComponent(Graphics g, int startRes, int endRes) { + if (av.updatingConsensus || av.updatingConservation) + { + if (image == null) + { + return; + } + //We'll keep a record of the old image, + //and draw a faded image until the calculation + //has completed + if (fadedImage == null + || fadedImage.getWidth() != imgWidth + || fadedImage.getHeight() != image.getHeight()) + { + fadedImage = new BufferedImage( + imgWidth, image.getHeight(), + BufferedImage.TYPE_INT_RGB); + + Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics(); + + fadedG.setColor(Color.white); + fadedG.fillRect(0, 0, imgWidth, image.getHeight()); + + fadedG.setComposite( + AlphaComposite.getInstance( + AlphaComposite.SRC_OVER, .3f)); + fadedG.drawImage(image, 0, 0, this); + + } + + } + else + { + fadedImage = null; + } + g.setColor(Color.white); g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight()); + g.setFont(av.getFont()); + if (fm == null) + { + fm = g.getFontMetrics(); + } + if ( (av.alignment.getAlignmentAnnotation() == null) || (av.alignment.getAlignmentAnnotation().length < 1)) { g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); 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; - int x = 0; - int y = 0; - char[] lastSS = new char[aa.length]; - int[] lastSSX = new int[aa.length]; - int iconOffset = av.charHeight / 2; + int x = 0, y=0; + int column = 0; + char lastSS; + int lastSSX; + int iconOffset = 0; boolean validRes = false; + boolean[] graphGroupDrawn = new boolean[aa.length]; + //\u03B2 \u03B1 for (int i = 0; i < aa.length; i++) { @@ -535,30 +706,94 @@ public class AnnotationPanel 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) { + iconOffset =av.charHeight -fm.getDescent(); y -= av.charHeight; } } - - if (row.hasText) + else if (row.hasText) { - iconOffset = av.charHeight / 2; + iconOffset = av.charHeight -fm.getDescent(); + } else { iconOffset = 0; } - for (j = startRes; j < endRes; j++) + + if (av.updatingConsensus && aa[i] == av.consensus) + { + y += av.charHeight; + + g.drawImage(fadedImage, + 0, y - row.height, imgWidth, y, + 0, y - row.height, imgWidth, y, this); + g.setColor(Color.black); + // g.drawString("Calculating Consensus....",20, y-row.height/2); + + continue; + } + else if (av.updatingConservation && aa[i].label.equals("Conservation")) + { + + y += av.charHeight; + g.drawImage(fadedImage, + 0, y - row.height, imgWidth, y, + 0, y - row.height, imgWidth, y, this); + + g.setColor(Color.black); + // g.drawString("Calculating Conservation.....",20, y-row.height/2); + + continue; + } + else if (av.updatingConservation && aa[i].label.equals("Quality")) + { + + y += av.charHeight; + g.drawImage(fadedImage, + 0, y - row.height, imgWidth, y, + 0, y - row.height, imgWidth, y, this); + g.setColor(Color.black); + /// g.drawString("Calculating Quality....",20, y-row.height/2); + + continue; + } + + + + 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; } @@ -567,72 +802,110 @@ 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.get(n).toString()); + int v = av.getColumnSelection().columnAt(n); - if (v == j) + 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 != null + && (row.annotations[column].displayCharacter.length() > 0)) { + int charOffset = (av.charWidth - - fm.charWidth(row.annotations[j].displayCharacter. - charAt( + fm.charWidth(row.annotations[column]. + displayCharacter.charAt( 0))) / 2; - g.setColor(row.annotations[j].colour); - if (j == 0) + 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[j].displayCharacter, - x, y + iconOffset + 2); + g.drawString(row.annotations[column].displayCharacter, + (x * av.charWidth) + charOffset, + y + iconOffset); } else if ( - ( (row.annotations[j - 1] == null) || - (row.annotations[j].displayCharacter != row.annotations[j - - 1].displayCharacter))) + 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, - y + iconOffset + 2); + g.drawString(row.annotations[column].displayCharacter, + x * av.charWidth + charOffset, + y + iconOffset); } - } if (row.hasIcons) { if (!validRes || - (row.annotations[j].secondaryStructure != lastSS[i])) + (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}, + { (x * av.charWidth) - 4, + (x * av.charWidth) - 4, + (x * av.charWidth)}, new int[] { y + iconOffset, y + 14 + iconOffset, @@ -641,128 +914,384 @@ public class AnnotationPanel break; - case 'C': - 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; + lastSSX = (x * av.charWidth); } } - 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); - } + column++; + x++; + } - g.setColor(row.annotations[j].colour); - g.fillRect(x, y - height, av.charWidth, height); - } + if (column >= row.annotations.length) + { + column = row.annotations.length - 1; } - x += av.charWidth; + // 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 + 1) * av.charWidth - lastSSX, 7); + } 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 (row.isGraph && row.hasText) + 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.isGraph) + 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; + } + + int x = 0; + + //Adjustment for fastpaint to left + if (eRes < av.endRes) + { + eRes++; + } + + eRes = Math.min(eRes, aa.annotations.length); + + if (sRes == 0) + { + x++; + } + + 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 + 1) * 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); + Graphics2D g2 = (Graphics2D) g; + g2.setStroke(new BasicStroke(1, + BasicStroke.CAP_SQUARE, + BasicStroke.JOIN_ROUND, 3f, + new float[] + {5f, 3f}, 0f)); + + y2 = (int) (y - ( (aa.threshold.value - min) / range) * graphHeight); + g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2); + g2.setStroke(new BasicStroke()); + } + } + + 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); + + y1 = y - + (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight); + + 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); + } + + x++; + + } + if (aa.threshold != null) + { + g.setColor(aa.threshold.colour); + Graphics2D g2 = (Graphics2D) g; + g2.setStroke(new BasicStroke(1, + BasicStroke.CAP_SQUARE, + BasicStroke.JOIN_ROUND, 3f, + new float[] + {5f, 3f}, 0f)); + + y2 = (int) (y - ( (aa.threshold.value - min) / range) * aa.graphHeight); + g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2); + g2.setStroke(new BasicStroke()); + } + } + // used by overview window - public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y) + 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; + int x = 0, height; - for (int j = 0; j < aa.annotations.length; j++) + for (int j = sRes; j < eRes; j++) { - g.setColor(new Color(0, 0, 180)); + if (aa.annotations[j] != null) + { + if (aa.annotations[j].colour == null) + g.setColor(Color.black); + else + g.setColor(aa.annotations[j].colour); - int height = (int) ( (aa.annotations[j].value / aa.graphMax) * - GRAPH_HEIGHT); - g.fillRect(x, y - height, av.charWidth, height); + height = (int) ( (aa.annotations[j].value / aa.graphMax) * y); + if (height > y) + { + height = y; + } + + g.fillRect(x, y - height, av.charWidth, height); + } x += av.charWidth; } } + }