- 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;
- }
-
- // first pass sets up state for drawing continuation from left-hand column
- // of startRes
- x = (startRes == 0) ? 0 : -1;
- while (x < endRes - startRes)
- {
- if (av.hasHiddenColumns)
- {
- column = av.getColumnSelection().adjustForHiddenColumns(
- startRes + x);
- if (column > row.annotations.length - 1)
- {
- break;
- }
- }
- else
- {
- column = startRes + x;
- }
-
- if ((row.annotations == null) || (row.annotations.length <= column)
- || (row.annotations[column] == null))
- {
- validRes = false;
- }
- else
- {
- validRes = true;
- }
- if (x > -1)
- {
- if (activeRow == i)
- {
- g.setColor(Color.red);
-
- if (av.getColumnSelection() != null)
- {
- for (int n = 0; n < av.getColumnSelection().size(); n++)
- {
- int v = av.getColumnSelection().columnAt(n);
-
- if (v == column)
- {
- g.fillRect(x * av.charWidth, y, av.charWidth,
- av.charHeight);
- }
- }
- }
- }
-
- if (av.validCharWidth
- && validRes
- && row.annotations[column].displayCharacter != null
- && (row.annotations[column].displayCharacter.length() > 0))
- {
-
- if (centreColLabels || scaleColLabel)
- {
- fmWidth = (float) fm.charsWidth(
- row.annotations[column].displayCharacter
- .toCharArray(), 0,
- row.annotations[column].displayCharacter.length());
-
- if (scaleColLabel)
- {
- // justify the label and scale to fit in column
- if (fmWidth > av.charWidth)
- {
- // scale only if the current font isn't already small enough
- fmScaling = av.charWidth;
- fmScaling /= fmWidth;
- g.setFont(ofont.deriveFont(AffineTransform
- .getScaleInstance(fmScaling, 1.0)));
- // and update the label's width to reflect the scaling.
- fmWidth = av.charWidth;
- }
- }
- }
- else
- {
- fmWidth = (float) fm
- .charWidth(row.annotations[column].displayCharacter
- .charAt(0));
- }
- charOffset = (int) ((av.charWidth - fmWidth) / 2f);
-
- 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[column].displayCharacter,
- (x * av.charWidth) + charOffset, y + iconOffset);
- }
- else if (row.annotations[column - 1] == null
- || (labelAllCols
- || !row.annotations[column].displayCharacter
- .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter
- .length() < 2 && row.annotations[column].secondaryStructure == ' ')))
- {
- g.drawString(row.annotations[column].displayCharacter, x
- * av.charWidth + charOffset, y + iconOffset);
- }
- g.setFont(ofont);
- }
- }
- if (row.hasIcons)
- {
- char ss = validRes ? row.annotations[column].secondaryStructure
- : ' ';
- if (ss == 'S')
- {
- // distinguish between forward/backward base-pairing
- if (row.annotations[column].displayCharacter.indexOf(')') > -1)
- {
- ss = 's';
- }
- }
- if (!validRes || (ss != lastSS))
- {
- if (x > -1)
- {
- switch (lastSS)
- {
- case 'H':
- drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
-
- case 'E':
- drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
-
- case 'S': // Stem case for RNA secondary structure
- case 's': // and opposite direction
- drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
-
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
- - lastSSX, 2);
-
- break;
- }
- }
- if (validRes)
- {
- lastSS = ss;
- }
- else
- {
- lastSS = ' ';
- }
- if (x > -1)
- {
- lastSSX = (x * av.charWidth);
- }
- }
- }
- column++;
- x++;
- }
- if (column >= row.annotations.length)
- {
- column = row.annotations.length - 1;
- validEnd = false;
- }
- else
- {
- validEnd = true;
- }
-
- // x ++;
-
- if (row.hasIcons)
- {
- switch (lastSS)
- {
- case 'H':
- drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
-
- case 'E':
- drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
- case 's':
- case 'S': // Stem case for RNA secondary structure
- drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
- default:
- drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
- }
- }
-
- 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.graph == 0)
- {
- y += aa[i].height;
- }
- }
- }
-
- private void drawStemAnnot(Graphics g, AlignmentAnnotation row,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
- {
- g.setColor(STEM_COLOUR);
- int sCol = (lastSSX / av.charWidth) + startRes;
- int x1 = lastSSX;
- int x2 = (x * av.charWidth);
- Regex closeparen = new Regex("(\\))");
-
- String dc = column == 0 ? ""
- : row.annotations[column - 1].displayCharacter;
-
- boolean diffupstream = sCol == 0 || row.annotations[sCol - 1] == null
- || !dc.equals(row.annotations[sCol - 1].displayCharacter);
- boolean diffdownstream = !validRes || !validEnd
- || row.annotations[column] == null
- || !dc.equals(row.annotations[column].displayCharacter);
- // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
- // If a closing base pair half of the stem, display a backward arrow
- if (column > 0 && closeparen.search(dc))
- {
- if (diffupstream)
- // if (validRes && column>1 && row.annotations[column-2]!=null &&
- // dc.equals(row.annotations[column-2].displayCharacter))
- {
- g.fillPolygon(new int[]
- { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
- x1 += 5;
- }
- if (diffdownstream)
- {
- x2 -= 1;
- }
- }
- else
- {
- // display a forward arrow
- if (diffdownstream)
- {
- g.fillPolygon(new int[]
- { x2 - 5, x2 - 5, x2 }, new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
- x2 -= 5;
- }
- if (diffupstream)
- {
- x1 += 1;
- }
- }
- // draw arrow body
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
- }
-
- private void drawGlyphLine(Graphics g, AlignmentAnnotation row,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
- {
- g.setColor(Color.gray);
- g
- .fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
- - lastSSX, 2);
- }
-
- private void drawSheetAnnot(Graphics g, AlignmentAnnotation row,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
- {
- g.setColor(SHEET_COLOUR);
-
- if (!validEnd || !validRes || row.annotations[column] == null
- || row.annotations[column].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);
- }
-
- }
-
- private void drawHelixAnnot(Graphics g, AlignmentAnnotation row,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
- {
- g.setColor(HELIX_COLOUR);
-
- int sCol = (lastSSX / av.charWidth) + startRes;
- int x1 = lastSSX;
- int x2 = (x * av.charWidth);
-
- if (MAC)
- {
- int ofs = av.charWidth / 2;
- // Off by 1 offset when drawing rects and ovals
- // to offscreen image on the MAC
- g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
- if (sCol == 0 || row.annotations[sCol - 1] == null
- || row.annotations[sCol - 1].secondaryStructure != 'H')
- {
- }
- else
- {
- // g.setColor(Color.orange);
- g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
- 0, 0);
- }
- if (!validRes || row.annotations[column] == null
- || row.annotations[column].secondaryStructure != 'H')
- {
-
- }
- else
- {
- // g.setColor(Color.magenta);
- g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
- + 1, 8, 0, 0);
-
- }
-
- return;
- }
-
- 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 (!validRes || 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);
- }
-
- public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
- int eRes, int y, float min, float max, int graphHeight)