/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.datamodel.*;\r
+import java.util.*;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
\r
-public class AnnotationPanel extends Panel implements AdjustmentListener\r
+import jalview.datamodel.*;\r
+\r
+public class AnnotationPanel\r
+ extends Panel implements AdjustmentListener\r
{\r
AlignViewport av;\r
AlignmentPanel ap;\r
- int activeRow =-1;\r
+ int activeRow = -1;\r
\r
Vector activeRes;\r
- static String HELIX ="Helix";\r
- static String SHEET ="Sheet";\r
- static String LABEL ="Label";\r
- static String REMOVE="Remove Annotation";\r
- static String COLOUR="Colour";\r
+ static String HELIX = "Helix";\r
+ static String SHEET = "Sheet";\r
+ static String LABEL = "Label";\r
+ static String REMOVE = "Remove Annotation";\r
+ static String COLOUR = "Colour";\r
static Color HELIX_COLOUR = Color.red.darker();\r
static Color SHEET_COLOUR = Color.green.darker().darker();\r
\r
-\r
Image image;\r
Graphics gg;\r
FontMetrics fm;\r
- int imgWidth=0;\r
+ int imgWidth = 0;\r
\r
boolean fastPaint = false;\r
\r
public static int GRAPH_HEIGHT = 40;\r
\r
-\r
+ boolean MAC = false;\r
\r
public AnnotationPanel(AlignmentPanel ap)\r
{\r
+ if (System.getProperty("os.name").startsWith("Mac"))\r
+ {\r
+ MAC = true;\r
+ }\r
+\r
this.ap = ap;\r
av = ap.av;\r
- this.setLayout(null);\r
+ setLayout(null);\r
adjustPanelHeight();\r
\r
addMouseMotionListener(new MouseMotionAdapter()\r
- {public void mouseMoved(MouseEvent evt)\r
- { doMouseMoved(evt); }\r
+ {\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ doMouseMoved(evt);\r
+ }\r
});\r
\r
- // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );\r
+ // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );\r
+ }\r
+\r
+ public AnnotationPanel(AlignViewport av)\r
+ {\r
+ this.av = av;\r
}\r
\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\r
- ap.alabels.setScrollOffset( -evt.getValue() );\r
+ ap.alabels.setScrollOffset( -evt.getValue());\r
}\r
\r
- public void adjustPanelHeight()\r
+ public int adjustPanelHeight()\r
{\r
// setHeight of panels\r
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+\r
int height = 0;\r
- if(aa!=null)\r
- for (int i = 0; i < aa.length; i++)\r
+ if (aa != null)\r
{\r
- if(!aa[i].visible)\r
- continue;\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (!aa[i].visible)\r
+ {\r
+ continue;\r
+ }\r
\r
- aa[i].height = 0;\r
+ aa[i].height = 0;\r
\r
- if(aa[i].hasText)\r
- aa[i].height += av.charHeight;\r
- if (aa[i].hasIcons)\r
- aa[i].height += 16;\r
+ if (aa[i].hasText)\r
+ {\r
+ aa[i].height += av.charHeight;\r
+ }\r
+ if (aa[i].hasIcons)\r
+ {\r
+ aa[i].height += 16;\r
+ }\r
\r
- if (aa[i].isGraph)\r
- aa[i].height += GRAPH_HEIGHT;\r
+ if (aa[i].graph > 0)\r
+ {\r
+ aa[i].height += GRAPH_HEIGHT;\r
+ }\r
\r
- if(aa[i].height==0)\r
- aa[i].height = 20;\r
- height += aa[i].height;\r
+ if (aa[i].height == 0)\r
+ {\r
+ aa[i].height = 20;\r
+ }\r
+ height += aa[i].height;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ height = 20;\r
}\r
- else height=20;\r
\r
- this.setSize(getSize().width, height);\r
- ap.annotationScroller.setSize(getSize().width, height);\r
+ this.setSize(getSize().width, height);\r
\r
-// ap.annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);\r
+ repaint();\r
\r
- repaint();\r
+ return height;\r
\r
}\r
\r
public void addEditableColumn(int i)\r
{\r
- if(activeRow==-1)\r
+ if (activeRow == -1)\r
{\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- for(int j=0; j<aa.length; j++)\r
- if(aa[j].editable)\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ if (aa == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ for (int j = 0; j < aa.length; j++)\r
+ {\r
+ if (aa[j].editable)\r
{\r
activeRow = j;\r
break;\r
}\r
+ }\r
}\r
\r
- if(activeRes==null)\r
+ if (activeRes == null)\r
{\r
activeRes = new Vector();\r
activeRes.addElement(String.valueOf(i));\r
activeRes.addElement(String.valueOf(i));\r
}\r
\r
- public void doMouseMoved(MouseEvent evt)\r
- {\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- if(aa==null)\r
- return;\r
+ public void doMouseMoved(MouseEvent evt)\r
+ {\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ if (aa == null)\r
+ {\r
+ return;\r
+ }\r
\r
- int row = -1;\r
- int height=0;\r
- for(int i=0; i<aa.length; i++)\r
- {\r
+ int row = -1;\r
+ int height = 0;\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
\r
- if( aa[i].visible )\r
- height += aa[i].height;\r
+ if (aa[i].visible)\r
+ {\r
+ height += aa[i].height;\r
+ }\r
\r
- if(evt.getY()<height)\r
- {\r
- row = i;\r
- break;\r
- }\r
- }\r
+ if (evt.getY() < height)\r
+ {\r
+ row = i;\r
+ break;\r
+ }\r
+ }\r
\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
- if(row>-1 && res<aa[row].annotations.length && aa[row].annotations[res]!=null)\r
- {\r
- StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +\r
- " " +\r
- aa[row].annotations[res].description);\r
- ap.alignFrame.statusBar.setText(text.toString());\r
- }\r
- }\r
+ int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+ }\r
\r
+ if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null)\r
+ {\r
+ StringBuffer text = new StringBuffer("Sequence position " + (res + 1));\r
+ if (aa[row].annotations[res].description != null)\r
+ {\r
+ text.append(" " + aa[row].annotations[res].description);\r
+ }\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+ }\r
+ }\r
\r
public void update(Graphics g)\r
{\r
\r
public void paint(Graphics g)\r
{\r
- imgWidth = (av.endRes-av.startRes+1) *av.charWidth;\r
\r
- if(image==null || imgWidth != image.getWidth(this))\r
- {\r
- image = createImage(imgWidth, ap.annotationPanel.getSize().height);\r
- gg = image.getGraphics();\r
- gg.setFont(av.getFont());\r
- fm = gg.getFontMetrics();\r
- fastPaint = false;\r
+ imgWidth = getSize().width;\r
+ //(av.endRes - av.startRes + 1) * av.charWidth;\r
+\r
+ if (image == null || imgWidth != image.getWidth(this))\r
+ {\r
+ image = createImage(imgWidth, ap.annotationPanel.getSize().height);\r
+ gg = image.getGraphics();\r
+ gg.setFont(av.getFont());\r
+ fm = gg.getFontMetrics();\r
+ fastPaint = false;\r
}\r
\r
- if(fastPaint)\r
+ if (fastPaint)\r
{\r
g.drawImage(image, 0, 0, this);\r
fastPaint = false;\r
return;\r
}\r
\r
- drawComponent( gg, av.startRes, av.endRes+1);\r
- g.drawImage( image, 0, 0, this);\r
+ gg.setColor(Color.white);\r
+ gg.fillRect(0, 0, getSize().width, getSize().height);\r
+ drawComponent(gg, av.startRes, av.endRes + 1);\r
\r
+ g.drawImage(image, 0, 0, this);\r
}\r
\r
public void fastPaint(int horizontal)\r
-{\r
- if( horizontal == 0\r
- || av.alignment.getAlignmentAnnotation()==null\r
- || av.alignment.getAlignmentAnnotation().length<1\r
- )\r
{\r
- repaint();\r
- return;\r
- }\r
-\r
- gg.copyArea( 0,0, imgWidth, getSize().height, -horizontal*av.charWidth, 0 );\r
- int sr=av.startRes, er=av.endRes+1, transX=0;\r
-\r
- if(horizontal>0) // scrollbar pulled right, image to the left\r
- {\r
- transX = (er-sr-horizontal)*av.charWidth;\r
- sr = er - horizontal ;\r
- }\r
- else if(horizontal<0)\r
- {\r
- er = sr-horizontal;\r
- }\r
+ if (horizontal == 0\r
+ || av.alignment.getAlignmentAnnotation() == null\r
+ || av.alignment.getAlignmentAnnotation().length < 1\r
+ )\r
+ {\r
+ repaint();\r
+ return;\r
+ }\r
\r
+ gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal * av.charWidth, 0);\r
+ int sr = av.startRes, er = av.endRes + 1, transX = 0;\r
\r
- gg.translate(transX, 0);\r
+ if (horizontal > 0) // scrollbar pulled right, image to the left\r
+ {\r
+ transX = (er - sr - horizontal) * av.charWidth;\r
+ sr = er - horizontal;\r
+ }\r
+ else if (horizontal < 0)\r
+ {\r
+ er = sr - horizontal;\r
+ }\r
\r
- drawComponent(gg, sr, er);\r
+ gg.translate(transX, 0);\r
\r
- gg.translate( -transX, 0 );\r
+ drawComponent(gg, sr, er);\r
\r
- fastPaint = true;\r
- repaint();\r
-}\r
+ gg.translate( -transX, 0);\r
\r
+ fastPaint = true;\r
+ repaint();\r
+ }\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param startRes DOCUMENT ME!\r
+ * @param endRes DOCUMENT ME!\r
+ */\r
public void drawComponent(Graphics g, int startRes, int endRes)\r
{\r
+ g.setFont(av.getFont());\r
+\r
g.setColor(Color.white);\r
- g.fillRect(0,0,(endRes-startRes) *av.charWidth, getSize().height);\r
- if(av.alignment.getAlignmentAnnotation()==null || av.alignment.getAlignmentAnnotation().length<1)\r
+ g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);\r
+\r
+ if (fm == null)\r
+ {\r
+ fm = g.getFontMetrics();\r
+ }\r
+\r
+ if ( (av.alignment.getAlignmentAnnotation() == null) ||\r
+ (av.alignment.getAlignmentAnnotation().length < 1))\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0,getSize().width, getSize().height);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
g.setColor(Color.black);\r
- g.drawString("Alignment has no annotations",20,15);\r
+ if (av.validCharWidth)\r
+ {\r
+ g.drawString("Alignment has no annotations", 20, 15);\r
+ }\r
+\r
return;\r
}\r
\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
- int j, x=0, y=0;\r
- char [] lastSS = new char[aa.length];\r
- int [] lastSSX= new int[aa.length] ;\r
- int iconOffset = av.charHeight/2;\r
+ int x = 0;\r
+ int y = 0;\r
+ int column = 0;\r
+ char lastSS;\r
+ int lastSSX;\r
+ int iconOffset = av.charHeight / 2;\r
boolean validRes = false;\r
- //\u03B2 \u03B1\r
\r
- for(int i=0; i<aa.length; i++)\r
+ boolean[] graphGroupDrawn = new boolean[aa.length];\r
+\r
+ //\u03B2 \u03B1\r
+ for (int i = 0; i < aa.length; i++)\r
{\r
AlignmentAnnotation row = aa[i];\r
- if(!row.visible)\r
+\r
+ if (!row.visible)\r
+ {\r
continue;\r
+ }\r
+\r
+ lastSS = ' ';\r
+ lastSSX = 0;\r
\r
- if(row.isGraph)\r
+ if (row.graph > 0)\r
{\r
+ if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])\r
+ {\r
+ continue;\r
+ }\r
+\r
// this is so that we draw the characters below the graph\r
y += row.height;\r
- if(row.hasText)\r
+\r
+ if (row.hasText)\r
+ {\r
y -= av.charHeight;\r
+ }\r
+ }\r
+\r
+ if (row.hasText)\r
+ {\r
+ iconOffset = av.charHeight / 2;\r
}\r
- if(row.hasText)\r
- iconOffset = av.charHeight/2;\r
else\r
+ {\r
iconOffset = 0;\r
+ }\r
\r
- for(j=startRes; j<endRes; j++)\r
+ x = 0;\r
+ while (x < endRes - startRes)\r
{\r
- if(row.annotations.length<=j || row.annotations[j]==null)\r
- validRes = false;\r
- else\r
- validRes = true;\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(startRes + x);\r
+ if (column > row.annotations.length - 1)\r
+ {\r
+ break;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ column = startRes + x;\r
+ }\r
\r
- x = (j-startRes)*av.charWidth;\r
+ if ( (row.annotations.length <= column) ||\r
+ (row.annotations[column] == null))\r
+ {\r
+ validRes = false;\r
+ }\r
+ else\r
+ {\r
+ validRes = true;\r
+ }\r
\r
+ if (av.validCharWidth && validRes &&\r
+ (row.annotations[column].displayCharacter.length() > 0))\r
+ {\r
+ int charOffset = (av.charWidth -\r
+ fm.charWidth(row.annotations[column].\r
+ displayCharacter.charAt(\r
+ 0))) / 2;\r
+ g.setColor(row.annotations[column].colour);\r
\r
- if(activeRow==i)\r
- {\r
+ if (column == 0 || row.graph > 0)\r
+ {\r
+ g.drawString(row.annotations[column].displayCharacter,\r
+ (x * av.charWidth) + charOffset,\r
+ y + iconOffset + 3);\r
+ }\r
+ else if (\r
+ row.annotations[column - 1] == null\r
+ || (!row.annotations[column].displayCharacter.equals(\r
+ row.annotations[column - 1].displayCharacter)\r
+ ||\r
+ (row.annotations[column].displayCharacter.length() < 2 &&\r
+ row.annotations[column].secondaryStructure == ' ')))\r
+ {\r
+ g.drawString(row.annotations[column].displayCharacter,\r
+ (x * av.charWidth) + charOffset,\r
+ y + iconOffset + 3);\r
+ }\r
+ }\r
\r
- g.setColor(Color.red);\r
+ if (row.hasIcons)\r
+ {\r
+ if (!validRes ||\r
+ (row.annotations[column].secondaryStructure != lastSS))\r
+ {\r
+ switch (lastSS)\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ if (MAC)\r
+ {\r
+ //Off by 1 offset when drawing rects and ovals\r
+ //to offscreen image on the MAC\r
+ g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
+ (x * av.charWidth) - lastSSX, 7, 8, 8);\r
+ break;\r
+ }\r
+\r
+ int sCol = (lastSSX / av.charWidth) + startRes;\r
+ int x1 = lastSSX;\r
+ int x2 = (x * av.charWidth);\r
+\r
+ if (sCol == 0 ||\r
+ row.annotations[sCol - 1] == null ||\r
+ row.annotations[sCol - 1].secondaryStructure != 'H')\r
+ {\r
+ g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,\r
+ 180);\r
+ x1 += av.charWidth / 2;\r
+ }\r
+\r
+ if (row.annotations[column] == null ||\r
+ row.annotations[column].secondaryStructure != 'H')\r
+ {\r
+ g.fillArc( (x * av.charWidth) - av.charWidth,\r
+ y + 4 + iconOffset, av.charWidth, 8, 270, 180);\r
+ x2 -= av.charWidth / 2;\r
+ }\r
+\r
+ g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);\r
+ break;\r
+\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+ g.fillRect(lastSSX, y + 4 + iconOffset,\r
+ (x * av.charWidth) - lastSSX - 4, 7);\r
+ g.fillPolygon(new int[]\r
+ { (x * av.charWidth) - 4,\r
+ (x * av.charWidth) - 4,\r
+ (x * av.charWidth)},\r
+ new int[]\r
+ {\r
+ y + iconOffset, y + 14 + iconOffset,\r
+ y + 8 + iconOffset\r
+ }, 3);\r
+\r
+ break;\r
+\r
+ default:\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX, y + 6 + iconOffset,\r
+ (x * av.charWidth) - lastSSX, 2);\r
+\r
+ break;\r
+ }\r
+\r
+ if (validRes)\r
+ {\r
+ lastSS = row.annotations[column].secondaryStructure;\r
+ }\r
+ else\r
+ {\r
+ lastSS = ' ';\r
+ }\r
+\r
+ lastSSX = (x * av.charWidth);\r
+ }\r
+ }\r
\r
- if(activeRes!=null)\r
- for (int n = 0; n < activeRes.size(); n++)\r
- {\r
- int v = Integer.parseInt(activeRes.elementAt(n).toString()) ;\r
- if (v == j)\r
- g.fillRect( (j-startRes) * av.charWidth, y, av.charWidth, row.height);\r
- }\r
- }\r
+ column++;\r
+ x++;\r
+ }\r
\r
+ if (column >= row.annotations.length)\r
+ {\r
+ column = row.annotations.length - 1;\r
+ }\r
+\r
+ // x ++;\r
\r
+ if (row.hasIcons)\r
+ {\r
+ switch (lastSS)\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ if (MAC)\r
+ {\r
+ //Off by 1 offset when drawing rects and ovals\r
+ //to offscreen image on the MAC\r
+ g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
+ (x * av.charWidth) - lastSSX, 7, 8, 8);\r
+ break;\r
+ }\r
+\r
+ int sCol = (lastSSX / av.charWidth) + startRes;\r
+ int x1 = lastSSX;\r
+ int x2 = (x * av.charWidth);\r
+\r
+ if (sCol == 0 ||\r
+ row.annotations[sCol - 1] == null ||\r
+ row.annotations[sCol - 1].secondaryStructure != 'H')\r
+ {\r
+ g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);\r
+ x1 += av.charWidth / 2;\r
+ }\r
+\r
+ if (row.annotations[column] == null ||\r
+ row.annotations[column].secondaryStructure != 'H')\r
+ {\r
+ g.fillArc( (x * av.charWidth) - av.charWidth,\r
+ y + 4 + iconOffset, av.charWidth, 8, 270,\r
+ 180);\r
+ x2 -= av.charWidth / 2;\r
+ }\r
+\r
+ g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);\r
+\r
+ break;\r
+\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+\r
+ if (row.annotations[endRes] == null\r
+ || row.annotations[endRes].secondaryStructure != 'E')\r
+ {\r
+ g.fillRect(lastSSX, y + 4 + iconOffset,\r
+ (x * av.charWidth) - lastSSX - 4, 7);\r
+ g.fillPolygon(new int[]\r
+ { (x * av.charWidth) - 4,\r
+ (x * av.charWidth) - 4,\r
+ (x * av.charWidth)},\r
+ new int[]\r
+ {\r
+ y + iconOffset, y + 14 + iconOffset,\r
+ y + 7 + iconOffset\r
+ }, 3);\r
+ }\r
+ else\r
+ {\r
+ g.fillRect(lastSSX, y + 4 + iconOffset,\r
+ x * av.charWidth - lastSSX, 7);\r
+ }\r
+ break;\r
+\r
+ default:\r
+ g.setColor(Color.gray);\r
+ if (!av.wrapAlignment || endRes == av.endRes)\r
+ {\r
+ g.fillRect(lastSSX, y + 6 + iconOffset,\r
+ (x * av.charWidth) - lastSSX, 2);\r
+ }\r
+\r
+ break;\r
+ }\r
+ }\r
\r
- if(validRes && row.annotations[j].displayCharacter.length()>0)\r
- {\r
- int charOffset = (av.charWidth - fm.charWidth(row.annotations[j].displayCharacter.charAt(0)))/2;\r
- g.setColor( row.annotations[j].colour);\r
- if(j==0)\r
+ if (row.graph > 0)\r
+ {\r
+ if (row.graph == AlignmentAnnotation.LINE_GRAPH)\r
+ {\r
+ if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])\r
{\r
- if (row.annotations[0].secondaryStructure == 'H'\r
- || row.annotations[0].secondaryStructure == 'E')\r
- g.drawString(row.annotations[j].displayCharacter, x,\r
- y + iconOffset + 2);\r
+ float groupmax = -999999, groupmin = 9999999;\r
+ for (int gg = 0; gg < aa.length; gg++)\r
+ {\r
+ if (aa[gg].graphGroup != row.graphGroup)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (aa[gg] != row)\r
+ {\r
+ aa[gg].visible = false;\r
+ }\r
+\r
+ if (aa[gg].graphMax > groupmax)\r
+ {\r
+ groupmax = aa[gg].graphMax;\r
+ }\r
+ if (aa[gg].graphMin < groupmin)\r
+ {\r
+ groupmin = aa[gg].graphMin;\r
+ }\r
+ }\r
+\r
+ for (int gg = 0; gg < aa.length; gg++)\r
+ {\r
+ if (aa[gg].graphGroup == row.graphGroup)\r
+ {\r
+ drawLineGraph(g, aa[gg], startRes, endRes, y,\r
+ groupmin, groupmax,\r
+ row.graphHeight);\r
+ }\r
+ }\r
+\r
+ graphGroupDrawn[row.graphGroup] = true;\r
}\r
- else if( (row.annotations[j].secondaryStructure=='H'\r
- || row.annotations[j].secondaryStructure=='E') &&\r
- (row.annotations[j-1]==null ||\r
- row.annotations[j].secondaryStructure!=row.annotations[j-1].secondaryStructure))\r
-\r
- g.drawString(row.annotations[j].displayCharacter, x, y + iconOffset + 2);\r
-\r
- if(!row.hasIcons)\r
- g.drawString(row.annotations[j].displayCharacter, x + charOffset,\r
- y + iconOffset + 2);\r
- }\r
-\r
- if(row.hasIcons)\r
- if(!validRes || row.annotations[j].secondaryStructure!=lastSS[i])\r
- {\r
- switch (lastSS[i])\r
- {\r
- case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y+4 + iconOffset, x-lastSSX[i], 7, 8, 8);\r
- break;\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset, x-lastSSX[i]-4, 7);\r
- g.fillPolygon(new int[] {x - 4, x- 4, x }\r
- , new int[]{y+ iconOffset, y + 14+ iconOffset, y + 8+ iconOffset}, 3);\r
- break;\r
- case 'C':\r
- break;\r
- default :\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
- break;\r
- }\r
-\r
- if(validRes)\r
- lastSS[i] = row.annotations[j].secondaryStructure;\r
else\r
- lastSS[i] = ' ';\r
- lastSSX[i] = x;\r
- }\r
+ {\r
+ drawLineGraph(g, row, startRes, endRes,\r
+ y, row.graphMin, row.graphMax, row.graphHeight);\r
+ }\r
+ }\r
+ else if (row.graph == AlignmentAnnotation.BAR_GRAPH)\r
+ {\r
+ drawBarGraph(g, row, startRes, endRes,\r
+ row.graphMin, row.graphMax, y);\r
+ }\r
+ }\r
+\r
+ if (row.graph > 0 && row.hasText)\r
+ {\r
+ y += av.charHeight;\r
+ }\r
+\r
+ if (row.graph == 0)\r
+ {\r
+ y += aa[i].height;\r
+ }\r
+ }\r
+ }\r
+\r
+ public void drawLineGraph(Graphics g, AlignmentAnnotation aa,\r
+ int sRes, int eRes,\r
+ int y,\r
+ float min, float max,\r
+ int graphHeight)\r
+ {\r
+ if (sRes > aa.annotations.length)\r
+ {\r
+ return;\r
+ }\r
+\r
+ int x = 0;\r
+\r
+ //Adjustment for fastpaint to left\r
+ if (eRes < av.endRes)\r
+ {\r
+ eRes++;\r
+ }\r
\r
- if (validRes && row.isGraph)\r
- {\r
- g.setColor(new Color(0,0,180));\r
- int height = (int)((row.annotations[j].value / row.graphMax)*GRAPH_HEIGHT);\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
\r
- if(row.windowLength>1)\r
- {\r
- int total =0;\r
- for(int i2=j- (row.windowLength/2); i2<j+(row.windowLength/2); i2++)\r
- {\r
- if(i2<0 || i2>=av.alignment.getWidth())\r
- continue;\r
+ if (sRes == 0)\r
+ {\r
+ sRes++;\r
+ x += av.charWidth;\r
+ }\r
\r
- total += row.annotations[i2].value;\r
- }\r
+ int y1 = y, y2 = y;\r
+ float range = max - min;\r
\r
- total/=row.windowLength;\r
- height = (int)( (total / row.graphMax) *GRAPH_HEIGHT);\r
+ ////Draw origin\r
+ if (min < 0)\r
+ {\r
+ y2 = y - (int) ( (0 - min / range) * graphHeight);\r
+ }\r
+\r
+ g.setColor(Color.gray);\r
+ g.drawLine(x - av.charWidth, y2, (eRes - sRes) * av.charWidth, y2);\r
\r
- }\r
- g.setColor(row.annotations[j].colour);\r
- g.fillRect(x, y-height, av.charWidth, height );\r
- }\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
\r
+ int column;\r
+ int aaMax = aa.annotations.length - 1;\r
\r
+ while (x < eRes - sRes)\r
+ {\r
+ column = sRes + x;\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(column);\r
}\r
\r
- x+=av.charWidth;\r
+ if (column > aaMax)\r
+ {\r
+ break;\r
+ }\r
\r
- if(row.hasIcons)\r
- switch (lastSS[i])\r
+ if (aa.annotations[column] == null || aa.annotations[column - 1] == null)\r
{\r
- case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y+4+ iconOffset, x - lastSSX[i], 7, 8, 8);\r
- break;\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
- g.fillRect(lastSSX[i], y + 4+ iconOffset, x - lastSSX[i] - 4, 7);\r
- g.fillPolygon(new int[]\r
- {x - 4, x - 4, x}\r
- , new int[]\r
- {y + iconOffset, y + 14+ iconOffset, y + 7+ iconOffset}\r
- , 3);\r
- break;\r
- case 'C':\r
- break;\r
- default:\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
- break;\r
+ x++;\r
+ continue;\r
+ }\r
+\r
+ g.setColor(aa.annotations[column].colour);\r
+ y1 = y -\r
+ (int) ( ( (aa.annotations[column - 1].value - min) / range) * graphHeight);\r
+ y2 = y -\r
+ (int) ( ( (aa.annotations[column].value - min) / range) * graphHeight);\r
+\r
+ g.drawLine(x * av.charWidth - av.charWidth / 2, y1,\r
+ x * av.charWidth + av.charWidth / 2, y2);\r
+ x++;\r
+ }\r
+\r
+ if (aa.threshold != null)\r
+ {\r
+ g.setColor(aa.threshold.colour);\r
+\r
+ y2 = (int) (y - ( (aa.threshold.value - min) / range) * graphHeight);\r
+ g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);\r
+ }\r
+ }\r
+\r
+ public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\r
+ int sRes, int eRes,\r
+ float min, float max,\r
+ int y)\r
+ {\r
+ if (sRes > aa.annotations.length)\r
+ {\r
+ return;\r
+ }\r
+\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
+\r
+ int x = 0, y1 = y, y2 = y;\r
+\r
+ float range = max - min;\r
+\r
+ if (min < 0)\r
+ {\r
+ y2 = y - (int) ( (0 - min / (range)) * aa.graphHeight);\r
+ }\r
\r
+ g.setColor(Color.gray);\r
+\r
+ g.drawLine(x, y2, (eRes - sRes) * av.charWidth, y2);\r
+\r
+ int column;\r
+ int aaMax = aa.annotations.length - 1;\r
+\r
+ while (x < eRes - sRes)\r
+ {\r
+ column = sRes + x;\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(column);\r
+ }\r
+\r
+ if (column > aaMax)\r
+ {\r
+ break;\r
+ }\r
+\r
+ if (aa.annotations[column] == null)\r
+ {\r
+ x++;\r
+ continue;\r
+ }\r
+\r
+ g.setColor(aa.annotations[column].colour);\r
+ y1 = y -\r
+ (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight);\r
+\r
+ if (y1 - y2 > 0)\r
+ {\r
+ g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);\r
}\r
+ else\r
+ {\r
+ g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);\r
+ }\r
+\r
+ x++;\r
\r
- if(row.isGraph && row.hasText)\r
- y+=av.charHeight;\r
- if(!row.isGraph)\r
- y+=aa[i].height;\r
+ }\r
+ if (aa.threshold != null)\r
+ {\r
+ g.setColor(aa.threshold.colour);\r
+ y2 = (int) (y - ( (aa.threshold.value - min) / range) * aa.graphHeight);\r
+ g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);\r
}\r
}\r
\r
// used by overview window\r
- public void drawGraph(Graphics g, AlignmentAnnotation aa,int width, int y)\r
+ public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y,\r
+ int sRes, int eRes)\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0,width, y);\r
- g.setColor(new Color(0,0,180));\r
- int x = 0;\r
- for(int j=0; j<aa.annotations.length; j++)\r
+ g.fillRect(0, 0, width, y);\r
+ g.setColor(new Color(0, 0, 180));\r
+\r
+ int x = 0, height;\r
+\r
+ for (int j = sRes; j < eRes; j++)\r
{\r
- g.setColor(new Color(0, 0, 180));\r
- int height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT );\r
+ g.setColor(aa.annotations[j].colour);\r
+\r
+ height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);\r
+ if (height > y)\r
+ {\r
+ height = y;\r
+ }\r
g.fillRect(x, y - height, av.charWidth, height);\r
- x+=av.charWidth;\r
+ x += av.charWidth;\r
}\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff