/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.gui;\r
\r
import org.exolab.castor.xml.*;\r
import jalview.binding.*;\r
import jalview.schemes.*;\r
+import jalview.util.jarInputStreamProvider;\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
+ * \r
* @author $author$\r
* @version $Revision$\r
*/\r
public class Jalview2XML_V1\r
{\r
+ boolean raiseGUI = true;\r
+\r
+ public Jalview2XML_V1()\r
+ {\r
+\r
+ };\r
+\r
+ public Jalview2XML_V1(boolean raiseGUI)\r
+ {\r
+ this.raiseGUI = raiseGUI;\r
+ };\r
+\r
jalview.schemes.UserColourScheme GetUserColourScheme(\r
- JalviewModelSequence jms, String id)\r
+ JalviewModelSequence jms, String id)\r
{\r
UserColours[] uc = jms.getUserColours();\r
UserColours colours = null;\r
\r
for (int i = 0; i < csize; i++)\r
{\r
- newColours[i] = new java.awt.Color(Integer.parseInt(\r
- colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
+ newColours[i] = new java.awt.Color(Integer.parseInt(colours\r
+ .getUserColourScheme().getColour(i).getRGB(), 16));\r
}\r
\r
return new jalview.schemes.UserColourScheme(newColours);\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param file DOCUMENT ME!\r
+ * \r
+ * @param file\r
+ * DOCUMENT ME!\r
*/\r
- public AlignFrame LoadJalviewAlign(final String file)\r
+ public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)\r
{\r
-\r
+ final String file = jprovider.getFilename();\r
jalview.gui.AlignFrame af = null;\r
\r
try\r
{\r
- //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
- URL url = null;\r
-\r
- if (file.startsWith("http://"))\r
- {\r
- url = new URL(file);\r
- }\r
-\r
JarInputStream jin = null;\r
JarEntry jarentry = null;\r
int entryCount = 1;\r
\r
do\r
{\r
- if (url != null)\r
- {\r
- jin = new JarInputStream(url.openStream());\r
- }\r
- else\r
- {\r
- jin = new JarInputStream(new FileInputStream(file));\r
- }\r
+ jin = jprovider.getJarInputStream();\r
\r
for (int i = 0; i < entryCount; i++)\r
{\r
jarentry = jin.getNextJarEntry();\r
}\r
\r
- class NoDescIDResolver\r
- implements IDResolver\r
+ class NoDescIDResolver implements IDResolver\r
{\r
public Object resolve(String idref)\r
{\r
af = LoadFromObject(object, file);\r
entryCount++;\r
}\r
- }\r
- while (jarentry != null);\r
- }\r
- catch (final java.net.UnknownHostException ex)\r
+ } while (jarentry != null);\r
+ } catch (final java.net.UnknownHostException ex)\r
{\r
ex.printStackTrace();\r
- javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ if (raiseGUI)\r
{\r
- public void run()\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
{\r
+ public void run()\r
+ {\r
\r
- System.err.println("Couldn't locate Jalview XML file : " +\r
- ex + "\n");\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Couldn't locate " + file,\r
- "URL not found",\r
- JOptionPane.WARNING_MESSAGE);\r
- }\r
- });\r
- }\r
- catch (Exception ex)\r
+ System.err.println("Couldn't locate Jalview XML file : " + ex\r
+ + "\n");\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Couldn't locate " + file, "URL not found",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ });\r
+ }\r
+ ;\r
+ } catch (Exception ex)\r
{\r
+ System.err.println("Exception whilst loading jalview XML file : ");\r
ex.printStackTrace();\r
- System.err.println("Exception whilst loading jalview XML file : " +\r
- ex + "\n");\r
- javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ if (raiseGUI)\r
{\r
- public void run()\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
{\r
+ public void run()\r
+ {\r
\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Error loading " + file,\r
- "Error loading Jalview file",\r
- JOptionPane.WARNING_MESSAGE);\r
- }\r
- });\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Error loading " + file, "Error loading Jalview file",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ });\r
+ }\r
}\r
\r
return af;\r
\r
JalviewModelSequence jms = object.getJalviewModelSequence();\r
\r
- //////////////////////////////////\r
- //LOAD SEQUENCES\r
- jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[\r
- vamsasSeq.length];\r
+ // ////////////////////////////////\r
+ // LOAD SEQUENCES\r
+ jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
for (int i = 0; i < vamsasSeq.length; i++)\r
{\r
jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
- vamsasSeq[i].getSequence());\r
+ vamsasSeq[i].getSequence());\r
jseqs[i].setStart(JSEQ[i].getStart());\r
jseqs[i].setEnd(JSEQ[i].getEnd());\r
seqids.add(jseqs[i]);\r
}\r
\r
- ///SequenceFeatures are added to the DatasetSequence,\r
+ // /SequenceFeatures are added to the DatasetSequence,\r
// so we must create the dataset before loading features\r
- /////////////////////////////////\r
+ // ///////////////////////////////\r
jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
al.setDataset(null);\r
- /////////////////////////////////\r
+ // ///////////////////////////////\r
\r
for (int i = 0; i < vamsasSeq.length; i++)\r
{\r
Features[] features = JSEQ[i].getFeatures();\r
for (int f = 0; f < features.length; f++)\r
{\r
- jalview.datamodel.SequenceFeature sf\r
- = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
- features[f].getDescription(), features[f].getStatus(),\r
- features[f].getBegin(), features[f].getEnd(),\r
- null);\r
+ jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(\r
+ features[f].getType(), features[f].getDescription(),\r
+ features[f].getStatus(), features[f].getBegin(),\r
+ features[f].getEnd(), null);\r
\r
al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
}\r
}\r
}\r
\r
- /////////////////////////////////\r
- //////////////////////////////////\r
- //LOAD ANNOTATIONS\r
+ // ///////////////////////////////\r
+ // ////////////////////////////////\r
+ // LOAD ANNOTATIONS\r
if (vamsasSet.getAnnotation() != null)\r
{\r
Annotation[] an = vamsasSet.getAnnotation();\r
for (int i = 0; i < an.length; i++)\r
{\r
AnnotationElement[] ae = an[i].getAnnotationElement();\r
- jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[\r
- al.getWidth()];\r
+ jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al\r
+ .getWidth()];\r
\r
for (int aa = 0; aa < ae.length; aa++)\r
{\r
- anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].\r
- getDisplayCharacter(),\r
- ae[aa].getDescription(),\r
- ae[aa].getSecondaryStructure().charAt(0),\r
- ae[aa].getValue());\r
+ anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(\r
+ ae[aa].getDisplayCharacter(), ae[aa].getDescription(),\r
+ ae[aa].getSecondaryStructure().charAt(0),\r
+ ae[aa].getValue());\r
}\r
\r
jalview.datamodel.AlignmentAnnotation jaa = null;\r
if (an[i].getGraph())\r
{\r
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
- an[i].getDescription(), anot, 0, 0,\r
- jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);\r
+ an[i].getDescription(), anot, 0, 0,\r
+ jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);\r
}\r
else\r
{\r
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
- an[i].getDescription(), anot);\r
+ an[i].getDescription(), anot);\r
}\r
\r
al.addAnnotation(jaa);\r
}\r
}\r
\r
- /////////////////////////////////\r
+ // ///////////////////////////////\r
// LOAD VIEWPORT\r
Viewport[] views = jms.getViewport();\r
Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
\r
for (int i = 0; i < JSEQ.length; i++)\r
{\r
- af.viewport.setSequenceColour(\r
- af.viewport.alignment.getSequenceAt(i),\r
- new java.awt.Color(\r
- JSEQ[i].getColour()));\r
+ af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),\r
+ new java.awt.Color(JSEQ[i].getColour()));\r
}\r
\r
- // af.changeColour() );\r
- /////////////////////////\r
- //LOAD GROUPS\r
+ // af.changeColour() );\r
+ // ///////////////////////\r
+ // LOAD GROUPS\r
if (jms.getJGroupCount() > 0)\r
{\r
JGroup[] groups = jms.getJGroup();\r
}\r
else\r
{\r
- cs = ColourSchemeProperty.getColour(al,\r
- groups[i].getColour());\r
+ cs = ColourSchemeProperty.getColour(al, groups[i].getColour());\r
}\r
\r
if (cs != null)\r
\r
for (int s = 0; s < ids.length; s++)\r
{\r
- seqs.addElement( (jalview.datamodel.SequenceI) seqids.elementAt(\r
- ids[s]));\r
+ seqs.addElement((jalview.datamodel.SequenceI) seqids\r
+ .elementAt(ids[s]));\r
}\r
\r
- jalview.datamodel.SequenceGroup sg = new jalview.datamodel.\r
- SequenceGroup(seqs,\r
- groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
- groups[i].getDisplayText(), groups[i].getColourText(),\r
- groups[i].getStart(), groups[i].getEnd());\r
+ jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(\r
+ seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
+ groups[i].getDisplayText(), groups[i].getColourText(),\r
+ groups[i].getStart(), groups[i].getEnd());\r
\r
- sg.setOutlineColour(new java.awt.Color(\r
- groups[i].getOutlineColour()));\r
+ sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));\r
\r
if (groups[i].getConsThreshold() != 0)\r
{\r
jalview.analysis.Conservation c = new jalview.analysis.Conservation(\r
- "All",\r
- ResidueProperties.propHash, 3, sg.getSequences(null), 0,\r
- sg.getWidth() - 1);\r
+ "All", ResidueProperties.propHash, 3,\r
+ sg.getSequences(null), 0, sg.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, 25);\r
sg.cs.setConservation(c);\r
}\r
\r
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
- view.getHeight());\r
+ view.getHeight());\r
af.viewport.setStartRes(view.getStartRes());\r
af.viewport.setStartSeq(view.getStartSeq());\r
af.viewport.setShowAnnotation(view.getShowAnnotation());\r
af.viewport.setColourText(view.getShowColourText());\r
af.viewport.setConservationSelected(view.getConservationSelected());\r
af.viewport.setShowJVSuffix(view.getShowFullId());\r
- af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
- view.getFontStyle(), view.getFontSize()));\r
+ af.viewport.setFont(new java.awt.Font(view.getFontName(), view\r
+ .getFontStyle(), view.getFontSize()));\r
af.alignPanel.fontChanged();\r
\r
af.viewport.setRenderGaps(view.getRenderGaps());\r
if (jms.getFeatureSettings() != null)\r
{\r
af.viewport.featuresDisplayed = new Hashtable();\r
- String[] renderOrder = new String[jms.getFeatureSettings().\r
- getSettingCount()];\r
+ String[] renderOrder = new String[jms.getFeatureSettings()\r
+ .getSettingCount()];\r
for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)\r
{\r
Setting setting = jms.getFeatureSettings().getSetting(fs);\r
\r
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.\r
- getType(),\r
- new java.awt.Color(setting.getColour()));\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(\r
+ setting.getType(), new java.awt.Color(setting.getColour()));\r
\r
renderOrder[fs] = setting.getType();\r
\r
if (setting.getDisplay())\r
{\r
- af.viewport.featuresDisplayed.put(\r
- setting.getType(), new Integer(setting.getColour()));\r
+ af.viewport.featuresDisplayed.put(setting.getType(), new Integer(\r
+ setting.getColour()));\r
}\r
}\r
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =\r
- renderOrder;\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
}\r
\r
af.setMenusFromViewport(af.viewport);\r
\r
- Desktop.addInternalFrame(af, view.getTitle(),\r
- view.getWidth(), view.getHeight());\r
+ Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),\r
+ view.getHeight());\r
\r
- //LOAD TREES\r
- ///////////////////////////////////////\r
+ // LOAD TREES\r
+ // /////////////////////////////////////\r
if (jms.getTreeCount() > 0)\r
{\r
try\r
\r
Tree tree = jms.getTree(t);\r
\r
- TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
- tree.getNewick()), tree.getTitle(),\r
- tree.getWidth(), tree.getHeight(),\r
- tree.getXpos(), tree.getYpos());\r
+ TreePanel tp = af.ShowNewickTree(\r
+ new jalview.io.NewickFile(tree.getNewick()),\r
+ tree.getTitle(), tree.getWidth(), tree.getHeight(),\r
+ tree.getXpos(), tree.getYpos());\r
\r
tp.fitToWindow.setState(tree.getFitToWindow());\r
tp.fitToWindow_actionPerformed(null);\r
\r
if (tree.getFontName() != null)\r
{\r
- tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
- tree.getFontStyle(),\r
- tree.getFontSize()));\r
+ tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree\r
+ .getFontStyle(), tree.getFontSize()));\r
}\r
else\r
{\r
- tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
- view.getFontStyle(),\r
- tree.getFontSize()));\r
+ tp.setTreeFont(new java.awt.Font(view.getFontName(), view\r
+ .getFontStyle(), tree.getFontSize()));\r
}\r
\r
tp.showPlaceholders(tree.getMarkUnlinked());\r
}\r
}\r
\r
- }\r
- catch (Exception ex)\r
+ } catch (Exception ex)\r
{\r
ex.printStackTrace();\r
}\r
git://source.jalview.org / jalview.git / blobdiff