From fa7f47950cccf7241aad97c1f6c99700e5a476f7 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 4 Aug 2011 17:16:33 +0100 Subject: [PATCH] JAL-883 - refactored and debugged arrow, stem and helix rendering code --- src/jalview/gui/AnnotationPanel.java | 422 ++++++++++++++++++---------------- 1 file changed, 227 insertions(+), 195 deletions(-) diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 6418c76..050e9f2 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -886,7 +886,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, scaleColLabel = row.scaleColLabel; lastSS = ' '; lastSSX = 0; - if (row.graph > 0) { if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup]) @@ -949,7 +948,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, continue; } - x = 0; + // 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) @@ -975,175 +976,117 @@ public class AnnotationPanel extends JPanel implements MouseListener, { validRes = true; } - - if (activeRow == i) + if (x > -1) { - g.setColor(Color.red); - - if (av.getColumnSelection() != null) + if (activeRow == i) { - for (int n = 0; n < av.getColumnSelection().size(); n++) - { - int v = av.getColumnSelection().columnAt(n); + g.setColor(Color.red); - if (v == column) + if (av.getColumnSelection() != null) + { + for (int n = 0; n < av.getColumnSelection().size(); n++) { - g.fillRect(x * av.charWidth, y, av.charWidth, av.charHeight); + 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) + if (av.validCharWidth + && validRes + && row.annotations[column].displayCharacter != null + && (row.annotations[column].displayCharacter.length() > 0)) { - fmWidth = (float) fm.charsWidth( - row.annotations[column].displayCharacter.toCharArray(), - 0, row.annotations[column].displayCharacter.length()); - if (scaleColLabel) + if (centreColLabels || scaleColLabel) { - // justify the label and scale to fit in column - if (fmWidth > av.charWidth) + fmWidth = (float) fm.charsWidth( + row.annotations[column].displayCharacter + .toCharArray(), 0, + row.annotations[column].displayCharacter.length()); + + if (scaleColLabel) { - // 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; + // 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); + 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 (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); + 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); } - g.setFont(ofont); } - if (row.hasIcons) { if (!validRes || (row.annotations[column].secondaryStructure != lastSS)) { - switch (lastSS) + if (x > -1) { - case 'H': - g.setColor(HELIX_COLOUR); - if (MAC) + switch (lastSS) { - // 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); + case 'H': + drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); 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; - } + case 'E': + drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); + break; - 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; - } + case 'S': // Stem case for RNA secondary structure + drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); + break; - g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); - break; + default: + g.setColor(Color.gray); + g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) + - lastSSX, 2); - case 'E': - g.setColor(SHEET_COLOUR); - 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 + 8 + iconOffset }, - 3); - - break; - - case 'S': // Stem case for RNA secondary structure - g.setColor(STEM_COLOUR); // row.annotations[column].colour for By - // RNA Helices colouring - // System.out.println("last SSX displayx" + - // row.annotations[column-1].displayCharacter +"x"); - Regex closeparen = new Regex("(\\))"); - - //If a closing base pair half of the stem, display a backward arrow - if (closeparen - .search(row.annotations[column - 1].displayCharacter))// row.annotations[column-1].displayCharacter)) - { - g.fillPolygon(new int[] - { lastSSX + 5, lastSSX + 5, lastSSX }, - new int[] - { y + iconOffset, y + 14 + iconOffset, - y + 8 + iconOffset }, 3); - g.fillRect(lastSSX + 2, y + 4 + iconOffset, - (x * av.charWidth) - lastSSX - 2, 7); - } - else //display a forward arrow - { - g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) - - lastSSX - 4, 7); - g.fillPolygon(new int[] - { (x * av.charWidth) - 5, (x * av.charWidth) - 5, - (x * av.charWidth) }, - new int[] - { y + iconOffset, y + 14 + iconOffset, - y + 8 + iconOffset }, 3); + break; } - break; - - default: - g.setColor(Color.gray); - g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) - - lastSSX, 2); - - break; } - if (validRes) { lastSS = row.annotations[column].secondaryStructure; @@ -1152,8 +1095,10 @@ public class AnnotationPanel extends JPanel implements MouseListener, { lastSS = ' '; } - - lastSSX = (x * av.charWidth); + if (x > -1) + { + lastSSX = (x * av.charWidth); + } } } @@ -1178,64 +1123,21 @@ public class AnnotationPanel extends JPanel implements MouseListener, switch (lastSS) { case 'H': - g.setColor(HELIX_COLOUR); - 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); - + drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); break; case 'E': - g.setColor(SHEET_COLOUR); - - if (!validEnd || 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); - } + drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); + break; + case 'S': // Stem case for RNA secondary structure + 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); - + drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); break; } } @@ -1305,7 +1207,137 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } - public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, + 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=""; + // If a closing base pair half of the stem, display a backward arrow + if (column>0 && closeparen.search(dc=row.annotations[column - 1].displayCharacter)) + { + if (sCol == 0 || row.annotations[sCol - 1] == null + || !dc.equals(row.annotations[sCol - 1].displayCharacter)) + //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; + } + } + else + { + // display a forward arrow + if (!validRes || row.annotations[column] == null + || !dc.equals(row.annotations[column].displayCharacter)) + { + g.fillPolygon( + new int[] + { x2 - 5, x2 - 5, + x2 }, new int[] + { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, + 3); + x2-=5; + } + } + // 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) { if (sRes > aa.annotations.length) -- 1.7.10.2