/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import javax.swing.*;
+import com.stevesoft.pat.Regex;
+
import jalview.analysis.AAFrequency;
+import jalview.analysis.StructureFrequency;
import jalview.datamodel.*;
import jalview.schemes.ColourSchemeI;
final String SHEET = "Sheet";
+ /**
+ * For RNA secondary structure "stems" aka helices
+ */
+ final String STEM = "RNA Helix";
+
final String LABEL = "Label";
final String REMOVE = "Remove Annotation";
final Color SHEET_COLOUR = Color.green.darker().darker();
+ final Color STEM_COLOUR = Color.blue.darker();
+
/** DOCUMENT ME!! */
AlignViewport av;
boolean MAC = false;
+ // for editing cursor
+ int cursorX = 0;
+
+ int cursorY = 0;
+
/**
* Creates a new AnnotationPanel object.
*
*/
public int adjustPanelHeight()
{
- int height=calcPanelHeight();
+ int height = calcPanelHeight();
this.setPreferredSize(new Dimension(1, height));
if (ap != null)
{
}
/**
- * calculate the height for visible annotation, revalidating bounds where necessary
- * ABSTRACT GUI METHOD
+ * calculate the height for visible annotation, revalidating bounds where
+ * necessary ABSTRACT GUI METHOD
+ *
* @return total height of annotation
*/
public int calcPanelHeight()
symbol = "\u03B2";
}
+ // Added by LML to color stems
+ else if (evt.getActionCommand().equals(STEM))
+ {
+ type = 'S';
+ symbol = "\u03C3";
+ }
+
if (!aa[activeRow].hasIcons)
{
aa[activeRow].hasIcons = true;
continue;
String tlabel = null;
if (anot[index] != null)
- {
+ { // LML added stem code
if (label2.equals(HELIX) || label2.equals(SHEET)
- || label2.equals(LABEL))
+ || label2.equals(STEM) || label2.equals(LABEL))
{
tlabel = anot[index].description;
if (tlabel == null || tlabel.length() < 1)
{
- if (label2.equals(HELIX) || label2.equals(SHEET))
+ if (label2.equals(HELIX) || label2.equals(SHEET)
+ || label2.equals(STEM))
{
tlabel = "" + anot[index].secondaryStructure;
}
}
JPopupMenu pop = new JPopupMenu("Structure type");
- JMenuItem item = new JMenuItem(HELIX);
- item.addActionListener(this);
- pop.add(item);
- item = new JMenuItem(SHEET);
- item.addActionListener(this);
- pop.add(item);
+ JMenuItem item;
+ /*
+ * Just display the needed structure options
+ */
+ if (av.alignment.isNucleotide() == true)
+ {
+ item = new JMenuItem(STEM);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ else
+ {
+ item = new JMenuItem(HELIX);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new JMenuItem(SHEET);
+ item.addActionListener(this);
+ pop.add(item);
+ }
item = new JMenuItem(LABEL);
item.addActionListener(this);
pop.add(item);
*/
public void mouseClicked(MouseEvent evt)
{
+ if (activeRow != -1)
+ {
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation anot = aa[activeRow];
+
+ if (anot.description.equals("secondary structure"))
+ {
+ // System.out.println(anot.description+" "+anot.getRNAStruc());
+ }
+ }
+ }
+
+ // TODO mouseClicked-content and drawCursor are quite experimental!
+ public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
+ int y1)
+ {
+ int pady = av.charHeight / 5;
+ int charOffset = 0;
+ graphics.setColor(Color.black);
+ graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+
+ if (av.validCharWidth)
+ {
+ graphics.setColor(Color.white);
+
+ char s = seq.getCharAt(res);
+
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s), charOffset + x1,
+ (y1 + av.charHeight) - pady);
+ }
+
}
/**
boolean[] graphGroupDrawn = new boolean[aa.length];
int charOffset = 0; // offset for a label
float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
- // column.
+ // column.
Font ofont = g.getFont();
// \u03B2 \u03B1
for (int i = 0; i < aa.length; i++)
scaleColLabel = row.scaleColLabel;
lastSS = ' ';
lastSSX = 0;
-
if (row.graph > 0)
{
if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])
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)
{
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))
+ 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))
{
- 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;
- }
- 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);
- break;
-
- 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);
+ case 'E':
+ drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
+ break;
- 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);
+ default:
+ g.setColor(Color.gray);
+ g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
+ - lastSSX, 2);
- break;
+ break;
+ }
}
-
if (validRes)
{
- lastSS = row.annotations[column].secondaryStructure;
+ lastSS = ss;
}
else
{
lastSS = ' ';
}
-
- lastSSX = (x * av.charWidth);
+ if (x > -1)
+ {
+ lastSSX = (x * av.charWidth);
+ }
}
}
-
column++;
x++;
}
-
if (column >= row.annotations.length)
{
column = row.annotations.length - 1;
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':
+ 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;
}
}
}
}
+ 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)
{
// draw profile if available
if (renderProfile && aa.annotations[column].value != 0)
{
+
int profl[] = getProfileFor(aa, column);
- int ht = y1, htn = y2 - y1;// aa.graphHeight;
- float wdth;
- double ht2 = 0;
- char[] dc = new char[1];
- LineMetrics lm;
- for (int c = 1; profl != null && c < profl[0];)
+ // just try to draw the logo if profl is not null
+ if (profl != null)
{
- dc[0] = (char) profl[c++];
- wdth = av.charWidth;
- wdth /= (float) fm.charsWidth(dc, 0, 1);
- if (c > 2)
+ int ht = y1, htn = y2 - y1;// aa.graphHeight;
+ float wdth;
+ double ht2 = 0;
+ char[] dc;
+
+ /**
+ * profl.length == 51 indicates that the profile of a secondary
+ * structure conservation row was accesed.
+ * Therefore dc gets length 2, to have space for a basepair instead of
+ * just a single nucleotide
+ */
+ if (profl.length == 51)
+ {
+ dc = new char[2];
+ }
+ else
{
- ht += (int) ht2;
+ dc = new char[1];
}
+
+ LineMetrics lm;
+ for (int c = 1; profl != null && c < profl[0];)
{
- // if (aa.annotations[column].value==0) {
- // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth,
- // (ht2=(aa.graphHeight*0.1/av.charHeight)))));
- // ht = y2-(int)ht2;
- // } else {
- g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
- wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0))
- / av.charHeight)));
- lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
- // htn -=ht2;
- // }
- g.setColor(profcolour.findColour(dc[0])); // (av.globalColourScheme!=null)
- // ? );// try to get a
- // colourscheme for the
- // group(aa.groupRef.cs==null)
- // ? av.textColour2 :
- // cs.findColour(dc));
- g.drawChars(dc, 0, 1, x * av.charWidth,
- (int) (ht + lm.getHeight()));
- // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent();
+ dc[0] = (char) profl[c++];
+
+ if (aa.label.startsWith("StrucConsensus"))
+ {
+ dc[1] = (char) profl[c++];
+ }
+
+ wdth = av.charWidth;
+ wdth /= (float) fm.charsWidth(dc, 0, dc.length);
+
+ if (c > 2)
+ {
+ ht += (int) ht2;
+ }
+ {
+ // if (aa.annotations[column].value==0) {
+ // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth,
+ // (ht2=(aa.graphHeight*0.1/av.charHeight)))));
+ // ht = y2-(int)ht2;
+ // } else {
+ g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
+ wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0))
+ / av.charHeight)));
+ lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
+ // htn -=ht2;
+ // }
+ g.setColor(profcolour.findColour(dc[0])); // (av.globalColourScheme!=null)
+ // ? );// try to get a
+ // colourscheme for the
+ // group(aa.groupRef.cs==null)
+ // ? av.textColour2 :
+ // cs.findColour(dc));
+ // System.out.println(dc[0]);
+
+ g.drawChars(dc, 0, dc.length, x * av.charWidth,
+ (int) (ht + lm.getHeight()));
+
+ // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent();
+ }
}
+ g.setFont(ofont);
}
- g.setFont(ofont);
}
x++;
}
&& aa.groupRef.isShowSequenceLogo())
{
return AAFrequency.extractProfile(
- aa.groupRef.consensusData[column],
- aa.groupRef.getIgnoreGapsConsensus());
+ aa.groupRef.consensusData[column], aa.groupRef
+ .getIgnoreGapsConsensus());
}
// TODO extend annotation row to enable dynamic and static profile data to
// be stored
if (aa.groupRef == null && aa.sequenceRef == null
&& av.isShowSequenceLogo())
{
- return AAFrequency.extractProfile(av.hconsensus[column],
- av.getIgnoreGapsConsensus());
+ return AAFrequency.extractProfile(av.hconsensus[column], av
+ .getIgnoreGapsConsensus());
+ }
+ }
+ else
+ {
+ if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
+ {
+ if (aa.groupRef != null && aa.groupRef.consensusData != null
+ && aa.groupRef.isShowSequenceLogo())
+ {
+ //TODO check what happens for group selections
+ return StructureFrequency.extractProfile(
+ aa.groupRef.consensusData[column], aa.groupRef
+ .getIgnoreGapsConsensus());
+ }
+ // TODO extend annotation row to enable dynamic and static profile data
+ // to
+ // be stored
+ if (aa.groupRef == null && aa.sequenceRef == null
+ && av.isShowSequenceLogo())
+ {
+ return StructureFrequency.extractProfile(av.hStrucConsensus[column],
+ av.getIgnoreGapsConsensus());
+ }
}
}
return null;
git://source.jalview.org / jalview.git / blobdiff