jalview.release=Release_2_9_0b1_Branch
-jalview.version=2.9.0b1
+jalview.version=2.9.0b2
<echo message="build - compiles all necessary files for Application" />
<echo message="makedist - compiles and places all necessary jar files into directory dist" />
<echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
- <echo message=" this needs a keystore and key. See docs/building.html for more information." />
+ <echo message=" this needs a keystore and key. Add -Dtimestamp to timestamp signed jars"/>
+ <echo message=" See docs/building.html for more information." />
<echo message="compileApplet - compiles all necessary files for Applet" />
<echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
<echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
<property name="jalview.key" value="jalview" />
<!-- Key Password -->
<property name="jalview.key.pass" value="alignmentisfun" />
+ <!-- time stamp server URL -->
+ <property name="jalview.tsaurl" value="" />
+ <!-- locally valid proxy for signing with external time server -->
+ <property name="proxyPort" value="80"/>
+ <property name="proxyHost" value="sqid"/>
+ <!-- default TestNG groups to run -->
<property name="testng-groups" value="Functional" />
<!-- Don't change anything below here unless you know what you are doing! -->
</java>
</target>
- <target name="makefulldist" depends="makedist">
+ <target name="preparejnlp" depends="makedist">
<copy todir="${packageDir}">
<fileset dir="${resourceDir}/images">
<include name="${WebStartImage}" />
<association mime-type="application-x/ext-file" extensions="amsa"/>
<association mime-type="application-x/ext-file" extensions="stk"/>
<association mime-type="application-x/ext-file" extensions="jar"/>-->
- <!-- and sign the jars -->
- <!-- the default keystore details might need to be edited here -->
+ </target>
+
+ <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA"
+ tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ </fileset>
+ </signjar>
+ </target>
+ <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
<fileset dir="${packageDir}">
<include name="*.jar" />
</signjar>
</target>
+ <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
+ <!-- and sign the jars -->
+ <!-- the default keystore details might need to be edited here -->
+ </target>
+
<target name="runenv" depends="init">
<path id="run.classpath">
<pathelement location="${outputDir}" />
<exclude name="jalview.jar" />
<exclude name="*jnilib.jar" />
</fileset>
+ <property name="jalview.version" value="${JALVIEW_VERSION}" />
</resources>
<resources os="Mac OS X">
- <property name="jalview.version" value="${JALVIEW_VERSION}" />
<fileset dir="${packageDir}">
<include name="*quaqua*.jnilib.jar" />
</fileset>
</tarfileset>
</tar>
</target>
-<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
+<target name="prepubapplet_1" depends="makeApplet">
<copy todir="${packageDir}/examples">
<fileset dir="examples">
<include name="**/*" />
<attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
</manifest>
</jar>
- <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
- <fileset dir="${packageDir}/examples">
- <include name="*.jar" />
- </fileset>
- </signjar>
+
<presetdef name="ap_applet.jar">
<!-- build a signed applet with 'all-permissions' -
Needs 'param name="permissions' value="all-permissions"' in applet tag
<applet.jar jarfile="${packageDir}/examples/${javaJson}" />
<applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
- <!-- todo - write examples/downloads for alternate versions of the applet -->
+ <!-- todo - write examples/downloads for alternate versions of the applet
+ probably don't need to do this now since we don't have alternate versions anymore !-->
+</target>
+<target name="-signapplet" depends="prepubapplet_1">
+ <fileset id="signappletjarset" dir="${packageDir}/examples">
+ <exclude name="u_*.jar" />
+ <include name="${jalviewLiteJar}" />
+ <include name="${jmolJar}" />
+ <include name="${javaJson}" />
+ <include name="${jsonSimple}" />
+ <include name="to_${jalviewLiteJar}" />
+ <include name="to_${jmolJar}" />
+ <include name="to_${javaJson}" />
+ <include name="to_${jsonSimple}" />
+ <include name="tl_${jalviewLiteJar}" />
+ <include name="tl_${jmolJar}" />
+ <include name="tl_${javaJson}" />
+ <include name="tl_${jsonSimple}" />
+ <include name="ap_${jalviewLiteJar}" />
+ <include name="ap_${jmolJar}" />
+ <include name="ap_${javaJson}" />
+ <include name="ap_${jsonSimple}" />
+ </fileset>
+</target>
+<target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+ <fileset refid="signappletjarset" />
+ </signjar>
+</target>
- <fileset dir="${packageDir}/examples">
- <exclude name="u_*.jar" />
- <include name="${jalviewLiteJar}" />
- <include name="${jmolJar}" />
- <include name="${javaJson}" />
- <include name="${jsonSimple}" />
- <include name="to_${jalviewLiteJar}" />
- <include name="to_${jmolJar}" />
- <include name="to_${javaJson}" />
- <include name="to_${jsonSimple}" />
- <include name="tl_${jalviewLiteJar}" />
- <include name="tl_${jmolJar}" />
- <include name="tl_${javaJson}" />
- <include name="tl_${jsonSimple}" />
- <include name="ap_${jalviewLiteJar}" />
- <include name="ap_${jmolJar}" />
- <include name="ap_${javaJson}" />
- <include name="ap_${jsonSimple}" />
- </fileset>
+<target name="-signapplettsa" if="timestamp" depends="-signapplet">
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
+ <fileset refid="signappletjarset" />
</signjar>
+</target>
+
+<target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
+
+<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
+
<!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
<copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
<!-- finally, replace any launchApp servlet tags with a version specification -->
"Deselect All" to deselect all columns.</em></li>
<li><strong>Remove Right (Control R)<br>
</strong><em>If the alignment has marked columns, the alignment will
- be trimmed to the left of the leftmost marked column. To
+ be trimmed to the right of the rightmost marked column. To
mark a column, mouse click the scale bar above the
alignment. Click again to unmark a column, or select
"Deselect All" to deselect all columns.</em></li>
deselect all columns.</em></li>
<li><strong>Remove Right (Control R)<br>
</strong><em>If the alignment has marked columns, the alignment will be
- trimmed to the left of the leftmost marked column. To mark a
+ trimmed to the right of the rightmost marked column. To mark a
column, mouse click the scale bar above the alignment. Click
again to unmark a column, or select "Deselect All" to
deselect all columns.</em></li>
<tr>
<td width="60" nowrap>
<div align="center">
+ <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
+ <em>16/10/2015</em></strong>
+ </div>
+ </td>
+ <td>
+ <em>General</em>
+ <ul>
+ <li>Time stamps for signed Jalview application and applet jars</li>
+ </ul>
+ </td>
+ <td>
+ <div align="left">
+ <em>Application</em><ul>
+ <li>Duplicate group consensus and conservation rows shown when tree is partitioned</li>
+ <li>Erratic behaviour when tree partitions made with multiple cDNA/Protein split views</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
<strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
<em>8/10/2015</em></strong>
</div>
<strong>What's new ?</strong>
</p>
<p>
- 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
+ Jalview 2.9.0b2 is a bug fix release for Jalview 2.9.
+ The release of Jalview 2.9 in September 2015 included
+ 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 patches since version 2.9 was release, see the
- <a href="releases.html#Jalview.2.9.0b1">Jalview 2.9.0b1 Release Notes</a>.
+ structural data.</p><p>For the patches since version 2.9 was released, see the
+ <a href="releases.html#Jalview.2.9.0b2">Jalview 2.9.0b2 Release Notes</a>.
</p>
<p>
<strong>Highlights in Jalview 2.9</strong>
TrimRegionCommand trimRegion;
if (trimLeft)
{
- trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
+ trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
+ column, viewport.getAlignment());
viewport.setStartRes(0);
}
else
{
- trimRegion = new TrimRegionCommand("Remove Right",
- TrimRegionCommand.TRIM_RIGHT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
+ trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
+ column, viewport.getAlignment());
}
statusBar.setText(MessageManager.formatMessage(
}
+ @Override
public void changeColour(ColourSchemeI cs)
{
this.add(statusBar, BorderLayout.SOUTH);
}
+ @Override
public void setStatus(String string)
{
statusBar.setText(string);
package jalview.commands;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.util.ShiftList;
-
-import java.util.List;
public class TrimRegionCommand extends EditCommand
{
- public static String TRIM_LEFT = "TrimLeft";
-
- public static String TRIM_RIGHT = "TrimRight";
-
- public ColumnSelection colSel = null;
-
- int[] start;
-
- ShiftList shiftList;
-
- SequenceGroup selectionGroup;
-
- List<int[]> deletedHiddenColumns;
-
int columnsDeleted;
- public TrimRegionCommand(String description, String command,
- SequenceI[] seqs, int column, AlignmentI al,
- ColumnSelection colSel, SequenceGroup selectedRegion)
+ /**
+ * Constructs and performs a trim alignment command
+ *
+ * @param description
+ * (to show in Undo/Redo menu)
+ * @param trimLeft
+ * if true trim to left of column, else to right
+ * @param seqs
+ * the sequences to trim
+ * @param column
+ * the alignment column (base 0) from which to trim
+ * @param al
+ */
+ public TrimRegionCommand(String description, boolean trimLeft,
+ SequenceI[] seqs, int column, AlignmentI al)
{
this.description = description;
- this.selectionGroup = selectedRegion;
- this.colSel = colSel;
- if (command.equalsIgnoreCase(TRIM_LEFT))
+ if (trimLeft)
{
if (column == 0)
{
setEdit(new Edit(Action.CUT, seqs, 0, column, al));
}
- else if (command.equalsIgnoreCase(TRIM_RIGHT))
+ else
{
int width = al.getWidth() - column - 1;
- if (width < 2)
+ if (width < 1)
{
return;
}
- columnsDeleted = width - 1;
+ columnsDeleted = width;
setEdit(new Edit(Action.CUT, seqs, column + 1, width, al));
}
- // We need to keep a record of the sequence start
- // in order to restore the state after a redo
- int i, isize = getEdit(0).seqs.length;
- start = new int[isize];
- for (i = 0; i < isize; i++)
- {
- start[i] = getEdit(0).seqs[i].getStart();
- }
performEdit(0, null);
}
- void cut(Edit command)
- {
- int column, j, jSize = command.seqs.length;
- for (j = 0; j < jSize; j++)
- {
- if (command.position == 0)
- {
- // This is a TRIM_LEFT command
- column = command.seqs[j].findPosition(command.number);
- command.seqs[j].setStart(column);
- }
- else
- {
- // This is a TRIM_RIGHT command
- column = command.seqs[j].findPosition(command.position) - 1;
- command.seqs[j].setEnd(column);
- }
- }
-
- super.cut(command, null);
-
- if (command.position == 0)
- {
- deletedHiddenColumns = colSel.compensateForEdit(0, command.number);
- if (selectionGroup != null)
- {
- selectionGroup.adjustForRemoveLeft(command.number);
- }
- }
- else
- {
- deletedHiddenColumns = colSel.compensateForEdit(command.position,
- command.number);
- if (selectionGroup != null)
- {
- selectionGroup.adjustForRemoveRight(command.position);
- }
- }
- }
-
- void paste(Edit command)
- {
- super.paste(command, null);
- int column, j, jSize = command.seqs.length;
- for (j = 0; j < jSize; j++)
- {
- if (command.position == 0)
- {
- command.seqs[j].setStart(start[j]);
- }
- else
- {
- column = command.seqs[j].findPosition(command.number
- + command.position) - 1;
- command.seqs[j].setEnd(column);
- }
- }
-
- if (command.position == 0)
- {
- colSel.compensateForEdit(0, -command.number);
- if (selectionGroup != null)
- {
- selectionGroup.adjustForRemoveLeft(-command.number);
- }
- }
-
- if (deletedHiddenColumns != null)
- {
- int[] region;
- for (int i = 0; i < deletedHiddenColumns.size(); i++)
- {
- region = deletedHiddenColumns.get(i);
- colSel.hideColumns(region[0], region[1]);
- }
- }
- }
-
+ @Override
public int getSize()
{
return columnsDeleted;
TrimRegionCommand trimRegion;
if (trimLeft)
{
- trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
+ trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
+ column, viewport.getAlignment());
viewport.setStartRes(0);
}
else
{
- trimRegion = new TrimRegionCommand("Remove Right",
- TrimRegionCommand.TRIM_RIGHT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
+ trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
+ column, viewport.getAlignment());
}
statusBar.setText(MessageManager.formatMessage(
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import java.io.InputStreamReader;
+import java.io.Reader;
+import java.net.UnknownHostException;
import java.util.Hashtable;
import java.util.Vector;
import java.util.jar.JarEntry;
import javax.swing.JOptionPane;
-import org.exolab.castor.xml.IDResolver;
-
/**
* DOCUMENT ME!
*
jarentry = jin.getNextJarEntry();
}
- class NoDescIDResolver implements IDResolver
- {
- public Object resolve(String idref)
- {
- System.out.println(idref + " used");
- return null;
- }
- }
-
if (jarentry != null)
{
- InputStreamReader in = new InputStreamReader(jin, "UTF-8");
- JalviewModel object = new JalviewModel();
+ entryCount++;
+ if (jarentry.getName().endsWith(".xml"))
+ {
+ Reader in = new InputStreamReader(jin, "UTF-8");
+ JalviewModel object = new JalviewModel();
- object = object.unmarshal(in);
+ object = object.unmarshal(in);
- af = LoadFromObject(object, file);
- entryCount++;
+ af = LoadFromObject(object, file);
+ }
}
+ jin.close();
} while (jarentry != null);
- } catch (final java.net.UnknownHostException ex)
+ } catch (final UnknownHostException ex)
{
ex.printStackTrace();
if (raiseGUI)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
}
// put printing in a thread to avoid painting problems
+ @Override
public void run()
{
PrinterJob printJob = PrinterJob.getPrinterJob();
* @throws PrinterException
* DOCUMENT ME!
*/
+ @Override
public int print(Graphics pg, PageFormat pf, int pi)
throws PrinterException
{
* @param g
* DOCUMENT ME!
*/
+ @Override
public void paintComponent(Graphics g)
{
super.paintComponent(g);
* @param fontSize
* DOCUMENT ME!
*/
+ @Override
public void setFont(Font font)
{
this.font = font;
* @param e
* DOCUMENT ME!
*/
+ @Override
public void mouseReleased(MouseEvent e)
{
}
* @param e
* DOCUMENT ME!
*/
+ @Override
public void mouseEntered(MouseEvent e)
{
}
* @param e
* DOCUMENT ME!
*/
+ @Override
public void mouseExited(MouseEvent e)
{
}
* @param e
* DOCUMENT ME!
*/
+ @Override
public void mouseClicked(MouseEvent evt)
{
if (highlightNode != null)
}
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
av.setCurrentTree(tree);
}
}
+ @Override
public void mouseDragged(MouseEvent ect)
{
}
* @param e
* DOCUMENT ME!
*/
+ @Override
public void mousePressed(MouseEvent e)
{
av.setCurrentTree(tree);
aps[a].av.setSelectionGroup(null);
aps[a].av.getAlignment().deleteAllGroups();
aps[a].av.clearSequenceColours();
- }
- if (av.getCodingComplement() != null)
- {
- av.getCodingComplement().setSelectionGroup(null);
- av.getCodingComplement().getAlignment().deleteAllGroups();
- av.getCodingComplement().clearSequenceColours();
+ if (aps[a].av.getCodingComplement() != null)
+ {
+ aps[a].av.getCodingComplement().setSelectionGroup(null);
+ aps[a].av.getCodingComplement().getAlignment()
+ .deleteAllGroups();
+ aps[a].av.getCodingComplement().clearSequenceColours();
+ }
}
colourGroups();
}
}
aps[a].av.getAlignment().addGroup(new SequenceGroup(sg));
- }
-
- // TODO can we push all of the below into AlignViewportI?
- av.getAlignment().addGroup(sg);
- final AlignViewportI codingComplement = av.getCodingComplement();
- if (codingComplement != null)
- {
- SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,
- codingComplement);
- if (mappedGroup.getSequences().size() > 0)
+ // TODO can we push all of the below into AlignViewportI?
+ final AlignViewportI codingComplement = aps[a].av
+ .getCodingComplement();
+ if (codingComplement != null)
{
- codingComplement.getAlignment().addGroup(mappedGroup);
- for (SequenceI seq : mappedGroup.getSequences())
+ if (codingComplement != null)
{
- codingComplement.setSequenceColour(seq, col.brighter());
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
+ av, codingComplement);
+ if (mappedGroup.getSequences().size() > 0)
+ {
+ codingComplement.getAlignment().addGroup(mappedGroup);
+ for (SequenceI seq : mappedGroup.getSequences())
+ {
+ codingComplement.setSequenceColour(seq, col.brighter());
+ }
+ }
}
}
}
}
- // notify the panel to redo any group specific stuff.
+ // notify the panel(s) to redo any group specific stuff.
for (int a = 0; a < aps.length; a++)
{
aps[a].updateAnnotation();
// TODO: JAL-868 - need to ensure view colour change message is broadcast
// to any Jmols listening in
- }
+ final AlignViewportI codingComplement = aps[a].av
+ .getCodingComplement();
+ if (codingComplement != null)
+ {
+ ((AlignViewport) codingComplement).getAlignPanel()
+ .updateAnnotation();
+
+ }
- if (av.getCodingComplement() != null)
- {
- ((AlignViewport) av.getCodingComplement()).getAlignPanel()
- .updateAnnotation();
- /*
- * idPanel. repaint ()
- */
}
+
}
/**
import jalview.util.MessageManager;
import java.io.IOException;
-import java.util.Hashtable;
-import java.util.StringTokenizer;
-import java.util.Vector;
+import java.util.ArrayList;
+import java.util.HashMap;
public class PfamFile extends AlignFile
{
super(source);
}
+ @Override
public void initData()
{
super.initData();
}
+ @Override
public void parse() throws IOException
{
int i = 0;
String line;
- Hashtable seqhash = new Hashtable();
- Vector headers = new Vector();
-
+ HashMap<String, StringBuffer> seqhash = new HashMap<String, StringBuffer>();
+ ArrayList<String> headers = new ArrayList<String>();
+ boolean useTabs = false;
+ int spces;
while ((line = nextLine()) != null)
{
- if (line.indexOf(" ") != 0)
+ if (line.indexOf("#") == 0)
+ {
+ // skip comment lines
+ continue;
+ }
+ // locate first space or (if already checked), tab
+ if (useTabs)
+ {
+ spces = line.indexOf("\t");
+ }
+ else
{
- if (line.indexOf("#") != 0)
+ spces = line.indexOf(" ");
+ // check to see if we ought to split on tabs instead.
+ if (!useTabs && spces == -1)
{
- // TODO: verify pfam format requires spaces and not tab characters -
- // if not upgrade to use stevesoft regex and look for whitespace.
- StringTokenizer str = new StringTokenizer(line, " ");
- String id = "";
-
- if (str.hasMoreTokens())
- {
- id = str.nextToken();
-
- StringBuffer tempseq;
-
- if (seqhash.containsKey(id))
- {
- tempseq = (StringBuffer) seqhash.get(id);
- }
- else
- {
- tempseq = new StringBuffer();
- seqhash.put(id, tempseq);
- }
-
- if (!(headers.contains(id)))
- {
- headers.addElement(id);
- }
- if (str.hasMoreTokens())
- {
- tempseq.append(str.nextToken());
- }
- }
+ useTabs = true;
+ spces = line.indexOf("\t");
}
}
+ if (spces <= 0)
+ {
+ // no sequence data to split on
+ continue;
+ }
+ String id = line.substring(0, spces);
+ StringBuffer tempseq;
+
+ if (seqhash.containsKey(id))
+ {
+ tempseq = seqhash.get(id);
+ }
+ else
+ {
+ tempseq = new StringBuffer();
+ seqhash.put(id, tempseq);
+ }
+
+ if (!(headers.contains(id)))
+ {
+ headers.add(id);
+ }
+ if (spces + 1 < line.length())
+ {
+ tempseq.append(line.substring(spces + 1));
+ }
}
this.noSeqs = headers.size();
for (i = 0; i < headers.size(); i++)
{
- if (seqhash.get(headers.elementAt(i)) != null)
+ if (seqhash.get(headers.get(i)) != null)
{
- if (maxLength < seqhash.get(headers.elementAt(i)).toString()
+ if (maxLength < seqhash.get(headers.get(i)).toString()
.length())
{
- maxLength = seqhash.get(headers.elementAt(i)).toString().length();
+ maxLength = seqhash.get(headers.get(i)).toString().length();
}
- Sequence newSeq = parseId(headers.elementAt(i).toString());
- newSeq.setSequence(seqhash.get(headers.elementAt(i).toString())
+ Sequence newSeq = parseId(headers.get(i).toString());
+ newSeq.setSequence(seqhash.get(headers.get(i).toString())
.toString());
seqs.addElement(newSeq);
}
else
{
System.err.println("PFAM File reader: Can't find sequence for "
- + headers.elementAt(i));
+ + headers.get(i));
}
}
}
return out.toString();
}
+ @Override
public String print()
{
return print(getSeqsAsArray());
--- /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.commands;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ * Unit tests for TrimRegionCommand
+ *
+ * @author gmcarstairs
+ *
+ */
+public class TrimRegionCommandTest
+{
+ private AlignmentI al;
+
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ SequenceI[] seqs = new SequenceI[2];
+ seqs[0] = new Sequence("seq0", "abcde-");
+ seqs[1] = new Sequence("seq1", "-ghjkl");
+ al = new Alignment(seqs);
+ al.setDataset(null);
+ }
+
+ /**
+ * Test performing, undoing and redoing a 'trim left'
+ */
+ @Test(groups = { "Functional" })
+ public void testTrimLeft_withUndoAndRedo()
+ {
+ TrimRegionCommand cmd = new TrimRegionCommand("Remove Left", true,
+ al.getSequencesArray(), 2, al);
+ assertEquals(2, cmd.getSize());
+ assertEquals("cde-", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("hjkl", al.getSequenceAt(1).getSequenceAsString());
+
+ /*
+ * undo and verify
+ */
+ cmd.undoCommand(new AlignmentI[] { al });
+ assertEquals("abcde-", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-ghjkl", al.getSequenceAt(1).getSequenceAsString());
+
+ /*
+ * redo and verify
+ */
+ cmd.doCommand(new AlignmentI[] { al });
+ assertEquals("cde-", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("hjkl", al.getSequenceAt(1).getSequenceAsString());
+ }
+
+ /**
+ * Trim left of no columns - should do nothing. This is the case where the
+ * first column is selected and 'Remove Left' is selected.
+ */
+ @Test(groups = { "Functional" })
+ public void testTrimLeft_noColumns()
+ {
+ TrimRegionCommand cmd = new TrimRegionCommand("Remove Left", true,
+ al.getSequencesArray(), 0, al);
+ assertEquals(0, cmd.getSize());
+ assertEquals("abcde-", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-ghjkl", al.getSequenceAt(1).getSequenceAsString());
+ }
+
+ /**
+ * Trim left of a single column
+ */
+ @Test(groups = { "Functional" })
+ public void testTrimLeft_oneColumn()
+ {
+ TrimRegionCommand cmd = new TrimRegionCommand("Remove Left", true,
+ al.getSequencesArray(), 1, al);
+ assertEquals(1, cmd.getSize());
+ assertEquals("bcde-", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("ghjkl", al.getSequenceAt(1).getSequenceAsString());
+ }
+
+ /**
+ * Trim right of no columns - should do nothing. This is the case where the
+ * last column is selected and 'Remove Right' is selected.
+ */
+ @Test(groups = { "Functional" })
+ public void testTrimRight_noColumns()
+ {
+ TrimRegionCommand cmd = new TrimRegionCommand("Remove Right", false,
+ al.getSequencesArray(), 5, al);
+ assertEquals(0, cmd.getSize());
+ assertEquals("abcde-", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-ghjkl", al.getSequenceAt(1).getSequenceAsString());
+ }
+
+ /**
+ * Trim right of a single column
+ */
+ @Test(groups = { "Functional" })
+ public void testTrimRight_oneColumn()
+ {
+ TrimRegionCommand cmd = new TrimRegionCommand("Remove Right", false,
+ al.getSequencesArray(), 4, al);
+ assertEquals(1, cmd.getSize());
+ assertEquals("abcde", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-ghjk", al.getSequenceAt(1).getSequenceAsString());
+ }
+
+ /**
+ * Test performing, undoing and redoing a 'trim right'
+ */
+ @Test(groups = { "Functional" })
+ public void testTrimRight_withUndoAndRedo()
+ {
+ TrimRegionCommand cmd = new TrimRegionCommand("Remove Right", false,
+ al.getSequencesArray(), 2, al);
+ assertEquals(3, cmd.getSize());
+ assertEquals("abc", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-gh", al.getSequenceAt(1).getSequenceAsString());
+
+ /*
+ * undo and verify
+ */
+ cmd.undoCommand(new AlignmentI[] { al });
+ assertEquals("abcde-", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-ghjkl", al.getSequenceAt(1).getSequenceAsString());
+
+ /*
+ * redo and verify
+ */
+ cmd.doCommand(new AlignmentI[] { al });
+ assertEquals("abc", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-gh", al.getSequenceAt(1).getSequenceAsString());
+ }
+}
--- /dev/null
+package jalview.io;
+
+import jalview.datamodel.AlignmentI;
+
+import java.io.IOException;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+public class PfamFormatInputTest
+{
+ @Test
+ public void testPfamFormatNoLimits() throws IOException
+ {
+ AlignmentI al = new jalview.io.AppletFormatAdapter().readFile("ASEQ"
+ + '\t' + "...--FFAFAFF--", AppletFormatAdapter.PASTE, "PFAM");
+ Assert.assertEquals(1, al.getHeight(), "Wrong number of sequences");
+ Assert.assertTrue(al.hasValidSequence(),
+ "Didn't extract limits from PFAM ID");
+ }
+
+ @Test
+ public void testPfamFormatValidLimits() throws IOException
+ {
+ AlignmentI al = new jalview.io.AppletFormatAdapter().readFile(
+ "ASEQ/15-25" + '\t' + "...--FFAFAFF--",
+ AppletFormatAdapter.PASTE, "PFAM");
+ Assert.assertEquals(1, al.getHeight(), "Wrong number of sequences");
+ Assert.assertTrue(al.hasValidSequence(),
+ "Didn't extract limits from PFAM ID");
+ }
+}
}
/**
- * Test percentage identity calculation for two sequences.
+ * Test the percentage identity calculation for two sequences
*/
@Test(groups = { "Functional" })
- public void testPID_matchGaps()
+ public void testPID_includingGaps()
{
String seq1 = "ABCDEF";
String seq2 = "abcdef";
seq2 = "abcdefghijklmnopqrstuvwxyz";
assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
- seq2 = "a---bcdef";
+ // 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
+ seq1 = "a--b-cdefh";
+ seq2 = "a---bcdefg";
+ int length = seq1.length();
+
+ // match gap-residue, match gap-gap: 9/10 identical
+ assertEquals(90f, Comparison.PID(seq1, seq2, 0, length, true, false),
+ 0.001f);
+ // overloaded version of the method signature above:
+ assertEquals(90f, Comparison.PID(seq1, seq2), 0.001f);
+
+ // don't match gap-residue, match gap-gap: 7/10 identical
+ assertEquals(70f, Comparison.PID(seq1, seq2, 0, length, false, false),
+ 0.001f);
+ }
+
+ /**
+ * Test the percentage identity calculation for two sequences
+ */
+ @Test(groups = { "Functional" })
+ public void testPID_ungappedOnly()
+ {
+ // 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
+ String seq1 = "a--b-cdefh";
+ String seq2 = "a---bcdefg";
+ int length = seq1.length();
+
+ /*
+ * As currently coded, 'ungappedOnly' ignores gap-residue but counts
+ * gap-gap. Is this a bug - should gap-gap also be ignored, giving a PID of
+ * 5/6?
+ *
+ * Note also there is no variant of the calculation that penalises
+ * gap-residue i.e. counts it as a mismatch. This would give a score of 5/8
+ * (if we ignore gap-gap) or 5/10 (if we count gap-gap as a match).
+ */
+ // match gap-residue, match gap-gap: 7/8 identical
+ assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, true, true),
+ 0.001f);
+
+ // don't match gap-residue with 'ungapped only' - same as above
+ assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, false, true),
+ 0.001f);
}
}
git://source.jalview.org / jalview.git / commitdiff