/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.appletgui;
int imgWidth = 0;
boolean fastPaint = false;
- //Used For mouse Dragging and resizing graphs
+
+ // Used For mouse Dragging and resizing graphs
int graphStretch = -1;
int graphStretchY = -1;
-
- boolean mouseDragging=false;
-
+
+ boolean mouseDragging = false;
+
public static int GRAPH_HEIGHT = 40;
boolean MAC = false;
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void actionPerformed(ActionEvent evt)
{
{
activeRow = i;
}
- else if (aa[i].graph > 0)
+ else if (aa[i].graph > 0)
{
// Stretch Graph
graphStretch = i;
graphStretchY = evt.getY();
}
-
break;
}
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param startRes
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param endRes
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void drawComponent(Graphics g, int startRes, int endRes)
{
boolean validRes = false;
boolean validEnd = false;
boolean labelAllCols = false;
- boolean centreColLabels,centreColLabelsDef = av.getCentreColumnLabels();
- boolean scaleColLabel=false;
+ boolean centreColLabels, centreColLabelsDef = av
+ .getCentreColumnLabels();
+ boolean scaleColLabel = false;
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.
+ float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
+ // column.
// \u03B2 \u03B1
for (int i = 0; i < aa.length; i++)
{
y -= av.charHeight;
}
}
- //TODO: else is the logic used in application, applet had no 'else'
+ // TODO: else is the logic used in application, applet had no 'else'
else if (row.hasText)
{
iconOffset = av.charHeight - fm.getDescent();
&& (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());
+ fmWidth = (float) fm.charsWidth(
+ row.annotations[column].displayCharacter.toCharArray(),
+ 0, row.annotations[column].displayCharacter.length());
- if ( scaleColLabel ) {
+ if (scaleColLabel)
+ {
// justify the label and scale to fit in column
- if (fmWidth > av.charWidth) {
+ if (fmWidth > av.charWidth)
+ {
// scale only if the current font isn't already small enough
fmScaling = av.charWidth;
fmScaling /= fmWidth;
- // not 1.1 // g.setFont(new Font(ofont,AffineTransform.getScaleInstance(fmScaling, 1.0)));
+ // not 1.1 // g.setFont(new
+ // Font(ofont,AffineTransform.getScaleInstance(fmScaling,
+ // 1.0)));
// and update the label's width to reflect the scaling.
fmWidth = av.charWidth;
}
}
- } else {
+ }
+ else
+ {
fmWidth = (float) fm
- .charWidth(row.annotations[column].displayCharacter.charAt(0));
+ .charWidth(row.annotations[column].displayCharacter
+ .charAt(0));
}
- charOffset = (int) ((av.charWidth - fmWidth) / 2f);
-
+ charOffset = (int) ((av.charWidth - fmWidth) / 2f);
+
if (row.annotations[column].colour == null)
g.setColor(Color.black);
else
if (column == 0 || row.graph > 0)
{
g.drawString(row.annotations[column].displayCharacter,
- (x * av.charWidth) + charOffset, y + iconOffset + 3); // + 3?
+ (x * av.charWidth) + charOffset, y + iconOffset + 3); // +
+ // 3?
}
else if (row.annotations[column - 1] == null
- || (labelAllCols||!row.annotations[column].displayCharacter
- .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter
+ || (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,
}
}
- if (row.graph > 0 && row.graphHeight> 0)
+ if (row.graph > 0 && row.graphHeight > 0)
{
if (row.graph == AlignmentAnnotation.LINE_GRAPH)
{
}
if (aa.annotations[column] == null) // || coaa.annotations[column - 1] ==
- // null)
+ // null)
{
x++;
continue;
int eRes, float min, float max, int y)
{
ColourSchemeI profcolour = av.getGlobalColourScheme();
- if (profcolour==null)
+ if (profcolour == null)
{
profcolour = new jalview.schemes.ZappoColourScheme();
}
int column;
int aaMax = aa.annotations.length - 1;
boolean renderHistogram = true, renderProfile = false;
- /* Logos are disabled for 2.5 release : Bug # 0060064
- * if (aa.autoCalculated && aa.label.startsWith("Consensus")) {
- // TODO: generalise this to have render styles for consensus/profile data
- if (aa.groupRef!=null)
- {
- renderHistogram = aa.groupRef.isShowConsensusHistogram();
- renderProfile = aa.groupRef.isShowSequenceLogo();
- } else {
- renderHistogram = av.isShowConsensusHistogram();
- renderProfile = av.isShowSequenceLogo();
- }
- }*/
+ /*
+ * Logos are disabled for 2.5 release : Bug # 0060064 if (aa.autoCalculated
+ * && aa.label.startsWith("Consensus")) { // TODO: generalise this to have
+ * render styles for consensus/profile data if (aa.groupRef!=null) {
+ * renderHistogram = aa.groupRef.isShowConsensusHistogram(); renderProfile =
+ * aa.groupRef.isShowSequenceLogo(); } else { renderHistogram =
+ * av.isShowConsensusHistogram(); renderProfile = av.isShowSequenceLogo(); }
+ * }
+ */
while (x < eRes - sRes)
{
column = sRes + x;
- (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
if (renderHistogram)
- {
- if (y1 - y2 > 0)
{
- g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);
- }
- else
- {
- g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);
- }
+ if (y1 - y2 > 0)
+ {
+ g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);
+ }
+ else
+ {
+ g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);
+ }
}
// draw profile if available
// Disabled for 2.5 release: see bug #0060064
/**
- if (aa.annotations[column].value!=0 && renderProfile)
- {
- 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];)
- {
- dc[0] = (char) profl[c++];
- wdth = av.charWidth;
- wdth/=(float) fm
- .charsWidth(dc,0,1);
-
- if (c>2)
- {
- ht+=(int)ht2;
- }
- {
- // not java 1.1 compatible: Bug # 0060064
- g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, (ht2=(htn*((double)profl[c++])/100.0))/av.charHeight)));
- lm = g.getFontMetrics().getLineMetrics(dc,0,1, g);
- g.setColor(profcolour.findColour(dc[0]));
- g.drawChars(dc,0,1,x*av.charWidth, (int) (ht+lm.getHeight()));
- }
- }
- g.setFont(ofont);
- }
- **/
+ * if (aa.annotations[column].value!=0 && renderProfile) { 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];) { dc[0] = (char) profl[c++];
+ * wdth = av.charWidth; wdth/=(float) fm .charsWidth(dc,0,1);
+ *
+ * if (c>2) { ht+=(int)ht2; } { // not java 1.1 compatible: Bug # 0060064
+ * g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth,
+ * (ht2=(htn*((double)profl[c++])/100.0))/av.charHeight))); lm =
+ * g.getFontMetrics().getLineMetrics(dc,0,1, g);
+ * g.setColor(profcolour.findColour(dc[0]));
+ * g.drawChars(dc,0,1,x*av.charWidth, (int) (ht+lm.getHeight())); } }
+ * g.setFont(ofont); }
+ **/
x++;
}
}
/*
- * Disabled for 2.5 release - see bug #0060064
- private int[] getProfileFor(AlignmentAnnotation aa, int column)
- {
-// if (aa.autoCalculated && aa.label.startsWith("Consensus")) {
- if (aa.groupRef!=null && aa.groupRef.consensusData!=null) { // && aa.groupRef.isShowSequenceLogo()) {
- return AAFrequency.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 AAFrequency.extractProfile(av.hconsensus[column],av.getIgnoreGapsConsensus());
- }
- // }
- return null;
- }
+ * Disabled for 2.5 release - see bug #0060064 private int[]
+ * getProfileFor(AlignmentAnnotation aa, int column) { // if
+ * (aa.autoCalculated && aa.label.startsWith("Consensus")) { if
+ * (aa.groupRef!=null && aa.groupRef.consensusData!=null) { // &&
+ * aa.groupRef.isShowSequenceLogo()) { return
+ * AAFrequency.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
+ * AAFrequency.extractProfile(av.hconsensus[column
+ * ],av.getIgnoreGapsConsensus()); } // } return null; }
*/
// used by overview window
git://source.jalview.org / jalview.git / blobdiff