X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=1b4a230a526f78d0d50d6dfe7a7d906372bc5fd0;hb=b437b816507d2acc59e34f70a9cf8c7f81921681;hp=5f0d3c88798bd7d80aa60d6dd0cda7d7cacbe87c;hpb=21930635bd32076820fe0f474bd8f8f89b84dff2;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 5f0d3c8..1b4a230 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -24,8 +24,6 @@ import java.awt.*; import java.awt.event.*; import java.awt.image.*; -import java.util.*; - import javax.swing.*; @@ -38,26 +36,31 @@ import javax.swing.*; 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(); + 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!! */ - public static int GRAPH_HEIGHT = 40; AlignViewport av; AlignmentPanel ap; int activeRow = -1; - Vector activeRes; BufferedImage image; 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; + /** * Creates a new AnnotationPanel object. * @@ -76,6 +79,12 @@ public class AnnotationPanel extends JPanel implements MouseListener, ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this); } + public AnnotationPanel(AlignViewport av) + { + this.av = av; + } + + /** * DOCUMENT ME! * @@ -89,7 +98,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! */ - public void adjustPanelHeight() + public int adjustPanelHeight() { // setHeight of panels image = null; @@ -117,9 +126,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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) @@ -136,76 +145,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, } this.setPreferredSize(new Dimension(1, height)); - } - - /** - * DOCUMENT ME! - * - * @param col DOCUMENT ME! - */ - public void removeEditableColumn(int col) - { - 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.contains(String.valueOf(col))) - { - activeRes.removeElement(String.valueOf(col)); - } - - repaint(); + return height; } - /** - * DOCUMENT ME! - * - * @param col DOCUMENT ME! - */ - public void addEditableColumn(int col) - { - 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(); - } - - if (!activeRes.contains(String.valueOf(col))) - { - activeRes.addElement(String.valueOf(col)); - } - - repaint(); - } /** * DOCUMENT ME! @@ -219,10 +163,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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)) @@ -240,9 +183,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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 (anot[index] == null) { @@ -257,9 +200,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, Color col = JColorChooser.showDialog(this, "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 (anot[index] == null) { @@ -302,9 +245,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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 (anot[index] == null) { @@ -317,7 +260,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, } adjustPanelHeight(); - activeRes = null; repaint(); return; @@ -334,6 +276,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, activeRow = -1; AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + if(aa==null) + return; for (int i = 0; i < aa.length; i++) { @@ -348,9 +292,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, { activeRow = i; } - else + else if(aa[i].graph>0) { - activeRes = null; + //Stretch Graph + graphStretch = i; + graphStretchY = evt.getY(); } break; @@ -359,7 +305,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (SwingUtilities.isRightMouseButton(evt)) { - if (activeRes == null) + if (av.getColumnSelection() == null) { return; } @@ -392,42 +338,28 @@ public class AnnotationPanel extends JPanel implements MouseListener, int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); - if (evt.isControlDown() || evt.isAltDown()) - { - addEditableColumn(res); - } - else if (evt.isShiftDown()) + min = res; + max = res; + + if (av.getColumnSelection().contains(res)) + av.getColumnSelection().removeElement(res); + else { - if (activeRes == null) + av.getColumnSelection().addElement(res); + SequenceGroup sg = new SequenceGroup(); + + for (int i = 0; i < av.alignment.getSequences().size(); i++) { - activeRes = new Vector(); + sg.addSequence(av.alignment.getSequenceAt(i), false); } - 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)); + sg.setStartRes(res); + sg.setEndRes(res); + av.setSelectionGroup(sg); } - repaint(); + ap.repaint(); + } /** @@ -437,6 +369,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void mouseReleased(MouseEvent evt) { + graphStretch = -1; + graphStretchY = -1; + mouseDragging = false; } /** @@ -446,6 +381,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void mouseEntered(MouseEvent evt) { + if(mouseDragging) + ap.seqPanel.scrollCanvas(null); } /** @@ -455,8 +392,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void mouseExited(MouseEvent evt) { + if(mouseDragging) + ap.seqPanel.scrollCanvas(evt); } + /** * DOCUMENT ME! * @@ -464,6 +404,65 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void mouseDragged(MouseEvent evt) { + if(graphStretch>-1) + { + av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY(); + if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <10) + av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 10; + graphStretchY = evt.getY(); + adjustPanelHeight(); + ap.repaint(); + } + else + { + mouseDragging = true; + + int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); + + SequenceGroup sg = av.getSelectionGroup(); + + if (res < min) + { + min = res; + } + + if (res > max) + { + max = res; + } + + if (sg != null) + { + if (!av.getColumnSelection().contains(res)) + { + av.getColumnSelection().addElement(res); + } + + if (res > sg.getStartRes()) + { + sg.setEndRes(res); + } + else if (res < sg.getStartRes()) + { + sg.setStartRes(res); + } + + for (int i = min; i <= max; i++) + { + if ((i < sg.getStartRes()) || (i > sg.getEndRes())) + { + av.getColumnSelection().removeElement(i); + } + else + { + av.getColumnSelection().addElement(i); + } + } + + ap.repaint(); + } + + } } /** @@ -500,14 +499,36 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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 (row > -1 && res-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) + this.setToolTipText(aa[row].annotations[res].description); - StringBuffer text = new StringBuffer("Sequence position " + - (res + 1) + " " + aa[row].annotations[res].description); - ap.alignFrame.statusBar.setText(text.toString()); + if(aa[row].annotations[res]!=null) + { + StringBuffer text = new StringBuffer("Sequence position " + + (res + 1) + " " + + aa[row].annotations[res].description); + + ap.alignFrame.statusBar.setText(text.toString()); + } } } @@ -530,20 +551,26 @@ public class AnnotationPanel extends JPanel implements MouseListener, g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); - if (fastPaint) - { - g.drawImage(image, 0, 0, this); - fastPaint = false; - return; + if(image!=null) + {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; - if (image == null || imgWidth != image.getWidth()) + 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); @@ -551,6 +578,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, fm = gg.getFontMetrics(); } + drawComponent(gg, av.startRes, av.endRes + 1); g.drawImage(image, 0, 0, this); } @@ -562,12 +590,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void fastPaint(int horizontal) { - if ((horizontal == 0) || + if ((horizontal == 0) || gg==null || (av.alignment.getAlignmentAnnotation() == null) || (av.alignment.getAlignmentAnnotation().length < 1)) { repaint(); - return; } @@ -606,8 +633,14 @@ public class AnnotationPanel extends JPanel implements MouseListener, * @param startRes DOCUMENT ME! * @param endRes DOCUMENT ME! */ - public void drawComponent(Graphics2D g, int startRes, int endRes) + 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, getHeight()); @@ -624,14 +657,16 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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]; + char lastSS; + int lastSSX; int iconOffset = av.charHeight / 2; boolean validRes = false; + boolean [] graphGroupDrawn = new boolean[aa.length]; + + //\u03B2 \u03B1 for (int i = 0; i < aa.length; i++) { @@ -642,9 +677,15 @@ public class AnnotationPanel extends JPanel implements MouseListener, continue; } + lastSS = ' '; + lastSSX = 0; + - if (row.isGraph) + 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; @@ -663,10 +704,24 @@ public class AnnotationPanel extends JPanel implements MouseListener, iconOffset = 0; } - for (j = startRes; j < endRes; j++) + int column = startRes; + int yPos = startRes; + + while (yPos < endRes) { - if ((row.annotations.length <= j) || - (row.annotations[j] == null)) + if (av.hasHiddenColumns) + { + column = av.getColumnSelection().adjustForHiddenColumns(yPos); + if (column > row.annotations.length-1) + { + break; + } + } + else + column = yPos; + + if ((row.annotations.length <= column) || + (row.annotations[column] == null)) { validRes = false; } @@ -675,21 +730,21 @@ public class AnnotationPanel extends JPanel implements MouseListener, validRes = true; } - x = (j - startRes) * av.charWidth; + x = (yPos - 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, + g.fillRect((column - startRes) * av.charWidth, y, av.charWidth, row.height); } } @@ -697,24 +752,25 @@ public class AnnotationPanel extends JPanel implements MouseListener, } if (validRes && - (row.annotations[j].displayCharacter.length() > 0)) + (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); + g.setColor(row.annotations[column].colour); - if (j == 0 || row.isGraph) + if (column == 0 || row.graph>0) { - g.drawString(row.annotations[j].displayCharacter, x+charOffset, + g.drawString(row.annotations[column].displayCharacter, x+charOffset, y + iconOffset + 3); } - else if (((row.annotations[j - 1] == null) || - (row.annotations[j].displayCharacter != row.annotations[j - - 1].displayCharacter))) + else if (((row.annotations[column - 1] == null) + || + (!row.annotations[column].displayCharacter.equals( + row.annotations[column - 1].displayCharacter)))) { - g.drawString(row.annotations[j].displayCharacter, x+charOffset, + g.drawString(row.annotations[column].displayCharacter, x+charOffset, y + iconOffset + 3); } } @@ -722,21 +778,21 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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); + g.fillRoundRect(lastSSX, y + 4 + iconOffset, + x - lastSSX, 7, 8, 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 - lastSSX - 4, 7); g.fillPolygon(new int[] { x - 4, x - 4, x }, new int[] { @@ -746,129 +802,305 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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 - 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; } } - 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); - } - - g.setColor(row.annotations[j].colour); - g.fillRect(x, y - height, av.charWidth, height); - } + yPos++; } x += av.charWidth; 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); + g.fillRoundRect(lastSSX, y + 4 + iconOffset, + x - lastSSX, 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 + 7 + iconOffset - }, 3); - break; + if (row.annotations[endRes] !=null + && row.annotations[endRes].secondaryStructure != 'E') + { + g.fillRect(lastSSX, y + 4 + iconOffset, + x - lastSSX - 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, y + 4 + iconOffset, + x - lastSSX, 7); - 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 - lastSSX, 2); break; } } - if (row.isGraph && row.hasText) + 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.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; + + eRes = Math.min(eRes, aa.annotations.length); + + int x = 0; + //Adjustment for fastpaint to left + if(eRes aaMax) + { + break; + } + } + else + column = yPos; - height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT); - if(height>y) - height = y; + yPos ++; - g.fillRect(x, y - height, av.charWidth, height); - x += av.charWidth; + if(aa.annotations[column]==null || aa.annotations[column-1]==null) + { + x+=av.charWidth; + continue; } + + 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/2, y1, x+av.charWidth/2, y2); + x += av.charWidth; + } + 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, 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); + + + int column = sRes; + int yPos = sRes; + int aaMax = aa.annotations.length-1; + + while( yPos < eRes ) + { + if(av.hasHiddenColumns) + { + column = av.getColumnSelection().adjustForHiddenColumns(yPos); + if(column > aaMax) + { + break; + } + } + else + column = yPos; + + yPos ++; + + if (aa.annotations[column] == null) + { + x += av.charWidth; + continue; + } + + + g.setColor(aa.annotations[column].colour); + y1 = y - (int) (((aa.annotations[column].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); + 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, 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) * y); + if(height>y) + height = y; + + g.fillRect(x, y - height, av.charWidth, height); + x += av.charWidth; + } + } + }