<classpathentry kind="con" path="org.testng.TESTNG_CONTAINER"/>
<classpathentry kind="lib" path="lib/biojava-core-4.1.0.jar"/>
<classpathentry kind="lib" path="lib/biojava-ontology-4.1.0.jar"/>
- <classpathentry kind="lib" path="lib/groovy-all-2.4.6-indy.jar"/>
+ <classpathentry kind="lib" path="lib/groovy-all-2.4.12-indy.jar"/>
<classpathentry kind="output" path="classes"/>
</classpath>
To set up benchmarking:
-1. In the jalview directory run
+You will need to install Maven: https://maven.apache.org/install.html
+
+1. Run the makedist target of build.xml in Eclipse, or in the jalview directory run
ant makedist
This builds a jalview.jar file and puts it into dist/
-2. Make a lib directory in benchmarking/ if not already present.
+2. Make a lib directory in benchmarking/ if not already present and cd into this directory.
3. Purge any previous maven dependencies:
mvn dependency:purge-local-repository -DactTransitively=false -DreResolve=false
@Measurement(iterations = 10, time = 500, timeUnit = TimeUnit.MILLISECONDS)
@Fork(1)
public class HiddenColumnsBenchmark
-{
- /*
- * State with multiple hidden columns and a start position set
- */
- @State(Scope.Thread)
- public static class HiddenColsAndStartState
- {
- @Param({"300", "10000", "100000"})
- public int maxcols;
-
- @Param({"1", "50", "90"})
- public int startpcnt; // position as percentage of maxcols
-
- @Param({"1","15","100"})
- public int hide;
-
- HiddenColumns h = new HiddenColumns();
- Random rand = new Random();
-
- public int hiddenColumn;
- public int visibleColumn;
-
- @Setup
- public void setup()
- {
- rand.setSeed(1234);
- int lastcol = 0;
- while (lastcol < maxcols)
- {
- int count = rand.nextInt(100);
- lastcol += count;
- h.hideColumns(lastcol, lastcol+hide);
- lastcol+=hide;
- }
-
- // make sure column at start is hidden
- hiddenColumn = (int)(maxcols * startpcnt/100.0);
- h.hideColumns(hiddenColumn, hiddenColumn);
-
- // and column <hide> after start is visible
- ColumnSelection sel = new ColumnSelection();
- h.revealHiddenColumns(hiddenColumn+hide, sel);
- visibleColumn = hiddenColumn+hide;
-
- System.out.println("Maxcols: " + maxcols + " HiddenCol: " + hiddenColumn + " Hide: " + hide);
- System.out.println("Number of hidden columns: " + h.getSize());
- }
- }
-
- /* Convention: functions in alphabetical order */
-
- @Benchmark
- @BenchmarkMode({Mode.Throughput})
- public int benchAdjustForHiddenColumns(HiddenColsAndStartState tstate)
- {
- return tstate.h.adjustForHiddenColumns(tstate.visibleColumn);
- }
-
- @Benchmark
- @BenchmarkMode({Mode.Throughput})
- public int benchFindColumnPosition(HiddenColsAndStartState tstate)
- {
- return tstate.h.findColumnPosition(tstate.visibleColumn);
- }
-
- @Benchmark
- @BenchmarkMode({Mode.Throughput})
- public List<Integer> benchFindHiddenRegionPositions(HiddenColsAndStartState tstate)
- {
- return tstate.h.findHiddenRegionPositions();
- }
-
- @Benchmark
- @BenchmarkMode({Mode.Throughput})
- public ArrayList<int[]> benchGetHiddenColumnsCopy(HiddenColsAndStartState tstate)
- {
- return tstate.h.getHiddenColumnsCopy();
- }
-
-
- @Benchmark
- @BenchmarkMode({Mode.Throughput})
- public int benchGetSize(HiddenColsAndStartState tstate)
- {
- return tstate.h.getSize();
- }
+{
+ /*
+ * State with multiple hidden columns and a start position set
+ */
+ @State(Scope.Thread)
+ public static class HiddenColsAndStartState
+ {
+ @Param({ "300", "10000", "100000" })
+ public int maxcols;
- @Benchmark
- @BenchmarkMode({Mode.Throughput})
- public HiddenColumns benchHideCols(HiddenColsAndStartState tstate)
- {
- tstate.h.hideColumns(tstate.visibleColumn,
- tstate.visibleColumn+2000);
- return tstate.h;
- }
-
- @Benchmark
- @BenchmarkMode({Mode.Throughput})
- public boolean benchIsVisible(HiddenColsAndStartState tstate)
- {
- return tstate.h.isVisible(tstate.hiddenColumn);
- }
-
- @Benchmark
- @BenchmarkMode({Mode.Throughput})
- public HiddenColumns benchReveal(HiddenColsAndStartState tstate)
- {
- ColumnSelection sel = new ColumnSelection();
- tstate.h.revealHiddenColumns(tstate.hiddenColumn, sel);
- return tstate.h;
- }
-
- @Benchmark
- @BenchmarkMode({Mode.Throughput})
- public HiddenColumns benchRevealAll(HiddenColsAndStartState tstate)
+ @Param({ "1", "50", "90" })
+ public int startpcnt; // position as percentage of maxcols
+
+ @Param({ "1", "15", "100" })
+ public int hide;
+
+ HiddenColumns h = new HiddenColumns();
+
+ Random rand = new Random();
+
+ public int hiddenColumn;
+
+ public int visibleColumn;
+
+ @Setup
+ public void setup()
{
- ColumnSelection sel = new ColumnSelection();
- tstate.h.revealAllHiddenColumns(sel);
- return tstate.h;
+ rand.setSeed(1234);
+ int lastcol = 0;
+ while (lastcol < maxcols)
+ {
+ int count = rand.nextInt(100);
+ lastcol += count;
+ h.hideColumns(lastcol, lastcol + hide);
+ lastcol += hide;
+ }
+
+ // make sure column at start is hidden
+ hiddenColumn = (int) (maxcols * startpcnt / 100.0);
+ h.hideColumns(hiddenColumn, hiddenColumn);
+
+ // and column <hide> after start is visible
+ ColumnSelection sel = new ColumnSelection();
+ h.revealHiddenColumns(hiddenColumn + hide, sel);
+ visibleColumn = hiddenColumn + hide;
+
+ System.out.println("Maxcols: " + maxcols + " HiddenCol: "
+ + hiddenColumn + " Hide: " + hide);
+ System.out.println("Number of hidden columns: " + h.getSize());
}
-
-
+ }
+
+ /* Convention: functions in alphabetical order */
+
+ @Benchmark
+ @BenchmarkMode({ Mode.Throughput })
+ public int benchAdjustForHiddenColumns(HiddenColsAndStartState tstate)
+ {
+ return tstate.h.adjustForHiddenColumns(tstate.visibleColumn);
+ }
+
+ @Benchmark
+ @BenchmarkMode({ Mode.Throughput })
+ public int benchFindColumnPosition(HiddenColsAndStartState tstate)
+ {
+ return tstate.h.findColumnPosition(tstate.visibleColumn);
+ }
+
+ @Benchmark
+ @BenchmarkMode({ Mode.Throughput })
+ public List<Integer> benchFindHiddenRegionPositions(
+ HiddenColsAndStartState tstate)
+ {
+ return tstate.h.findHiddenRegionPositions();
+ }
+
+ @Benchmark
+ @BenchmarkMode({ Mode.Throughput })
+ public ArrayList<int[]> benchGetHiddenColumnsCopy(
+ HiddenColsAndStartState tstate)
+ {
+ return tstate.h.getHiddenColumnsCopy();
+ }
+
+ @Benchmark
+ @BenchmarkMode({ Mode.Throughput })
+ public int benchGetSize(HiddenColsAndStartState tstate)
+ {
+ return tstate.h.getSize();
+ }
+
+ @Benchmark
+ @BenchmarkMode({ Mode.Throughput })
+ public HiddenColumns benchHideCols(HiddenColsAndStartState tstate)
+ {
+ tstate.h.hideColumns(tstate.visibleColumn, tstate.visibleColumn + 2000);
+ return tstate.h;
+ }
+
+ @Benchmark
+ @BenchmarkMode({ Mode.Throughput })
+ public boolean benchIsVisible(HiddenColsAndStartState tstate)
+ {
+ return tstate.h.isVisible(tstate.hiddenColumn);
+ }
+
+ @Benchmark
+ @BenchmarkMode({ Mode.Throughput })
+ public HiddenColumns benchReveal(HiddenColsAndStartState tstate)
+ {
+ ColumnSelection sel = new ColumnSelection();
+ tstate.h.revealHiddenColumns(tstate.hiddenColumn, sel);
+ return tstate.h;
+ }
+
+ @Benchmark
+ @BenchmarkMode({ Mode.Throughput })
+ public HiddenColumns benchRevealAll(HiddenColsAndStartState tstate)
+ {
+ ColumnSelection sel = new ColumnSelection();
+ tstate.h.revealAllHiddenColumns(sel);
+ return tstate.h;
+ }
+
}
\ No newline at end of file
<jnlpf toFile="${jnlpFile}" />
<!-- add the add-modules j2se attribute for java 9 -->
- <replace file="${jnlpFile}" value="j2se version="1.7+" initial-heap-size="${inih}" max-heap-size="${maxh}" java-vm-args="--add-modules=java.se.ee"">
+ <replace file="${jnlpFile}" value="j2se version="1.7+" initial-heap-size="${inih}" max-heap-size="${maxh}" java-vm-args="--add-modules=java.se.ee --illegal-access=warn"">
<replacetoken>j2se version="1.7+"</replacetoken>
</replace>
<tocitem text="Jalview Documentation" target="home" expand="true">
<tocitem text="What's new" target="new" expand="true">
<tocitem text="Latest Release Notes" target="release"/>
- <tocitem text="Calculations Dialog" target="calcs.dialog"/>
- <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
- <tocitem text="Custom Colourschemes in Groovy" target="groovy.colours"/>
- <tocitem text="Omit hidden regions in Overview" target="overview"/>
- <tocitem text="Show gaps as grey in overview" target="overviewprefs"/>
- <tocitem text="identifers.org for URL Links" target="linksprefs" />
- <tocitem text="New features in Split Frame View" target="splitframe.mirrorfonts" />
+
</tocitem>
<tocitem text="Editing Alignments" target="edit" />
<p>
To open the PDB Sequence Fetcher, select PDB as the database from
any <a href="seqfetch.html">Sequence Fetcher</a> dialog (opened <em>via</em>
- <strong>"File →Fetch Sequences"</strong>).
+ <strong>"File →Fetch Sequences"</strong>).
</p>
<img src="pdbseqfetcher.png" align="left"
alt="PDB sequence fetcher (introduced in Jalview 2.9)" />
<p>
<strong>Searching the PDB Database</strong>
</p>
+ <p>To search the PDB, begin typing in the text box. If the
+ 'autosearch' checkbox is enabled, then the results of your query
+ will be automatically updated and shown in the search results tab;
+ otherwise, press return to update the results. To access previous
+ searches, press the down-arrow or click the drop down menu icon at
+ the side of the search box. If you just want to paste in a list of
+ IDs, the 'Retrieve IDs' tab provides a batch-retrieval interface.</p>
<p>
- To search the PDB, begin typing in the text box. The results of your
- query are shown in the search results tab, which updates every time
- you type in the search text box. You can sort results according to
- the displayed columns, and select entries with the mouse and
- keyboard. Once you have selected one or more entries, hit the <strong>OK</strong>
- button to retrieve and view them in Jalview.
+ You can sort results according to the displayed columns, and select
+ entries with the mouse and keyboard. Once you have selected one or
+ more entries, hit the <strong>OK</strong> button to retrieve and
+ view them in Jalview.
</p>
<p>
<ul>
1xyz:A</li>
<li><strong>Bulk PDB retrieval</strong><br>Multiple PDB
- IDs can be specified by separating them with a semi-colon.<br />
- e.g. 1xyz;2xyz;3xyz<br />Hitting Return or OK will automatically
- fetch those IDs, like the default Sequence Fetcher interface.</li>
+ IDs can be specified for retrieval via the
+ <strong>Retrieve IDs</strong> tab.</li>
<li><strong>Wild card searching</strong><br>The following
wild cards are supported by the EMBL-EBI PDBe query service:
<p>
<strong>Searching the UniProt Database</strong>
</p>
- <p>
- To search UniProt, simply begin typing in the text box. After a
- short delay (about 1.5 seconds), results will be shown in the table
- below. You can sort results by clicking on the displayed columns,
+ <p>To search UniProt, simply begin typing in the text box. If the
+ 'autosearch' check box is enabled, then after a short delay (about
+ 1.5 seconds), results will be shown in the table below. Results are
+ also updated whenever you press Enter, and you can access previous
+ searches by pressing the 'Down' arrow or clicking the drop-down menu
+ icon at the side of the search box.</p>
+ <p>You can sort results by clicking on the displayed columns,
and select entries with the mouse or keyboard. Once you have
selected one or more entries, hit the <strong>OK</strong> button to
retrieve the sequences.
<li><strong>Bulk UniProt record retrieval</strong><br> To
- retrieve several uniprot accessions at once, first select <strong>UniProt
- ID</strong> from the dropdown menu, then paste in the accession IDs as a
- semi-colon separated list. (e.g. fila_human; mnt_human;
- mnt_mouse).<br />Hitting Return or OK will automatically fetch
- those IDs, like the default Sequence Fetcher interface.</li>
+ retrieve sequences for a list of Uniprot accessions, please enter
+ them via the 'Retrieve IDs' tab.</li>
<li><strong><a name="text-search">Complex queries
with the UniProt query Syntax</a></strong> The text box also allows complex
<li><!-- JAL-2617 -->Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references</li>
<li><!-- JAL-2685 -->Start/End limits are shown in Pairwise Alignment report</li>
+ <li><!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch' feature can be disabled</li>
+ <li><!-- JAL-2810 -->Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs</li>
+ <li><!-- JAL-2758 -->Short names for sequences retrieved from Uniprot</li>
+ </ul>
+ <em>Scripting</em>
+ <ul>
+ <li>Groovy interpreter updated to 2.4.12</li>
+ <li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li>
</ul>
- <ul><li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li></ul>
<em>Testing and Deployment</em>
- <ul><li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li></ul>
- </div>
+ <ul>
+ <li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li>
+ </ul>
+ </div>
</td>
<td><div align="left">
<em>General</em>
<li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
<li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
<li><!-- JAL-2548 -->Export of features doesn't always respect group visibility</li>
+ <li><!-- JAL-2541,JAL-2829,JAL-2830 -->Cuts and Sequence Edits don't properly relocate sequence features</li>
</ul>
<em>Desktop</em>
<ul>
<!-- JAL-2546 -->BioJSON export does not preserve non-positional features
</li>
</ul>
+ <strong>Known Java 9 Issues</strong>
+ <ul>
+ <li><!-- JAL-2902 -->Groovy Console very slow to open and is
+ not responsive when entering characters (Webstart, Java 9.01,
+ OSX 10.10)
+ </li>
+ </ul>
+ <strong>New Known Issues</strong>
+ <ul>
+ <li><!-- JAL- --></li>
+ </ul>
</div>
</td>
</tr>
<strong>What's new in Jalview 2.10.3 ?</strong>
</p>
<p>
- Version 2.10.3 is due for release in October 2017. The full list of
+ Version 2.10.3 was released in November 2017. The full list of
bug fixes and new features can be found in the <a
href="releases.html#Jalview.2.10.3"> 2.10.3 Release Notes</a>, but
the highlights are below.
</p>
+ <ul>
+ <li>Faster import and more responsive UI when working with wide alignments and handling hundreds and thousands of sequence features</li>
+ <li>
+ <li>Improved usability with <a href="features/pdbsequencefetcher.html">PDB</a> and
+ <a href="features/uniprotsequencefetcher.html">UniProt</a> Free Text Search
+ dialog, and new tab for retrieval of sequences for lists of IDs.</li>
+ <li>Short names assigned to sequences retrieved from UniProt</li>
+ </ul>
<p>
<strong><a name="experimental">Experimental Features</a></strong>
</p>
label.overview = Overview
label.reset_to_defaults = Reset to defaults
label.oview_calc = Recalculating overview...
+option.enable_disable_autosearch = When ticked, search is performed automatically.
+option.autosearch = Autosearch
+label.retrieve_ids = Retrieve IDs
\ No newline at end of file
*/
Vector<AlignmentAnnotation> annotation;
- /**
- * The index of the sequence in a MSA
- */
- int index = -1;
-
private SequenceFeaturesI sequenceFeatureStore;
/*
}
}
- /**
- * @return The index (zero-based) of this sequence in the MSA. It returns
- * {@code -1} if this information is not available.
- */
- @Override
- public int getIndex()
- {
- return index;
- }
-
- /**
- * Defines the (zero-based) position of this sequence in the MSA. Use the
- * value {@code -1} if this information is undefined.
- *
- * @param value
- */
- @Override
- public void setIndex(int value)
- {
- index = value;
- }
-
@Override
public void setRNA(RNA r)
{
public void transferAnnotation(SequenceI entry, Mapping mp);
/**
- * @param index
- * The sequence index in the MSA
- */
- public void setIndex(int index);
-
- /**
- * @return The index of the sequence in the alignment
- */
- public int getIndex();
-
- /**
* @return The RNA of the sequence in the alignment
*/
return "EnsemblGenomes";
}
- private String Wrong[];
@Override
public String getTestQuery()
{
- return "DDB_G0283883";
+ /*
+ * Salmonella gene, Uniprot Q8Z9G6, EMBLCDS CAD01290
+ */
+ return "CAD01290";
}
@Override
* @return
*/
public String getCacheKey();
+
+ /**
+ *
+ * @return user preference name for configuring this FTS search's autosearch
+ * checkbox
+ */
+ public String getAutosearchPreference();
}
import javax.swing.ImageIcon;
import javax.swing.JButton;
+import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JInternalFrame;
protected JInternalFrame mainFrame = new JInternalFrame(
getFTSFrameTitle());
+ protected JTabbedPane tabs = new JTabbedPane();
protected IProgressIndicator progressIndicator;
protected JComboBox<FTSDataColumnI> cmb_searchTarget = new JComboBox<FTSDataColumnI>();
protected JButton btn_cancel = new JButton();
+ protected JCheckBox btn_autosearch = new JCheckBox();
+
protected JvCacheableInputBox<String> txt_search;
protected SequenceFetcher seqFetcher;
public GFTSPanel()
{
+ this(null);
+ }
+
+ public GFTSPanel(SequenceFetcher fetcher)
+ {
try
{
+ if (fetcher == null)
+ {
+ tabs = null;
+ }
jbInit();
+ if (fetcher != null)
+ {
+ tabs.addTab(MessageManager.getString("label.retrieve_ids"),
+ fetcher);
+ fetcher.setDatabaseChooserVisible(false);
+ fetcher.embedWithFTSPanel(this);
+ }
mainFrame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+ final JPanel ftsPanel = this;
mainFrame.addFocusListener(new FocusAdapter()
{
@Override
public void focusGained(FocusEvent e)
{
- txt_search.requestFocusInWindow();
+ // TODO: make selected tab gain focus in correct widget
+ if (tabs != null
+ && tabs.getSelectedComponent() == ftsPanel)
+ {
+ txt_search.requestFocusInWindow();
+ }
}
});
mainFrame.invalidate();
}
});
+ btn_autosearch.setText(MessageManager.getString("option.autosearch"));
+ btn_autosearch.setToolTipText(
+ MessageManager.getString("option.enable_disable_autosearch"));
+ btn_autosearch.setSelected(
+ jalview.bin.Cache.getDefault(getAutosearchPreference(), true));
+ btn_autosearch.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ jalview.bin.Cache.setProperty(getAutosearchPreference(),
+ Boolean.toString(btn_autosearch.isSelected()));
+ }
+ });
btn_back.setFont(new java.awt.Font("Verdana", 0, 12));
btn_back.setText(MessageManager.getString("action.back"));
btn_back.addActionListener(new java.awt.event.ActionListener()
if (primaryKeyName.equalsIgnoreCase(getCmbSearchTarget()
.getSelectedItem().toString()))
{
+ // TODO: nicer to show the list in the result set before
+ // viewing in Jalview perhaps ?
transferToSequenceFetcher(getTypedText());
}
+ else
+ {
+ performSearchAction();
+ }
}
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- String typed = getTypedText();
- if (!typed.equalsIgnoreCase(lastSearchTerm))
+ if (btn_autosearch.isSelected()
+ || txt_search.wasEnterPressed())
{
- searchAction(true);
- paginatorCart.clear();
- lastSearchTerm = typed;
+ performSearchAction();
}
}
}, false);
}
});
+ txt_search.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ performSearchAction();
+ }
+ });
final String searchTabTitle = MessageManager
.getString("label.search_result");
final String configureCols = MessageManager
pnl_results.add(tabbedPane);
pnl_inputs.add(cmb_searchTarget);
pnl_inputs.add(txt_search);
+ pnl_inputs.add(btn_autosearch);
pnl_inputs.add(lbl_loading);
pnl_inputs.add(lbl_warning);
pnl_inputs.add(lbl_blank);
this.add(pnl_results, java.awt.BorderLayout.CENTER);
this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
mainFrame.setVisible(true);
- mainFrame.setContentPane(this);
+ if (tabs != null)
+ {
+ tabs.setOpaque(true);
+ tabs.insertTab("Free Text Search", null, this, "", 0);
+ mainFrame.setContentPane(tabs);
+ tabs.setVisible(true);
+ }
+ else
+ {
+ mainFrame.setContentPane(this);
+ }
mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
mainFrame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
closeAction();
}
});
- mainFrame.setVisible(true);
- mainFrame.setContentPane(this);
mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
Integer x = getTempUserPrefs().get("FTSPanel.x");
Integer y = getTempUserPrefs().get("FTSPanel.y");
}
+ void performSearchAction()
+ {
+ String typed = getTypedText();
+ if (typed != null && typed.length() > 0
+ && !typed.equalsIgnoreCase(lastSearchTerm))
+ {
+ searchAction(true);
+ paginatorCart.clear();
+ lastSearchTerm = typed;
+ }
+ }
+
public boolean wantedFieldsUpdated()
{
if (previousWantedFields == null)
}
}
- protected void btn_back_ActionPerformed()
+ public void btn_back_ActionPerformed()
{
closeAction();
new SequenceFetcher(progressIndicator);
btn_cancel.setEnabled(false);
}
- protected void btn_cancel_ActionPerformed()
+ public void btn_cancel_ActionPerformed()
{
closeAction();
}
private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
+ private static final String PDB_AUTOSEARCH = "FTS.PDB.AUTOSEARCH";
+
public PDBFTSPanel(SequenceFetcher fetcher)
{
- super();
+ super(fetcher);
pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
this.seqFetcher = fetcher;
this.progressIndicator = (fetcher == null) ? null
return PDB_FTS_CACHE_KEY;
}
-}
+ @Override
+ public String getAutosearchPreference()
+ {
+ return PDB_AUTOSEARCH;
+ }
+}
\ No newline at end of file
private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
+ private static final String UNIPROT_AUTOSEARCH = "FTS.UNIPROT.AUTOSEARCH";
+
public UniprotFTSPanel(SequenceFetcher fetcher)
{
- super();
+ super(fetcher);
pageLimit = UniProtFTSRestClient.getInstance()
.getDefaultResponsePageSize();
this.seqFetcher = fetcher;
{
return UNIPROT_FTS_CACHE_KEY;
}
+
+ @Override
+ public String getAutosearchPreference()
+ {
+ return UNIPROT_AUTOSEARCH;
+ }
}
{
ViewportRanges ranges = av.getRanges();
- if (Math.abs(scrollX) > ranges.getViewportWidth())
+ // if (Math.abs(scrollX) > ranges.getViewportWidth())
+ // JAL-2836, 2836 temporarily removed wrapped fastpaint for release 2.10.3
+ if (true)
{
/*
* shift of more than one view width is
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.fts.core.GFTSPanel;
import jalview.fts.service.pdb.PDBFTSPanel;
import jalview.fts.service.uniprot.UniprotFTSPanel;
import jalview.io.FileFormatI;
JButton close = new JButton();
+ JButton back = new JButton();
+
JPanel jPanel1 = new JPanel();
JTextArea textArea = new JTextArea();
.getString("label.additional_sequence_fetcher"));
}
+ GFTSPanel parentFTSframe = null;
+ /**
+ * change the buttons so they fit with the FTS panel.
+ */
+ public void embedWithFTSPanel(GFTSPanel toClose)
+ {
+ back.setVisible(true);
+ parentFTSframe = toClose;
+ }
private void jbInit() throws Exception
{
this.setLayout(borderLayout2);
example_actionPerformed();
}
});
- close.setText(MessageManager.getString("action.close"));
+ close.setText(MessageManager.getString("action.cancel"));
close.addActionListener(new ActionListener()
{
@Override
close_actionPerformed(e);
}
});
+ back.setText(MessageManager.getString("action.back"));
+ back.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ parentFTSframe.btn_back_ActionPerformed();
+ }
+ });
+ // back not visible unless embedded
+ back.setVisible(false);
textArea.setFont(JvSwingUtils.getLabelFont());
textArea.setLineWrap(true);
textArea.addKeyListener(new KeyAdapter()
});
jPanel3.setLayout(borderLayout1);
borderLayout1.setVgap(5);
- jPanel1.add(ok);
+ jPanel1.add(back);
jPanel1.add(example);
jPanel1.add(clear);
+ jPanel1.add(ok);
jPanel1.add(close);
jPanel2.setLayout(borderLayout3);
databaseButt = /*database.getDatabaseSelectorButton();
try
{
frame.setClosed(true);
+ if (parentFTSframe!=null)
+ {
+ parentFTSframe.btn_cancel_ActionPerformed();
+ }
} catch (Exception ex)
{
}
textArea.setEnabled(false);
ok.setEnabled(false);
close.setEnabled(false);
-
+ back.setEnabled(false);
Thread worker = new Thread(this);
worker.start();
}
textArea.setEnabled(true);
ok.setEnabled(true);
close.setEnabled(true);
+ back.setEnabled(parentFTSframe != null);
}
@Override
{
frame.setVisible(false);
}
+
+ public void setDatabaseChooserVisible(boolean b)
+ {
+ databaseButt.setVisible(b);
+ }
}
}
parseCalled = true;
parse();
- // sets the index of each sequence in the alignment
- for (int i = 0, c = seqs.size(); i < c; i++)
- {
- seqs.get(i).setIndex(i);
- }
}
/**
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
private JMenuItem menuItemClearCache = new JMenuItem();
+ volatile boolean enterWasPressed = false;
+
+ /**
+ * @return flag indicating if the most recent keypress was enter
+ */
+ public boolean wasEnterPressed()
+ {
+ return enterWasPressed;
+ }
+
public JvCacheableInputBox(String newCacheKey)
{
super();
this.cacheKey = newCacheKey;
setEditable(true);
+ addKeyListener(new KeyListener()
+ {
+
+ @Override
+ public void keyTyped(KeyEvent e)
+ {
+ enterWasPressed = false;
+ if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ enterWasPressed = true;
+ }
+ // let event bubble up
+ }
+
+ @Override
+ public void keyReleased(KeyEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+ });
setPrototypeDisplayValue(
"XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
appCache = AppCache.getInstance();
/**
*
* @param entry
- * UniportEntry
+ * UniprotEntry
* @return The accession id(s) and name(s) delimited by '|'.
*/
public static String getUniprotEntryId(UniprotEntry entry)
{
StringBuilder name = new StringBuilder(32);
- // name.append("UniProt/Swiss-Prot");
- // use 'canonicalised' name for optimal id matching
- name.append(DBRefSource.UNIPROT);
- for (String accessionId : entry.getAccession())
- {
- name.append(BAR_DELIMITER);
- name.append(accessionId);
- }
for (String n : entry.getName())
{
- name.append(BAR_DELIMITER);
+ if (name.length() > 0)
+ {
+ name.append(BAR_DELIMITER);
+ }
name.append(n);
}
return name.toString();
new StringReader(UNIPROT_XML)).get(0);
/*
- * name formatted as source | accession ids | names
- * source database converted to Jalview canonical name
+ * name formatted with Uniprot Entry name
*/
- String expectedName = "UNIPROT|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6";
- assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
+ String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
+ assertEquals(expectedName,
+ Uniprot.getUniprotEntryId(entry));
}
/**
git://source.jalview.org / jalview.git / commitdiff
