sp_cleanup.add_missing_deprecated_annotations=true
sp_cleanup.add_missing_methods=false
sp_cleanup.add_missing_nls_tags=false
-sp_cleanup.add_missing_override_annotations=false
+sp_cleanup.add_missing_override_annotations=true
sp_cleanup.add_missing_override_annotations_interface_methods=true
sp_cleanup.add_serial_version_id=false
sp_cleanup.always_use_blocks=true
There is as yet no properly defined scripting interface to Jalview,
but all the public methods of the jalview class hierarchy can be
called from Groovy scripts. The access point for this is the <strong>Jalview</strong>
- object defined in the groovy environent which corresponds to the
+ object defined in the groovy environment which corresponds to the
<pre>jalview.gui.Desktop</pre>
object which manages all the Jalview windows. Here's an example to get
you started:
<td width="60" nowrap>
<div align="center">
<strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
- <em>6/10/2015</em></strong>
+ <em>8/10/2015</em></strong>
</div>
</td>
<td>
</ul>
<em>Application</em><ul>
<!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
- <li>Signed OSX InstallAnywhere installer</li></ul>
+ <li>Signed OSX InstallAnywhere installer<br></li>
+ <li>Support for per-sequence based annotations in BioJSON</li></ul>
<em>Applet</em>
<ul><li>Split frame example added to applet examples page</li>
</ul>
<li>Disabled 'minimise' button on Jalview windows running on OSX to workaround redraw hang bug</li>
<li>Split cDNA/Protein view position and geometry not recovered from jalview project</li>
<li>Initial enabled/disabled state of annotation menu sorter 'show autocalculated first/last' corresponds to alignment view</li>
+ <li>Restoring of Clustal, RNA helix and TCoffee colour shcemes from BioJSON</li>
</ul>
<em>Applet</em><ul>
<li>Reorder sequences mirrored in cDNA/Protein split frame</li>
<strong>What's new ?</strong>
</p>
<p>
- Jalview 2.9 has been in development since December 2014. In addition
+ Jalview 2.9.0b1 is a bug fix release for Jalview 2.9, which has been in development since December 2014. In addition
to a multitude of bug fixes and minor improvements (both small, and
rather big!), it also brings major new capabilities for codon-level
analysis of protein alignments and the retrieval and manipulation of
- structural data.</p><p>For the full list of changes, see the
- <a href="releases.html#Jalview.2.9">Jalview 2.9 Release Notes</a>.
+ structural data.</p><p>For the patches since version 2.9 was release, see the
+ <a href="releases.html#Jalview.2.9.0b1">Jalview 2.9.0b1 Release Notes</a>.
</p>
<p>
<strong>Highlights in Jalview 2.9</strong>
* @param cdnaAlignment
* @return
*/
- public static boolean mapProteinAlignmentToCdna(final AlignmentI proteinAlignment,
- final AlignmentI cdnaAlignment)
+ public static boolean mapProteinAlignmentToCdna(
+ final AlignmentI proteinAlignment, final AlignmentI cdnaAlignment)
{
if (proteinAlignment == null || cdnaAlignment == null)
{
{
return null;
}
- if (!translatesAs(cdnaSeqChars, startOffset,
- aaSeqChars))
+ if (!translatesAs(cdnaSeqChars, startOffset, aaSeqChars))
{
return null;
}
infoPanel
.add(new Label(MessageManager.getString("warn.delete_all")));
- final JVDialog dialog = new JVDialog(this, title, true, 400,
- 200);
+ final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
dialog.setMainPanel(infoPanel);
dialog.ok.setLabel(MessageManager.getString("action.ok"));
dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
}
else
{
-
+ Desktop.setCurrentAlignFrame(af);
data = aparser.getValue("colour", true);
if (data != null)
{
return rtn;
} catch (Exception ex)
{
- System.out.println("Exception checking resources: " + f + " "
- + ex);
+ System.out.println("Exception checking resources: " + f + " " + ex);
return false;
}
}
}
+ /**
+ * When positional annotation and a sequence reference is present, clears and
+ * resizes the annotations array to the current alignment width, and adds
+ * annotation according to aligned positions of the sequenceRef given by
+ * sequenceMapping.
+ */
public void adjustForAlignment()
{
if (sequenceRef == null)
int position;
Annotation[] temp = new Annotation[aSize];
Integer index;
-
- for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
+ if (sequenceMapping != null)
{
- index = new Integer(a);
- if (sequenceMapping.containsKey(index))
+ for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
{
- position = sequenceRef.findIndex(a) - 1;
+ index = new Integer(a);
+ Annotation annot = sequenceMapping.get(index);
+ if (annot != null)
+ {
+ position = sequenceRef.findIndex(a) - 1;
- temp[position] = sequenceMapping.get(index);
+ temp[position] = annot;
+ }
}
}
-
annotations = temp;
}
}
/**
- * Associate this annotion with the aligned residues of a particular sequence.
- * sequenceMapping will be updated in the following way: null sequenceI -
- * existing mapping will be discarded but annotations left in mapped
- * positions. valid sequenceI not equal to current sequenceRef: mapping is
- * discarded and rebuilt assuming 1:1 correspondence TODO: overload with
+ * Associate this annotation with the aligned residues of a particular
+ * sequence. sequenceMapping will be updated in the following way: null
+ * sequenceI - existing mapping will be discarded but annotations left in
+ * mapped positions. valid sequenceI not equal to current sequenceRef: mapping
+ * is discarded and rebuilt assuming 1:1 correspondence TODO: overload with
* parameter to specify correspondence between current and new sequenceRef
*
* @param sequenceI
* allow for offset e.g. treat pos 8 as 2 if sequence starts at 7
*/
int truePos = sequencePos - (start - 1);
- while (alignedBases < truePos
- && alignedColumn < alignedSeq.length)
+ while (alignedBases < truePos && alignedColumn < alignedSeq.length)
{
if (alignedSeq[alignedColumn++] != gap)
{
}
}
-
/**
* DOCUMENT ME!
*
cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
}
+ if (cs instanceof TCoffeeColourScheme)
+ {
+ tcoffeeColour.setEnabled(true);
+ tcoffeeColour.setSelected(true);
+ }
}
viewport.setGlobalColourScheme(cs);
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
*/
public static AlignFrame[] getAlignFrames()
{
+ if (Jalview.isHeadlessMode())
+ {
+ // Desktop.desktop is null in headless mode
+ return new AlignFrame[] { currentAlignFrame };
+ }
+
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
if (frames == null)
AlignmentExportData exportData = jalview.gui.AlignFrame
.getAlignmentForExport(JSONFile.FILE_DESC,
ap.getAlignViewport(), exportSettings);
- String bioJSON = new FormatAdapter(ap,
- exportData.getSettings()).formatSequences(JSONFile.FILE_DESC,
- exportData.getAlignment(), exportData.getOmitHidden(),
- exportData.getStartEndPostions(), ap.getAlignViewport()
- .getColumnSelection());
+ String bioJSON = new FormatAdapter(ap, exportData.getSettings())
+ .formatSequences(JSONFile.FILE_DESC, exportData
+ .getAlignment(), exportData.getOmitHidden(),
+ exportData.getStartEndPostions(), ap
+ .getAlignViewport().getColumnSelection());
String bioJSTemplateString = getBioJsTemplateAsString();
String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
- .replaceAll("#sequenceData#", bioJSON)
- .toString();
+ .replaceAll("#sequenceData#", bioJSON).toString();
PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
outputFile));
* - process html strings into plain text
* @return true if features were added
*/
- public boolean parse(AlignmentI align, Map colours,
- boolean removeHTML)
+ public boolean parse(AlignmentI align, Map colours, boolean removeHTML)
{
return parse(align, colours, null, removeHTML, false);
}
import jalview.datamodel.SequenceI;
import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
import jalview.json.binding.biojson.v1.AlignmentPojo;
+import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
import jalview.json.binding.biojson.v1.AnnotationPojo;
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
import jalview.json.binding.biojson.v1.SequenceGrpPojo;
import jalview.json.binding.biojson.v1.SequencePojo;
import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import java.awt.Color;
private ArrayList<SequenceI> hiddenSequences;
+ private final static String TCOFFEE_SCORE = "TCoffeeScore";
+
public JSONFile()
{
super();
}
else
{
- if (globalColourScheme.equalsIgnoreCase("RNA Helices"))
+ // These color schemes require annotation, disable them if annotations
+ // are not exported
+ if (globalColourScheme.equalsIgnoreCase("RNA Helices")
+ || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
{
jsonAlignmentPojo.setGlobalColorScheme("None");
}
AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
alignAnnotPojo.setDescription(annot.description);
alignAnnotPojo.setLabel(annot.label);
+ if (!Double.isNaN(annot.score))
+ {
+ alignAnnotPojo.setScore(annot.score);
+ }
+ alignAnnotPojo.setCalcId(annot.getCalcId());
+ alignAnnotPojo.setGraphType(annot.graph);
+
+ AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
+ annotSetting.setBelowAlignment(annot.belowAlignment);
+ annotSetting.setCentreColLabels(annot.centreColLabels);
+ annotSetting.setScaleColLabel(annot.scaleColLabel);
+ annotSetting.setShowAllColLabels(annot.showAllColLabels);
+ annotSetting.setVisible(annot.visible);
+ annotSetting.setHasIcon(annot.hasIcons);
+ alignAnnotPojo.setAnnotationSettings(annotSetting);
+ SequenceI refSeq = annot.sequenceRef;
+ if (refSeq != null)
+ {
+ alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
+ }
for (Annotation annotation : annot.annotations)
{
AnnotationPojo annotationPojo = new AnnotationPojo();
annotationPojo.setValue(annotation.value);
annotationPojo
.setSecondaryStructure(annotation.secondaryStructure);
- annotationPojo.setDisplayCharacter(annotation.displayCharacter);
+ String displayChar = annotation.displayCharacter == null ? null
+ : annotation.displayCharacter;
+ // System.out.println("--------------------->[" + displayChar + "]");
+ annotationPojo.setDisplayCharacter(displayChar);
+ if (annotation.colour != null)
+ {
+ annotationPojo.setColour(jalview.util.Format
+ .getHexString(annotation.colour));
+ }
alignAnnotPojo.getAnnotations().add(annotationPojo);
}
else
{
- alignAnnotPojo.getAnnotations().add(annotationPojo);
+ if (annot.getCalcId() != null
+ && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
+ {
+ // do nothing
+ }
+ else
+ {
+ alignAnnotPojo.getAnnotations().add(annotationPojo);
+ }
}
}
jsonAnnotations.add(alignAnnotPojo);
seqMap.put(seqUniqueId, seq);
}
-
parseFeatures(jsonSeqArray);
for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
}
}
SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
- displayBoxes, displayText, colourText,
- startRes, endRes);
+ displayBoxes, displayText, colourText, startRes, endRes);
seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
seqGrp);
seqGrp.setShowNonconserved(showNonconserved);
: annot.get("displayCharacter").toString();
annotations[count] = new Annotation(displayChar, desc, ss, val);
+ if (annot.get("colour") != null)
+ {
+ Color color = UserColourScheme.getColourFromString(annot.get(
+ "colour").toString());
+ annotations[count].colour = color;
+ }
}
++count;
}
AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
.get("label").toString(), alAnnot.get("description")
.toString(), annotations);
+ alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
+ .valueOf(alAnnot.get("graphType").toString());
+
+ JSONObject diplaySettings = (JSONObject) alAnnot
+ .get("annotationSettings");
+ if (diplaySettings != null)
+ {
+
+ alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
+ : Boolean.valueOf(diplaySettings.get("scaleColLabel")
+ .toString());
+ alignAnnot.showAllColLabels = (diplaySettings
+ .get("showAllColLabels") == null) ? true : Boolean
+ .valueOf(diplaySettings.get("showAllColLabels")
+ .toString());
+ alignAnnot.centreColLabels = (diplaySettings
+ .get("centreColLabels") == null) ? true
+ : Boolean.valueOf(diplaySettings.get("centreColLabels")
+ .toString());
+ alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
+ : Boolean.valueOf(diplaySettings.get("belowAlignment")
+ .toString());
+ alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
+ : Boolean.valueOf(diplaySettings.get("visible")
+ .toString());
+ alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
+ : Boolean.valueOf(diplaySettings.get("hasIcon")
+ .toString());
+
+ }
+ if (alAnnot.get("score") != null)
+ {
+ alignAnnot.score = Double
+ .valueOf(alAnnot.get("score").toString());
+ }
+
+ String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
+ "calcId").toString();
+ alignAnnot.setCalcId(calcId);
+ String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
+ .get("sequenceRef").toString() : null;
+
+ Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
+ if (sequence != null)
+ {
+ alignAnnot.sequenceRef = sequence;
+ sequence.addAlignmentAnnotation(alignAnnot);
+ if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
+ {
+ alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
+ false);
+ sequence.addAlignmentAnnotation(alignAnnot);
+ alignAnnot.adjustForAlignment();
+ }
+ }
+ alignAnnot.validateRangeAndDisplay();
this.annotations.add(alignAnnot);
+
}
} catch (Exception e)
{
{
if (annot != null && !annot.autoCalculated)
{
- if (!annot.visible)
- {
- continue;
- }
annotations.add(annot);
}
}
import jalview.structure.StructureSelectionManager;
import jalview.util.HttpUtils;
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URL;
import java.util.ArrayList;
import java.util.List;
{
if (btn_view.isEnabled())
{
- btn_view.requestFocus();
+ btn_view.requestFocus();
}
else
{
@Attributes(
required = false,
- description = "Label for the Alignment Annotation")
+ description = "Label for the alignment annotation")
private String label;
@Attributes(
required = false,
- description = "Description for the Alignment Annotation")
+ description = "Description for the alignment annotation")
private String description;
@Attributes(required = false)
private List<AnnotationPojo> annotations = new ArrayList<AnnotationPojo>();
+ @Attributes(
+ required = false,
+ enums = { "0", "1", "2" },
+ description = "Determines the rendering for the annotation<br><ul><li>0 - No graph</li><li>1 - Bar Graph</li><li>2 - Line graph</li></ul>")
+ private int graphType;
+
+ @Attributes(
+ required = false,
+ description = "Reference to the sequence in the alignment<br> if per-sequence annotation")
+ private String sequenceRef;
+
+ @Attributes(
+ required = false,
+ description = "Stores display settings for an annotation")
+ private AnnotationDisplaySettingPojo annotationSettings;
+
+ @Attributes(required = false, description = "Score of the annotation")
+ private double score;
+
+ @Attributes(
+ required = false,
+ description = "The annotation generation source")
+ private String calcId;
+
public String getLabel()
{
return label;
this.annotations = annotations;
}
+ public String getSequenceRef()
+ {
+ return sequenceRef;
+ }
+
+ public void setSequenceRef(String sequenceRef)
+ {
+ this.sequenceRef = sequenceRef;
+ }
+
+ public int getGraphType()
+ {
+ return graphType;
+ }
+
+ public void setGraphType(int graphType)
+ {
+ this.graphType = graphType;
+ }
+
+ public AnnotationDisplaySettingPojo getAnnotationSettings()
+ {
+ return annotationSettings;
+ }
+
+ public void setAnnotationSettings(
+ AnnotationDisplaySettingPojo annotationSettings)
+ {
+ this.annotationSettings = annotationSettings;
+ }
+
+ public double getScore()
+ {
+ return score;
+ }
+
+ public void setScore(double score)
+ {
+ this.score = score;
+ }
+
+ public String getCalcId()
+ {
+ return calcId;
+ }
+
+ public void setCalcId(String calcId)
+ {
+ this.calcId = calcId;
+ }
+
}
--- /dev/null
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
+package jalview.json.binding.biojson.v1;
+
+import com.github.reinert.jjschema.Attributes;
+
+public class AnnotationDisplaySettingPojo
+{
+
+ @Attributes(
+ required = false,
+ description = "Indicates if column label is scaled to fit within the <br>alignment column")
+ private boolean scaleColLabel;
+
+ @Attributes(
+ required = false,
+ description = "Indicates if every column label is displayed.")
+ private boolean showAllColLabels;
+
+ @Attributes(
+ required = false,
+ description = "Indicates if column labels is centred relative to the <br>alignment column")
+ private boolean centreColLabels;
+
+ @Attributes(
+ required = false,
+ description = "Indicates if the Annotation is shown below the alignment")
+ private boolean belowAlignment;
+
+ @Attributes(
+ required = false,
+ description = "Indicates if the annotation row is visible")
+ private boolean visible;
+
+ @Attributes(
+ required = false,
+ description = "Indicates if annotation has a graphical symbol track")
+ private boolean hasIcon;
+
+ public boolean isScaleColLabel()
+ {
+ return scaleColLabel;
+ }
+
+ public void setScaleColLabel(boolean scaleColLabel)
+ {
+ this.scaleColLabel = scaleColLabel;
+ }
+
+ public boolean isShowAllColLabels()
+ {
+ return showAllColLabels;
+ }
+
+ public void setShowAllColLabels(boolean showAllColLabels)
+ {
+ this.showAllColLabels = showAllColLabels;
+ }
+
+ public boolean isCentreColLabels()
+ {
+ return centreColLabels;
+ }
+
+ public void setCentreColLabels(boolean centreColLabels)
+ {
+ this.centreColLabels = centreColLabels;
+ }
+
+ public boolean isBelowAlignment()
+ {
+ return belowAlignment;
+ }
+
+ public void setBelowAlignment(boolean belowAlignment)
+ {
+ this.belowAlignment = belowAlignment;
+ }
+
+ public boolean isVisible()
+ {
+ return visible;
+ }
+
+ public void setVisible(boolean visible)
+ {
+ this.visible = visible;
+ }
+
+ public boolean isHasIcon()
+ {
+ return hasIcon;
+ }
+
+ public void setHasIcon(boolean hasIcon)
+ {
+ this.hasIcon = hasIcon;
+ }
+
+}
@Attributes(required = false, description = "Value of the annotation")
private float value;
+ @Attributes(
+ required = false,
+ description = "Colour of the annotation position in hex string.")
+ private String colour;
+
public String getDisplayCharacter()
{
return displayCharacter;
this.value = value;
}
+ public String getColour()
+ {
+ return colour;
+ }
+
+ public void setColour(String colour)
+ {
+ this.colour = colour;
+ }
+
}
csPID = new PIDColourScheme();
csBlosum62 = new Blosum62ColourScheme();
}
+
public static ColourSchemeI getJalviewColourScheme(
String colourSchemeName, AnnotatedCollectionI annotCol)
{
//- Imported classes and packages -/
//---------------------------------/
-
/**
* Class AnnotationColoursDescriptor.
*
//- Imported classes and packages -/
//---------------------------------/
-
/**
* Class FeaturesDescriptor.
*
//- Imported classes and packages -/
//---------------------------------/
-
/**
* Class UserColourSchemeDescriptor.
*
//- Imported classes and packages -/
//---------------------------------/
-
/**
* Class VamsasModelDescriptor.
*
return schemeName;
}
- public Color getColourFromString(String colour)
+ public static Color getColourFromString(String colour)
{
colour = colour.trim();
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
package jalview.util;
import java.io.IOException;
// absStart = 0;
// create valid mapping between matching region of local sequence and
// the mapped sequence
- mp = new Mapping(null, new int[] {
- sequenceStart + absStart,
- sequenceStart + absStart + entrySeq.length() - 1 },
- new int[] { entry.getStart(),
- entry.getStart() + entrySeq.length() - 1 }, 1, 1);
+ mp = new Mapping(null, new int[] { sequenceStart + absStart,
+ sequenceStart + absStart + entrySeq.length() - 1 }, new int[]
+ { entry.getStart(), entry.getStart() + entrySeq.length() - 1 },
+ 1, 1);
updateRefFrame = false; // mapping is based on current start/end so
// don't modify start and end
}
*/
package jalview.ws.uimodel;
-
public class AlignAnalysisUIText
{
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
import java.util.List;
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
package jalview.bin;
import static org.testng.AssertJUnit.assertEquals;
import org.testng.annotations.Test;
-
public class JalviewLiteTest
{
assertNull(JalviewLite.separatorListToArray("|", "|"));
assertNull(JalviewLite.separatorListToArray("abc", "abc"));
- String [] array = JalviewLite.separatorListToArray("abc|def|ghi|", "|");
+ String[] array = JalviewLite.separatorListToArray("abc|def|ghi|", "|");
assertEquals(3, array.length);
assertEquals("abc", array[0]);
assertEquals("def", array[1]);
public class FeaturesFileTest
{
- static String TestFiles[][] = {
- { "Test example features import/export",
+ static String TestFiles[][] = { { "Test example features import/export",
"examples/uniref50.fa", "examples/exampleFeatures.txt" } };
@Test(groups = { "Functional" })
"Colourscheme is null, parsing failed!");
Assert.assertEquals(testJsonFile.getGlobalColourScheme(), "Zappo",
"Zappo colour scheme expected!");
- // Assert.assertTrue(
- // testJsonFile.getGlobalColourScheme() instanceof ZappoColourScheme,
- // "Zappo colour scheme expected!");
}
@Test(groups = { "Functional" })
// map second dna to second protein seq
map = new MapList(new int[] { 20, 20, 22, 23, 24, 26 }, new int[] { 50,
- 51 },
- 3, 1);
+ 51 }, 3, 1);
acf.addMap(cdna.getSequenceAt(1).getDatasetSequence(), protein
.getSequenceAt(1).getDatasetSequence(), map);
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
package jalview.util;
import static org.testng.AssertJUnit.assertEquals;
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
//
//========================================================================
//Copyright (c) 1995-2015 Mort Bay Consulting Pty. Ltd.
server.start();
server.join();
}
-}
\ No newline at end of file
+}
git://source.jalview.org / jalview.git / commitdiff