// ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );\r
}\r
\r
+\r
+ public AnnotationPanel(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ }\r
+\r
+\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\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
+\r
int height = 0;\r
if (aa != null)\r
{\r
}\r
\r
this.setSize(getSize().width, height);\r
- ap.annotationScroller.setSize(getSize().width, height);\r
+ if(ap!=null)\r
+ ap.annotationScroller.setSize(getSize().width, height);\r
\r
-// ap.annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);\r
\r
repaint();\r
\r
+ return height;\r
+\r
}\r
\r
public void addEditableColumn(int i)\r
if (activeRow == -1)\r
{\r
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ if(aa ==null)\r
+ return;\r
+\r
for (int j = 0; j < aa.length; j++)\r
{\r
if (aa[j].editable)\r
\r
public void paint(Graphics g)\r
{\r
+ g.setColor(Color.white);\r
+ g.fillRect(0,0, getSize().width, getSize().height);\r
imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
\r
if (image == null || imgWidth != image.getWidth(this))\r
\r
drawComponent(gg, av.startRes, av.endRes + 1);\r
g.drawImage(image, 0, 0, this);\r
-\r
}\r
\r
public void fastPaint(int horizontal)\r
\r
public void drawComponent(Graphics g, int startRes, int endRes)\r
{\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);\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.setColor(Color.black);\r
- g.drawString("Alignment has no annotations", 20, 15);\r
- return;\r
- }\r
+ g.setFont(av.getFont());\r
\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ if (fm == null)\r
+ fm = g.getFontMetrics();\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
- boolean validRes = false;\r
- //\u03B2 \u03B1\r
\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- AlignmentAnnotation row = aa[i];\r
- if (!row.visible)\r
- {\r
- continue;\r
- }\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);\r
\r
- if (row.isGraph)\r
- {\r
- // this is so that we draw the characters below the graph\r
- y += row.height;\r
- if (row.hasText)\r
- {\r
- y -= av.charHeight;\r
- }\r
- }\r
- if (row.hasText)\r
- {\r
- iconOffset = av.charHeight / 2;\r
- }\r
- else\r
+ if ((av.alignment.getAlignmentAnnotation() == null) ||\r
+ (av.alignment.getAlignmentAnnotation().length < 1))\r
{\r
- iconOffset = 0;\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
+ g.setColor(Color.black);\r
+ g.drawString("Alignment has no annotations", 20, 15);\r
+\r
+ return;\r
}\r
\r
- for (j = startRes; j < endRes; j++)\r
- {\r
- if (row.annotations.length <= j || row.annotations[j] == null)\r
- {\r
- validRes = false;\r
- }\r
- else\r
- {\r
- validRes = true;\r
- }\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
- x = (j - startRes) * av.charWidth;\r
+ int j;\r
+ int x = 0;\r
+ int y = 0;\r
+ char[] lastSS = new char[aa.length];\r
+ int[] lastSSX = new int[aa.length];\r
+ int iconOffset = av.charHeight / 2;\r
+ boolean validRes = false;\r
\r
- if (activeRow == i)\r
- {\r
+ //\u03B2 \u03B1\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ AlignmentAnnotation row = aa[i];\r
+\r
+ if (!row.visible)\r
+ {\r
+ continue;\r
+ }\r
\r
- g.setColor(Color.red);\r
\r
- if (activeRes != null)\r
+ if (row.isGraph)\r
{\r
- for (int n = 0; n < activeRes.size(); n++)\r
- {\r
- int v = Integer.parseInt(activeRes.elementAt(n).toString());\r
- if (v == j)\r
+ // this is so that we draw the characters below the graph\r
+ y += row.height;\r
+\r
+ if (row.hasText)\r
{\r
- g.fillRect( (j - startRes) * av.charWidth, y, av.charWidth,\r
- row.height);\r
+ y -= av.charHeight;\r
}\r
- }\r
}\r
- }\r
\r
- if (validRes && row.annotations[j].displayCharacter.length() > 0)\r
- {\r
- int charOffset = (av.charWidth -\r
- fm.charWidth(row.annotations[j].displayCharacter.\r
- charAt(0))) / 2;\r
- g.setColor(row.annotations[j].colour);\r
- if (j == 0 || row.isGraph)\r
+ if (row.hasText)\r
{\r
- if (row.annotations[0].secondaryStructure == 'H'\r
- || row.annotations[0].secondaryStructure == 'E')\r
- {\r
- g.drawString(row.annotations[j].displayCharacter, x,\r
- y + iconOffset + 3);\r
- }\r
+ iconOffset = av.charHeight / 2;\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 !=\r
- row.annotations[j - 1].secondaryStructure))\r
+ else\r
{\r
-\r
- g.drawString(row.annotations[j].displayCharacter, x + charOffset,\r
- y + iconOffset + 3);\r
+ iconOffset = 0;\r
}\r
\r
- if (!row.hasIcons)\r
+ for (j = startRes; j < endRes; j++)\r
{\r
- g.drawString(row.annotations[j].displayCharacter, x + charOffset,\r
- y + iconOffset + 3);\r
- }\r
- }\r
+ if ((row.annotations.length <= j) ||\r
+ (row.annotations[j] == null))\r
+ {\r
+ validRes = false;\r
+ }\r
+ else\r
+ {\r
+ validRes = true;\r
+ }\r
\r
- if (row.hasIcons)\r
- {\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],\r
- 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,\r
- 7);\r
- g.fillPolygon(new int[]\r
- {x - 4, x - 4, x}\r
- , new int[]\r
- {y + iconOffset, y + 14 + iconOffset,\r
- 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
- {\r
- lastSS[i] = row.annotations[j].secondaryStructure;\r
- }\r
- else\r
- {\r
- lastSS[i] = ' ';\r
- }\r
- lastSSX[i] = x;\r
- }\r
- }\r
+ x = (j - startRes) * av.charWidth;\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) *\r
- GRAPH_HEIGHT);\r
\r
- if (row.windowLength > 1)\r
- {\r
- int total = 0;\r
- for (int i2 = j - (row.windowLength / 2);\r
- i2 < j + (row.windowLength / 2); i2++)\r
- {\r
- if (i2 < 0 || i2 >= av.alignment.getWidth())\r
+ if (validRes &&\r
+ (row.annotations[j].displayCharacter.length() > 0))\r
+ {\r
+\r
+ int charOffset = (av.charWidth -\r
+ fm.charWidth(row.annotations[j].displayCharacter.charAt(\r
+ 0))) / 2;\r
+ g.setColor(row.annotations[j].colour);\r
+\r
+ if (j == 0 || row.isGraph)\r
+ {\r
+ g.drawString(row.annotations[j].displayCharacter, x+charOffset,\r
+ y + iconOffset + 3);\r
+ }\r
+ else if (((row.annotations[j - 1] == null) ||\r
+ (row.annotations[j].displayCharacter != row.annotations[j -\r
+ 1].displayCharacter)))\r
+ {\r
+ g.drawString(row.annotations[j].displayCharacter, x+charOffset,\r
+ y + iconOffset + 3);\r
+ }\r
+ }\r
+\r
+ if (row.hasIcons)\r
{\r
- continue;\r
+ if (!validRes ||\r
+ (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,\r
+ x - lastSSX[i], 7, 8, 8);\r
+\r
+ break;\r
+\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+ g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
+ x - lastSSX[i] - 4, 7);\r
+ g.fillPolygon(new int[] { x - 4, x - 4, x },\r
+ new int[]\r
+ {\r
+ y + iconOffset, y + 14 + iconOffset,\r
+ y + 8 + iconOffset\r
+ }, 3);\r
+\r
+ break;\r
+\r
+ case 'C':\r
+ break;\r
+\r
+ default:\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX[i], y + 6 + iconOffset,\r
+ x - lastSSX[i], 2);\r
+\r
+ break;\r
+ }\r
+\r
+ if (validRes)\r
+ {\r
+ lastSS[i] = row.annotations[j].secondaryStructure;\r
+ }\r
+ else\r
+ {\r
+ lastSS[i] = ' ';\r
+ }\r
+\r
+ lastSSX[i] = x;\r
+ }\r
}\r
\r
- total += row.annotations[i2].value;\r
- }\r
+ if (validRes && row.isGraph)\r
+ {\r
+ g.setColor(new Color(0, 0, 180));\r
+\r
+ int height = (int) ((row.annotations[j].value / row.graphMax) * GRAPH_HEIGHT);\r
+\r
+ if (row.windowLength > 1)\r
+ {\r
+ int total = 0;\r
+\r
+ for (int i2 = j - (row.windowLength / 2);\r
+ i2 < (j + (row.windowLength / 2)); i2++)\r
+ {\r
+ if ((i2 < 0) || (i2 >= av.alignment.getWidth()))\r
+ {\r
+ continue;\r
+ }\r
\r
- total /= row.windowLength;\r
- height = (int) ( (total / row.graphMax) * GRAPH_HEIGHT);\r
+ total += row.annotations[i2].value;\r
+ }\r
\r
+ total /= row.windowLength;\r
+ height = (int) ((total / row.graphMax) * GRAPH_HEIGHT);\r
+ }\r
+\r
+ g.setColor(row.annotations[j].colour);\r
+ g.fillRect(x, y - height, av.charWidth, height);\r
+ }\r
}\r
- g.setColor(row.annotations[j].colour);\r
- g.fillRect(x, y - height, av.charWidth, height);\r
- }\r
\r
- }\r
+ x += av.charWidth;\r
\r
- x += av.charWidth;\r
+ if (row.hasIcons)\r
+ {\r
+ switch (lastSS[i])\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
+ x - lastSSX[i], 7, 8, 8);\r
\r
- if (row.hasIcons)\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,\r
- 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,\r
- 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
+ break;\r
\r
- }\r
- }\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+ g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
+ x - lastSSX[i] - 4, 7);\r
+ g.fillPolygon(new int[] { x - 4, x - 4, x },\r
+ new int[]\r
+ {\r
+ y + iconOffset, y + 14 + iconOffset,\r
+ y + 7 + iconOffset\r
+ }, 3);\r
+\r
+ break;\r
\r
- if (row.isGraph && row.hasText)\r
- {\r
- y += av.charHeight;\r
- }\r
- if (!row.isGraph)\r
- {\r
- y += aa[i].height;\r
- }\r
- }\r
+ case 'C':\r
+ break;\r
+\r
+ default:\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);\r
+\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (row.isGraph && row.hasText)\r
+ {\r
+ y += av.charHeight;\r
+ }\r
+\r
+ if (!row.isGraph)\r
+ {\r
+ y += aa[i].height;\r
+ }\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, 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
- {\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, width, y);\r
g.setColor(new Color(0, 0, 180));\r
- int height = (int) ( (aa.annotations[j].value / aa.graphMax) *\r
- GRAPH_HEIGHT);\r
- g.fillRect(x, y - height, av.charWidth, height);\r
- x += av.charWidth;\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
+\r
+ height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);\r
+ if(height>y)\r
+ height = y;\r
+ g.fillRect(x, y - height, av.charWidth, height);\r
+ x += av.charWidth;\r
+ }\r
}\r
- }\r
}\r
git://source.jalview.org / jalview.git / blobdiff