String[] sargs = args.toArray(new String[args.size()]);
log.info("Running " + StringUtil.join(sargs, "\n "));
- return Runtime.getRuntime().exec(sargs, envp, getAppDir());
+ // don't set the working dir, leave it the same as the working dir of the invocation
+ //return Runtime.getRuntime().exec(sargs, envp, getAppDir());
+ return Runtime.getRuntime().exec(sargs, envp);
}
/**
#j2s.compiler.nonqualified.classes = null
#j2s.compiler.mode = debug
#a semicolon-separated list of package (foo.) or class (foo.bar) replacements to be made
-j2s.class.replacements = org.apache.log4j.->jalview.javascript.log4j.
+#j2s.class.replacements = org.apache.logging.log4j.->jalview.javascript.log4j.
j2s.template.html = utils/jalviewjs/template.html
j2s_coretemplate_html = utils/jalviewjs/coretemplate.html
#output file name for logging methods declared - delete the file to regenerate a listing
(http://www.cgl.ucsf.edu/chimera/) can be used for viewing
structures opened via the <a href="structurechooser.html"><strong>"View
Structure Data.."</strong> dialog</a>. In Jalview 2.11.2, support
- was also added for ChimeraX.
+ was also added for ChimeraX, and <a href="pymol.html">Pymol</a>.
</p>
<p>
You can set a default choice of Jmol or Chimera structure viewer in
<strong>The Pymol Viewer</strong>
</p>
<p>
- In Jalview 2.11.2, support was added for <a href="https://pymol.org/2/">Pymol</a>
- (https://pymol.org/2/) to be used for viewing
- structures opened via the <a href="structurechooser.html"><strong>"View
- Structure Data.."</strong> dialog</a>.
+ In Jalview 2.11.2, support was added for viewing structures opened
+ via the <a href="structurechooser.html"><strong>"View
+ Structure Data.."</strong> dialog</a> with <a
+ href="https://pymol.org/2/">Pymol</a> (https://pymol.org/2/). Like
+ with <a href="chimera.html">Chimera and ChimeraX</a>, Pymol views
+ can be saved and restored from Jalview Project files on any machine
+ with it installed, and structures can be coloured and superimposed
+ according to the alignment.
</p>
<p>
- You can configure Pymol as your preferred structure viewer in
- <a href="preferences.html#structure"> Preferences</a>. You can also
- optionally specify the path to the Pymol program here (if it differs
- from the standard paths searched by Jalview).<br /> <strong>Jalview
- requires Pymol's RPC interface, which is not available in older
- versions of the Pymol community edition.<br />Please make sure your
- version of Pymol is up to date.
- </strong>
- </p>
+ <em>Configuring Jalview to use Pymol</em><br /> You can configure
+ Pymol as your preferred structure viewer in <a
+ href="preferences.html#structure"> Preferences</a>. Jalview will
+ look for an existing installation, and will ask you to specify the
+ installation's path if it cannot be found. You can also optionally
+ specify the path to the Pymol program here if you want Jalview to
+ use a specific installation.
+ </p>
+ <p>
+ <strong>Jalview requires Pymol V 2.5.0 (community edition)
+ or later</strong> <br />Jalview requires Pymol's RPC interface, which is
+ not available in older versions of the Pymol community edition.
+ </p>
<p>
- If you save your Jalview session as a project file, the state of any
- open Pymol windows will also be saved, and can be reopened by
- loading the project file on any machine with Pymol installed.
- </p>
- <p>
- <strong>Known Limitations</strong><br /> Jalview provides an easy way
- to employ Pymol for linked analysis of sequences and structures in the
- same way as <a href="chimera.html">Chimera and ChimeraX</a>. There are
- some limitations, however:
- </p>
- <ul>
- <li>Pymol does not support some forms of legacy structural data
- (e.g. the 1A70 C-alpha only PDB file included in the Jalview example
- project).</li>
- <li>Pymol to Jalview communication does not support transfer of
- properties or highlighting sequence regions corresponding to
- structure selections or mouse-overs in Pymol.</li>
- </ul>
+ <strong>Known Limitations</strong><br />
+ </p>
+ <ul>
+ <li>Pymol does not support some forms of legacy structural data
+ (e.g. the 1A70 C-alpha only PDB file included in the Jalview
+ example project).</li>
+ <li>Pymol to Jalview communication does not support transfer of
+ properties or highlighting sequence regions corresponding to
+ structure selections or mouse-overs in Pymol.</li>
+ <li>Jalview to Pymol communication currently doesn't highlight
+ the positions on structures corresponding to moused-overs
+ in Jalview.</li>
+ </ul>
<p>
Basic screen operations (see <a
- href="https://pymol.org/dokuwiki/doku.php?id=mouse">Pymol Wiki</a> at
- https://pymol.org/dokuwiki/doku.php?id=mouse
- for full details).
+ href="https://pymol.org/dokuwiki/doku.php?id=mouse">Pymol Wiki</a>
+ at https://pymol.org/dokuwiki/doku.php?id=mouse for full details).
<table border="1">
<tr>
<td><strong>Action</strong></td>
colourschemes.<br>
</strong><em>The remaining entries apply the colourschemes available
from the standard and user defined <a
- href="../colourSchemes/index.html">amino acid
- colours</a>.
+ href="../colourSchemes/index.html">amino acid colours</a>.
</em></li>
</ul></li>
<li><strong>Pymol<br>
- </strong><em>This pulldown menu provides access to Pymol's capabilities from Jalview.</em>
+ </strong><em>This pulldown menu provides access to Pymol's capabilities
+ from Jalview.</em>
<ul>
<li><strong><a name="sAlign">Align</a> <br> </strong><em>
When selected, the associated alignment will be used to
superimpose all the structures in the view onto the first
- structure in the alignment. The regions used to calculate
+ structure in the alignment via the pair_fit command. The regions used to calculate
the superposition will be highlighted using the 'Cartoon'
rendering style, and the remaining data shown as a chain
- trace.<br />
- <br />
+ trace. RMSD values are output in the Pymol log.<br /> <br />
</em></li>
<li><a name="annotxfer"><strong>Write Jalview
features</strong></a><br /> <em>Selecting this option will create
new atom properties for any features currently visible in
- the associated alignment views. This allows those atoms to
- be selected and analysed in Pymol directly.
- </em><br>
- <ul><li>Feature transfer in Pymol is experimental.</li><li>To select by a particular feature use the string matching syntax:<br>
- select foo,p.jv_helix in helix
- </li>
- <li>To view transferred properties use Pymol's Properties Inspector</li><li>
- For more information see <a href="https://pymol.org/dokuwiki/doku.php?id=properties#selection_language">Property based selection in Pymol's Documentation</a>.
- </li>
- </ul>
- </li>
+ the associated alignment views. This allows those atoms to
+ be selected and analysed in Pymol directly. </em><br>
+ <ul>
+ <li>Feature transfer in Pymol is experimental.</li>
+ <li>To select by a particular feature use the string
+ matching syntax:<br> select foo,p.jv_helix in helix
+ </li>
+ <li>To view transferred properties use Pymol's
+ Properties Inspector</li>
+ <li>For more information see <a
+ href="https://pymol.org/dokuwiki/doku.php?id=properties#selection_language">Property
+ based selection in Pymol's Documentation</a>.
+ </li>
+ </ul></li>
</ul></li>
<li><strong>Help<br>
</strong>
<ul>
<li><strong>Pymol Help<br>
- </strong><em>Access the Pymol Help documentation in a new browser window.
- window.</em></li>
+ </strong><em>Access the Pymol Help documentation in a new browser
+ window. window.</em></li>
</ul></li>
</ul>
<p>
<strong>Pymol and Windows Firewall</strong>
</p>
- Jalview and Pymol communicate using the <a href="https://pymolwiki.org/index.php/RPC">Pymol's XML-RPC over HTTP interface</a>(https://pymolwiki.org/index.php/RPC).
-
-<br> Technically this requires both Pymol and Jalview to open
+ Jalview and Pymol communicate using the
+ <a href="https://pymolwiki.org/index.php/RPC">Pymol's XML-RPC over
+ HTTP interface</a>(https://pymolwiki.org/index.php/RPC).
+
+ <br> Technically this requires both Pymol and Jalview to open
ports on the local network, and this may be blocked by Windows
Firewall with a warning message such as
<br /> "Windows Firewall has blocked some features of this program"
<strong>Selection of the best structure for each sequence</strong>
</p>
<p>Jalview can automatically select the best structures according
- to meta-data provided by the PDB. For alignments with no existing
- structure data, the 'PDBe Best Quality' structure for each sequence will
- by default be selected, but clicking on the drop down menu allows
- other criteria to be chosen, including Resolution (only defined for
- X-Ray structures), Highest Protein Chain etc. When 'Invert' is
+ to meta-data provided by the search service. The 'PDBe Best Quality' structure for each sequence will
+ by default be selected when no other structure data is available. If 3D-models from other sources are also available, then 'Best 3D Beacons coverage' will be show.
+ <br/><br/>Clicking on the drop down menu allows
+ other criteria to be chosen. For the PDBe, these include including Resolution (only defined for
+ X-Ray structures), Highest Protein Chain etc. When 3D-Beacons results are available, structures can be selected based on their specific provider, or by their coverage of the aligned sequences.<br/>
+ <br/>When 'Invert' is
selected, structures are selected in reverse order for the current
criteria (e.g. worst quality rather than best).</p>
<p>
- <img src="schooser_main.png" style="width: 499px; height: 437px;">
+ <img src="schooser_main.png" style="width: 820px; height: 458px;">
<!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
<p><img src="schooser_drop-down.png" style="width: 464px; height: 368px; ">
<p><img src="schooser_enter-id.png" style="width: 467px; height: 373px; ">
<br/>
The 3D-Beacons Network search requires UniProt references and Jalview will ask
to attempt to fetch these references for the selected sequences.
- UniProt references might not always be found in which case you can revert to the PDB
- search.
+ If no UniProt references are found, Jalview will still search the PDB for potential matches for the sequence's ID string.
<br/>
<img src="3dbeacons_structurechooser.png"/>
<br/>
- If structures are found through the 3D-Beacons network you can filter which structures
- are shown using the drop-down filter at the top of the Structure Chooser window.
- <br/>
+ Structures found through the 3D-Beacons network can be filtered using the drop-down filter at the top of the Structure Chooser window.
You can view information about each related model, such as the resource providing
- each model, in the columns displayed. You can sort the list of models by clicking on
+ each model, in the displayed columns, and models can be reordered by clicking on
column headings.
<br/>
Select and view the structures in the usual way using the <a href="viewingpdbs.html#afterviewbutton">open structure options</a> at
</p>
<p>Information on each structure available is displayed in columns
in the dialog box. By default, only the title, resolution and PDB
- identifier are shown, but many more are provided by the PDBe. To
- configure which ones are displayed, select the 'Configure Displayed
- Columns' tab and tick the columns which you want to see.</p>
+ identifier are shown, but many more are provided by the PDBe.
+ 3D-Beacons structures have different data, including a quality score
+ (such as Qmeans_DISCO). To configure which ones are displayed,
+ select the 'Configure Displayed Columns' tab and tick the columns
+ which you want to see.</p>
<p>
<img src="schooser_enter-id.png"
- style="width: 464px; height: 173px;">
- <br/>
- <strong>Manual selection/association of PDB files with
- Sequences</strong>
+ style="width: 464px; height: 173px;"> <br /> <strong>Manual
+ selection/association of PDB files with Sequences</strong>
</p>
<p>To manually associate PDB files with a sequence, select 'From
File', or 'Enter PDB Id' from the drop-down menu:
Jalview.</p>
<p>
+ Jalview logging will automatically scroll the text in the Java Console
+ but if you want to examine a particular part of the logs whilst logging
+ is still going on you can click on any part of the text area to
+ stop this behaviour. A border should appear arround the
+ text area to signify that autoscroll has been turned off. You can
+ toggle the autoscroll behaviour on and off by clicking again on the
+ text area.
+ </p>
+ <p>
You can temporarily control the detail of what appears as output by
selecting a <em>Log level</em> using the drop-down list at the
bottom left of the console. There are several levels to choose from:
<tr>
<td width="60" align="center" nowrap><strong><a
id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
- <em>01/02/2022</em></strong></td>
+ <em>24/02/2022</em></strong></td>
<td align="left" valign="top">
<ul>
<li>
- <!-- -->
+ <!-- JAL- -->
</li>
- </ul> <!-- <em>Development</em>
+ <li>
+ <!-- JAL-3863 -->Support for Canonical Uniprot IDs
+ </li>
+ </ul> <em>JalviewJS</em>
+ <ul><li><!-- 3624 -->PDB structures mapped to Uniprot Sequences with SIFTS</li>
+ <li></li>
+ </ul> <em>Development</em>
<ul>
<li>Updated building instructions</li>
- </ul> -->
+ <li>First integrated JalviewJS and Jalview release</li>
+ </ul>
</td>
<td>
<ul>
<li>
- TO DOCUMENT: JAL-3700,JAL-3751,JAL-3763
+ <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not propagated between Linked CDS - Protein alignments and their trees (known defect from 2.11.1.3)
+ </li>
+ <li>
+ <!-- JAL-3761 -->Not all codon positions highlighted for
+ overlapping exon splice sites (e.g due to RNA slippage)
</li>
<li>
<!-- JAL-3915 -->Removed RNAview checkbox and logic from
Structure Preferences
</li>
+ <li><!-- JAL-3583 -->Tooltip behaviour improved (slightly)</li>
+ <li><!-- JAL-3162 -->Can edit a feature so that start > end</li>
+ <li><!-- JAL-2848 -->Cancel from Amend Features doesn't reset a modified graduated colour</li>
</ul> <em>Development</em>
<ul>
- <li>Fixed non-fatal gradle errors during build</li>
+ <li>Gradle<ul><li>Fixed non-fatal gradle errors during build</li>
+ <li><!-- JAL-3745 -->Updated build.gradle for use with Gradle v.6.6+</li></ul></li>
+
</ul>
</td>
</tr>
<p>
<strong>Highlights in 2.11.2</strong>
</p>
- <p><strong>New features for working with 3D Structure</strong><br/>
- Jalview 2.11.2 features a number of new capabilities:<ul><li><strong>Linked viewing with <em>ChimeraX</em> and <em>PyMol</em></strong><br/>Simply configure your prefered viewer for 3D molecular data in <a href="features/preferences.html#structure">Jalview's structure preferences</a>, make sure that Jalview can locate the viewer's installation, and open a new view via the 3D Structure Chooser!</li>
- <li><strong>View predicted protein structures via 3D-Beacons</strong><br/>
- Jalview 2.11.2's <a href="features/structurechooser.html">Structure Chooser includes a client for the 3D-Beacons Network</a>, a new service that allows predicted and observed 3D models for proteins in Uniprot from a range of resources, including AlphaFold DB, SWISS-MODEL and a growing number of other resources.
- </li>
- <p><strong>Retrieval
- </p>
- <p>
- For the full release notes, see <a
- href="releases.html#Jalview.2.11.1.4">the Jalview 2.11.1.4
- release notes</a>.
- </p>
<p>
- <strong>Known Issues</strong>
- </p>
- <p>New known issues in this release affect recovery of CDS/Protein
- relationships from project files, and interactive selection of
- protein sequences from a tree built on linked nucleotide sequences.
- We will provide patches for these issues as soon as possible.</p>
+ <strong>New features for working with 3D Structure</strong><br />
+ Jalview 2.11.2 features a number of new capabilities:
+
+ <ul>
+ <li><strong>Linked viewing with <em>ChimeraX</em> and
+ <em>PyMol</em></strong><br />Simply configure your prefered viewer for 3D
+ molecular data in <a href="features/preferences.html#structure">Jalview's
+ structure preferences</a>, make sure that Jalview can locate the
+ viewer's installation, and open a new view via the 3D Structure
+ Chooser!</li>
+ <li><strong>View predicted protein structures via
+ 3D-Beacons</strong><br /> Jalview 2.11.2's <a
+ href="features/structurechooser.html">Structure Chooser
+ includes a client for the 3D-Beacons Network</a>, a new service that
+ allows predicted and observed 3D models for proteins in Uniprot
+ from a range of resources, including AlphaFold DB, SWISS-MODEL and
+ a growing number of other resources.</li>
+ <p>
+ <strong>Retrieval of 3D models via 3D-Beacons</strong> <br>The
+ 3D-Beacons network (<a
+ href="https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/">www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/</a>)
+ provides a central point for the retrieval of predicted and
+ observed 3D structures for sequences in Uniprot, including
+ homology models from Swiss-model and deep learning based
+ predictions from the EBI's Alphafold database (Orengo et al. 2020,
+ <a href="https://doi.org/10.12688/f1000research.20559.1">doi:10.12688/f1000research.20559.1</a>).<br>
+ See the <a href="features/structurechooser.html">Structure
+ Chooser's documentation</a>.
+ </p>
+ <p>
+ <strong>Support for viewing structures with ChimeraX and
+ Pymol</strong><br> Structures Preferences tab provides new options
+ allowing ChimeraX and Pymol to be used for visualising external 3D
+ structures. Jalview 2.11.2 has been tested with Pymol 2.5.0
+ (community) and 2.5.2 (incentive). For ChimeraX, we recommend
+ using v1.3 or later. Jalview's 3D structure viewer system has been
+ re-architected to allow easier integration of external structure
+ viewers, and takes advantage of the strucViz2 Chimera
+ communications library developed by Scooter Morris (<a
+ href="https://doi.org/10.1093/bioinformatics/btm329">doi:10.1093/bioinformatics/btm329</a>).
+ </p>
+ <p>
+ For the full release notes, see <a
+ href="releases.html#Jalview.2.11.1.4">the Jalview 2.11.1.4
+ release notes</a>.
+ </p>
+ <p>
+ <strong>Known Issues</strong>
+ </p>
+ <p>New known issues in this release affect recovery of
+ CDS/Protein relationships from project files, and interactive
+ selection of protein sequences from a tree built on linked
+ nucleotide sequences. We will provide patches for these issues as
+ soon as possible.</p>
</ul>
</body>
</html>
import java.util.SortedMap;
import java.util.TreeMap;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.RemoveGapColCommand;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
}
else
{
- Cache.log.error(
+ Console.error(
"JAL-2154 regression: warning - found (and ignored) a duplicate CDS sequence:" + mtch.toString());
}
}
addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss,
retrievedDss);
}
+ // JBPNote: What assumptions are made for dbref structures on
+ // retrieved sequences ?
+ // addedXref will be true means importCrossRefSeq found
+ // sequences with dbrefs with mappings to sequences congruent with dss
+
if (!addedXref)
{
// try again, after looking for matching IDs
/**
* process sequence retrieved via a dbref on source sequence to resolve and
- * transfer data
+ * transfer data JBPNote: as of 2022-02-03 - this assumes retrievedSequence
+ * has dbRefs with Mapping references to a sequence congruent with
+ * sourceSequence
*
* @param cf
* @param sourceSequence
List<DBRefEntry> dbr = retrievedSequence.getDBRefs();
if (dbr != null)
{
- for (int ib = 0, nb = dbr.size(); ib < nb; ib++)
+ for (int ib = 0, nb = dbr.size(); ib < nb; ib++)
{
- DBRefEntry dbref = dbr.get(ib);
+ DBRefEntry dbref = dbr.get(ib);
+ // matched will return null if the dbref has no map
SequenceI matched = findInDataset(dbref);
if (matched == sourceSequence)
{
Mapping map = dbref.getMap();
if (map != null)
{
- SequenceI ms = map.getTo();
+ SequenceI ms = map.getTo();
if (ms != null && map.getMap() != null)
{
if (ms == sourceSequence)
* Returns null or the first sequence in the dataset which is identical to
* xref.mapTo, and has a) a primary dbref matching xref, or if none found, the
* first one with an ID source|xrefacc
- *
+ * JBPNote: Could refactor this to AlignmentI/DatasetI
* @param xref
* with map and mapped-to sequence
* @return
* Updates any empty mappings in the cross-references with one to a compatible
* retrieved sequence if found, and adds any new mappings to the
* AlignedCodonFrame
- *
+ * JBPNote: TODO: this relies on sequence IDs like UNIPROT|ACCESSION - which do not always happen.
* @param mapFrom
* @param xrefs
* @param retrieved
package jalview.analysis;
import java.util.Locale;
-
-import jalview.bin.Cache;
-
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.util.Map;
import java.util.StringTokenizer;
+import jalview.bin.Console;
+
/**
* A singleton that provides instances of genetic code translation tables
*
}
} catch (IOException | NullPointerException e)
{
- Cache.log.error(
+ Console.error(
"Error reading genetic codes data file " + fileName + ": "
+ e.getMessage());
}
}
} catch (IOException e)
{
- Cache.log.error(
+ Console.error(
"Error reading nucleotide ambiguity codes data file: "
+ e.getMessage());
}
line.lastIndexOf(QUOTE));
if (aminos.length() != NUCS_COUNT_CUBED) // 4 * 4 * 4 combinations
{
- Cache.log.error("wrong data length in code table: " + line);
+ Console.error("wrong data length in code table: " + line);
}
else
{
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Point;
import jalview.math.MatrixI;
eigenMatrix.tqli();
} catch (Exception q)
{
- Cache.log.error("Error computing PCA: " + q.getMessage());
+ Console.error("Error computing PCA: " + q.getMessage());
q.printStackTrace();
}
}
*/
package jalview.analysis;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.NodeTransformI;
if (one2many.contains(nam))
{
// countOne2Many++;
- // if (jalview.bin.Cache.log.isDebugEnabled())
- // jalview.bin.Cache.log.debug("One 2 many relationship for
+ // if (Cache.isDebugEnabled())
+ // Cache.debug("One 2 many relationship for
// "+nam.getName());
}
else
j.setPlaceholder(true);
}
}
- // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
- // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment
+ // if (Cache.isDebugEnabled() && countOne2Many>0) {
+ // Cache.debug("There were "+countOne2Many+" alignment
// sequence ids (out of "+one2many.size()+" unique ids) linked to two or
// more leaves.");
// }
import javax.swing.LookAndFeel;
import javax.swing.UIManager;
-import org.apache.log4j.ConsoleAppender;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
-import org.apache.log4j.SimpleLayout;
-import org.apache.log4j.builders.appender.ConsoleAppenderBuilder;
-import org.apache.logging.log4j.core.config.Configurator;
-import org.apache.logging.log4j.core.config.builder.api.AppenderComponentBuilder;
-import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilder;
-import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilderFactory;
-import org.apache.logging.log4j.core.config.builder.impl.BuiltConfiguration;
-
import jalview.datamodel.PDBEntry;
import jalview.gui.Preferences;
import jalview.gui.UserDefinedColours;
+import jalview.log.JLoggerLog4j;
import jalview.schemes.ColourSchemeLoader;
import jalview.schemes.ColourSchemes;
import jalview.schemes.UserColourScheme;
/**
* Initialises the Jalview Application Log
*/
- public static Logger log;
+
+ public final static String JALVIEW_LOGGER_NAME = "JalviewLogger";
// save the proxy properties set at startup
public final static String[] startupProxyProperties = {
private final static String JS_PROPERTY_PREFIX = "jalview_";
- public static void initLogger()
- {
- if (log != null)
- {
- return;
- }
- try
- {
- // configure the root logger to stderr
- ConfigurationBuilder<BuiltConfiguration> builder = ConfigurationBuilderFactory.newConfigurationBuilder();
- AppenderComponentBuilder consoleApp = builder.newAppender("stderr", "Console");
- builder.add(consoleApp);
- Configurator.initialize(builder.build());
- // log output
- Logger laxis = Logger.getLogger("org.apache.axis");
- jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
-
- laxis.setLevel(Level.toLevel(
- Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
- // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
- // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
- // Level.INFO.toString())));
- // we shouldn't need to do this
- org.apache.log4j.Logger.getRootLogger()
- .setLevel(org.apache.log4j.Level.INFO);
-
- jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
- .getDefault("logs.Jalview.level", Level.INFO.toString())));
- // laxis.addAppender(ap);
- // lcastor.addAppender(ap);
- // jalview.bin.Cache.log.addAppender(ap);
- // Tell the user that debug is enabled
- jalview.bin.Cache.log.debug(ChannelProperties.getProperty("app_name")
- + " Debugging Output Follows.");
- } catch (Exception ex)
- {
- System.err.println("Problems initializing the log4j system\n");
- ex.printStackTrace(System.err);
- }
- }
-
/**
- * Loads properties from the given properties file. Any existing properties are
- * first cleared.
+ * Loads properties from the given properties file. Any existing properties
+ * are first cleared.
*/
public static void loadProperties(String propsFile)
{
default:
String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
+ proxyType;
- Cache.warn(message);
+ Console.warn(message);
}
// LOAD THE AUTHORS FROM THE authors.props file
SiftsSettings
.setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
- SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
+ SiftsSettings.setSiftDownloadDirectory(Cache
.getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
SiftsSettings.setFailSafePIDThreshold(
- jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
+ Cache.getDefault("sifts_fail_safe_pid_threshold",
DEFAULT_FAIL_SAFE_PID_THRESHOLD));
SiftsSettings.setCacheThresholdInDays(
- jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
+ Cache.getDefault("sifts_cache_threshold_in_days",
DEFAULT_CACHE_THRESHOLD_IN_DAYS));
IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
"https://www.jalview.org/services/identifiers"));
IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
- StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
- .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+ StructureImportSettings.setDefaultStructureFileFormat(
+ Cache.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
StructureImportSettings
.setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
// StructureImportSettings
- // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+ // .setDefaultPDBFileParser(Cache.getDefault(
// "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
String jnlpVersion = System.getProperty("jalview.version");
}
/**
- * Gets Jalview application property of given key. Returns null if key not found
+ * Gets Jalview application property of given key. Returns null if key not
+ * found
*
* @param key
- * Name of property
+ * Name of property
*
* @return Property value
*/
}
/**
- * These methods are used when checking if the saved preference is different to
- * the default setting
+ * These methods are used when checking if the saved preference is different
+ * to the default setting
*/
public static boolean getDefault(String property, boolean def)
}
/**
- * Answers the value of the given property, or the supplied default value if the
- * property is not set
+ * Answers the value of the given property, or the supplied default value if
+ * the property is not set
*/
public static String getDefault(String property, String def)
{
* Stores property in the file "HOME_DIR/.jalview_properties"
*
* @param key
- * Name of object
+ * Name of object
* @param obj
- * String value of property
+ * String value of property
*
* @return previous value of property (or null)
*/
if (jalview.jbgui.GDesktop.class.getClassLoader()
.loadClass("uk.ac.vamsas.client.VorbaId") != null)
{
- jalview.bin.Cache.log.debug(
- "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+ Console.debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
vamsasJarsArePresent = 1;
- Logger lvclient = Logger.getLogger("uk.ac.vamsas");
- lvclient.setLevel(Level.toLevel(Cache
- .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
-
- lvclient.addAppender(log.getAppender("JalviewLogger"));
+ JLoggerLog4j lvclient = JLoggerLog4j.getLogger("uk.ac.vamsas",
+ Console.getCachedLogLevel("logs.Vamsas.Level"));
+ JLoggerLog4j.addAppender(lvclient, Console.log, JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
lvclient.debug(ChannelProperties.getProperty("app_name")
+ " Vamsas Client Debugging Output Follows.");
} catch (Exception e)
{
vamsasJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Vamsas Classes are not present");
+ Console.debug("Vamsas Classes are not present");
}
}
return (vamsasJarsArePresent > 0);
if (Cache.class.getClassLoader()
.loadClass("groovy.lang.GroovyObject") != null)
{
- jalview.bin.Cache.log.debug(
- "Found Groovy (groovy.lang.GroovyObject can be loaded)");
+ Console.debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
groovyJarsArePresent = 1;
- Logger lgclient = Logger.getLogger("groovy");
- lgclient.setLevel(Level.toLevel(Cache
- .getDefault("logs.Groovy.Level", Level.INFO.toString())));
-
- lgclient.addAppender(log.getAppender("JalviewLogger"));
+ JLoggerLog4j lgclient = JLoggerLog4j.getLogger("groovy",
+ Console.getCachedLogLevel("logs.Groovy.Level"));
+ JLoggerLog4j.addAppender(lgclient, Console.log, JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
lgclient.debug(ChannelProperties.getProperty("app_name")
+ " Groovy Client Debugging Output Follows.");
} catch (Error e)
{
groovyJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
+ Console.debug("Groovy Classes are not present", e);
} catch (Exception e)
{
groovyJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Groovy Classes are not present");
+ Console.debug("Groovy Classes are not present");
}
}
return (groovyJarsArePresent > 0);
.loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
} catch (Exception e)
{
- log.debug(
- "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+ Console.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
tracker = null;
jgoogleanalyticstracker = null;
trackerfocus = null;
{ String.class, String.class, String.class })
.newInstance(new Object[]
{ ChannelProperties.getProperty("app_name") + " Desktop",
- (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
- + jalview.bin.Cache.getDefault("BUILD_DATE",
- "unknown")),
+ (vrs = Cache.getProperty("VERSION") + "_"
+ + Cache.getDefault("BUILD_DATE", "unknown")),
"UA-9060947-1" });
jgoogleanalyticstracker
.getMethod("trackAsynchronously", new Class[]
}
if (re != null || ex != null || err != null)
{
- if (log != null)
+ if (re != null)
{
- if (re != null)
- {
- log.debug("Caught runtime exception in googletracker init:",
- re);
- }
- if (ex != null)
- {
- log.warn(
- "Failed to initialise GoogleTracker for Jalview Desktop with version "
- + vrs,
- ex);
- }
- if (err != null)
- {
- log.error(
- "Whilst initing GoogleTracker for Jalview Desktop version "
- + vrs,
- err);
- }
+ Console.debug("Caught runtime exception in googletracker init:", re);
}
- else
+ if (ex != null)
{
- if (re != null)
- {
- System.err.println(
- "Debug: Caught runtime exception in googletracker init:"
- + vrs);
- re.printStackTrace();
- }
- if (ex != null)
- {
- System.err.println(
- "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
- + vrs);
- ex.printStackTrace();
- }
-
- if (err != null)
- {
- System.err.println(
- "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
- + vrs);
- err.printStackTrace();
- }
+ Console.warn("Failed to initialise GoogleTracker for Jalview Desktop with version "
+ + vrs, ex);
+ }
+ if (err != null)
+ {
+ Console.error("Whilst initing GoogleTracker for Jalview Desktop version "
+ + vrs, err);
}
}
else
{
- log.debug("Successfully initialised tracker.");
+ Console.debug("Successfully initialised tracker.");
}
}
}
Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
- log.warn("Couldn't parse '" + colprop + "' as a colour for "
- + property);
+ Console.warn("Couldn't parse '" + colprop + "' as a colour for " + property);
}
return (col == null) ? defcolour : col;
}
* Loads in user colour schemes from files.
*
* @param files
- * a '|'-delimited list of file paths
+ * a '|'-delimited list of file paths
*/
public static void initUserColourSchemes(String files)
{
StringBuilder sb = new StringBuilder();
sb.append(ChannelProperties.getProperty("app_name"))
.append(" Version: ");
- sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
+ sb.append(Cache.getDefault("VERSION", "TEST"));
sb.append("\n");
sb.append(ChannelProperties.getProperty("app_name"))
.append(" Installation: ");
- sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+ sb.append(Cache.getDefault("INSTALLATION", "unknown"));
sb.append("\n");
sb.append("Build Date: ");
- sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+ sb.append(Cache.getDefault("BUILD_DATE", "unknown"));
sb.append("\n");
sb.append("Java version: ");
sb.append(System.getProperty("java.version"));
// Not displayed in release version ( determined by possible version number
// regex 9[9.]*9[.-_a9]* )
if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
- jalview.bin.Cache.getDefault("VERSION", "TEST")))
+ Cache.getDefault("VERSION", "TEST")))
{
appendIfNotNull(sb, "Getdown appdir: ",
System.getProperty("getdownappdir"), "\n", null);
{
// consider returning more human friendly info
// eg 'built from Source' or update channel
- return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
+ return Cache.getDefault("INSTALLATION", "unknown");
}
public static String getStackTraceString(Throwable t)
? " [" + startupProxyProperties[6] + "]"
: "");
- Cache.debug(sb.toString());
+ Console.debug(sb.toString());
}
public static void setProxyPropertiesFromPreferences()
case Cache.PROXYTYPE_NONE:
if (!previousProxyType.equals(proxyType))
{
- Cache.log.info("Setting no proxy settings");
+ Console.info("Setting no proxy settings");
Cache.setProxyProperties(null, null, null, null, null, null, null,
null, null);
}
case Cache.PROXYTYPE_CUSTOM:
// always re-set a custom proxy -- it might have changed, particularly
// password
- Cache.log.info("Setting custom proxy settings");
+ Console.info("Setting custom proxy settings");
boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false);
Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null),
Cache.getDefault("PROXY_PORT", null),
proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
break;
default: // system proxy settings by default
- Cache.log.info("Setting system proxy settings");
+ Console.info("Setting system proxy settings");
Cache.resetProxyProperties();
}
}
char[] displayHttpPw = new char[httpPassword == null ? 0
: httpPassword.length];
Arrays.fill(displayHttpPw, '*');
- Cache.debug("CACHE Proxy: setting new Authenticator with httpUser='"
+ Console.debug("CACHE Proxy: setting new Authenticator with httpUser='"
+ httpUser + "' httpPassword='" + displayHttpPw + "'");
if (!Platform.isJS())
/* *
&& getRequestingPort() == Integer
.valueOf(httpPort))
{
- Cache.debug(
+ Console.debug(
"AUTHENTICATOR returning PasswordAuthentication(\""
+ httpUser + "\", '"
+ new String(displayHttpPw) + "')");
{
char[] displayHttpsPw = new char[httpPassword.length];
Arrays.fill(displayHttpsPw, '*');
- Cache.debug(
+ Console.debug(
"AUTHENTICATOR returning PasswordAuthentication(\""
+ httpsUser + "\", '" + displayHttpsPw
+ "'");
}
} catch (NumberFormatException e)
{
- Cache.error("Problem with proxy port values [http:"
+ Console.error("Problem with proxy port values [http:"
+ httpPort + ", https:" + httpsPort + "]");
}
- Cache.debug(
+ Console.debug(
"AUTHENTICATOR after trying to get PasswordAuthentication");
}
}
// non proxy request
- Cache.debug("AUTHENTICATOR returning null");
+ Console.debug("AUTHENTICATOR returning null");
return null;
}
});
// required to re-enable basic authentication (should be okay for a
// local proxy)
- Cache.debug(
+ Console.debug(
"AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\"");
System.setProperty("jdk.http.auth.tunneling.disabledSchemes", "");
} catch (SecurityException e)
{
- Cache.error("Could not set default Authenticator");
- Cache.debug(getStackTraceString(e));
+ Console.error("Could not set default Authenticator");
+ Console.debug(getStackTraceString(e));
}
}
else
*
*/
{
- Cache.debug("AUTHENTICATOR setting default Authenticator to null");
+ Console.debug("AUTHENTICATOR setting default Authenticator to null");
Authenticator.setDefault(null);
}
}
// nonProxyHosts not currently configurable in Preferences
- Cache.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
+ Console.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
+ nonProxyHosts + "\"");
setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
}
}
}
- public final static int TRACE = 10;
-
- public final static int DEBUG = 20;
-
- public final static int INFO = 30;
-
- public final static int WARN = 40;
-
- public final static int ERROR = 50;
-
- public static boolean println(int level, String message)
- {
- if (Cache.log == null)
- {
- if (level >= WARN)
- System.err.println(message);
- else if (level >= INFO)
- System.out.println(message);
- // not printing debug or trace messages
- return false;
- }
- if (level >= ERROR)
- {
- Cache.log.error(message);
- }
- else if (level >= WARN)
- {
- Cache.log.warn(message);
- }
- else if (level >= INFO)
- {
- Cache.log.info(message);
- }
- else if (level >= DEBUG)
- {
- Cache.log.debug(message);
- }
- else
- {
- Cache.log.trace(message);
- }
- return true;
- }
-
- public static void trace(String message)
- {
- println(TRACE, message);
- }
-
- public static void debug(String message)
- {
- println(DEBUG, message);
- }
-
- public static void info(String message)
- {
- println(INFO, message);
- }
-
- public static void warn(String message)
- {
- println(WARN, message);
- }
-
- public static void error(String message)
- {
- println(ERROR, message);
- }
-
/**
* Getdown appbase methods
*/
--- /dev/null
+package jalview.bin;
+
+import jalview.log.JLogger;
+import jalview.log.JLoggerI.LogLevel;
+import jalview.log.JLoggerLog4j;
+import jalview.util.ChannelProperties;
+import jalview.util.Log4j;
+import jalview.util.Platform;
+
+public class Console
+{
+
+ public static JLoggerLog4j log;
+
+ public static void debug(String message, Throwable t)
+ {
+ if (Console.initLogger())
+ {
+ log.debug(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
+
+ }
+
+ public static void info(String message)
+ {
+ if (Console.initLogger())
+ {
+ log.info(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
+
+ }
+
+ public static void trace(String message, Throwable t)
+ {
+ if (Console.initLogger())
+ {
+ log.trace(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
+ }
+
+ public static void debug(String message)
+ {
+ if (Console.initLogger())
+ {
+ log.debug(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
+
+ }
+
+ public static void info(String message, Throwable t)
+ {
+ if (Console.initLogger())
+ {
+ log.info(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
+
+ }
+
+ public static void warn(String message)
+ {
+ if (Console.initLogger())
+ {
+ log.warn(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
+
+ }
+
+ public static void trace(String message)
+ {
+ if (Console.initLogger())
+ {
+ log.trace(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
+ }
+
+ public static void warn(String message, Throwable t)
+ {
+ if (Console.initLogger())
+ {
+ log.warn(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
+
+ }
+
+ public static void error(String message)
+ {
+ if (Console.initLogger())
+ {
+ log.error(message, null);
+ }
+ else
+ {
+ System.err.println(message);
+ }
+
+ }
+
+ public static void error(String message, Throwable t)
+ {
+ if (Console.initLogger())
+ {
+ log.error(message, t);
+ }
+ else
+ {
+ System.err.println(message);
+ t.printStackTrace(System.err);
+ }
+
+ }
+
+ public static void fatal(String message)
+ {
+ if (Console.initLogger())
+ {
+ log.fatal(message, null);
+ }
+ else
+ {
+ System.err.println(message);
+ }
+
+ }
+
+ public static void fatal(String message, Throwable t)
+ {
+ if (Console.initLogger())
+ {
+ log.fatal(message, t);
+ }
+ else
+ {
+ System.err.println(message);
+ t.printStackTrace(System.err);
+ }
+
+ }
+
+ public static boolean isDebugEnabled()
+ {
+ return log == null ? false : log.isDebugEnabled();
+ }
+
+ public static boolean isTraceEnabled()
+ {
+ return log == null ? false : log.isTraceEnabled();
+ }
+
+ public static JLogger.LogLevel getCachedLogLevel()
+ {
+ return Console.getCachedLogLevel(Cache.JALVIEWLOGLEVEL);
+ }
+
+ public static JLogger.LogLevel getCachedLogLevel(String key)
+ {
+ return JLogger.toLevel(Cache.getDefault(key, "INFO"));
+ }
+
+ public static boolean initLogger()
+ {
+ if (log != null)
+ {
+ return true;
+ }
+ try
+ {
+ JLogger.LogLevel cachedLevel = getCachedLogLevel();
+ if (!Platform.isJS())
+ {
+ Log4j.init(cachedLevel);
+ }
+ // log output
+ // is laxis used? Does getLogger do anything without a Logger object?
+ // Logger laxis = Log4j.getLogger("org.apache.axis", myLevel);
+ JLoggerLog4j.getLogger("org.apache.axis", cachedLevel);
+
+ // The main application logger
+ log = JLoggerLog4j.getLogger(Cache.JALVIEW_LOGGER_NAME, cachedLevel);
+ } catch (NoClassDefFoundError e)
+ {
+ System.err.println("Could not initialise the logger framework");
+ e.printStackTrace();
+ }
+
+ // Test message
+ if (log != null)
+ {
+ // Logging test message should got through the logger object
+ if (log.loggerExists())
+ log.debug(Console.LOGGING_TEST_MESSAGE);
+ // Tell the user that debug is enabled
+ debug(ChannelProperties.getProperty("app_name")
+ + " Debugging Output Follows.");
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ public final static String LOGGING_TEST_MESSAGE = "Logging to STDERR";
+
+}
*/
package jalview.bin;
-import java.util.Locale;
-
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.security.Permissions;
import java.security.Policy;
import java.util.HashMap;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
import java.util.logging.ConsoleHandler;
static
{
Platform.getURLCommandArguments();
+ Platform.addJ2SDirectDatabaseCall("https://www.jalview.org");
+ Platform.addJ2SDirectDatabaseCall("http://www.jalview.org");
+ Platform.addJ2SDirectDatabaseCall("http://www.compbio.dundee.ac.uk");
+ Platform.addJ2SDirectDatabaseCall("https://www.compbio.dundee.ac.uk");
}
/*
}
System.setProperty("http.agent",
"Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
+
try
{
- Cache.initLogger();
+ Console.initLogger();
} catch (NoClassDefFoundError error)
{
error.printStackTrace();
JalviewTaskbar.setTaskbar(this);
} catch (Exception e)
{
- Cache.log.info("Cannot set Taskbar");
- Cache.log.error(e.getMessage());
+ Console.info("Cannot set Taskbar");
+ Console.error(e.getMessage());
// e.printStackTrace();
} catch (Throwable t)
{
- Cache.log.info("Cannot set Taskbar");
- Cache.log.error(t.getMessage());
+ Console.info("Cannot set Taskbar");
+ Console.error(t.getMessage());
// t.printStackTrace();
}
{
// Start the desktop questionnaire prompter with the specified
// questionnaire
- Cache.log.debug("Starting questionnaire url at " + url);
+ Console.debug("Starting questionnaire url at " + url);
desktop.checkForQuestionnaire(url);
System.out.println("CMD questionnaire[-" + url
+ "] executed successfully!");
// "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
// //
String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
- Cache.log.debug(
+ Console.debug(
"Starting questionnaire with default url: " + defurl);
desktop.checkForQuestionnaire(defurl);
}
* @j2sIgnore
*/
{
- file = jalview.bin.Cache.getDefault("STARTUP_FILE",
- jalview.bin.Cache.getDefault("www.jalview.org",
- "https://www.jalview.org")
+ file = Cache.getDefault("STARTUP_FILE",
+ Cache.getDefault("www.jalview.org", "https://www.jalview.org")
+ "/examples/exampleFile_2_7.jvp");
- if (file.equals(
- "http://www.jalview.org/examples/exampleFile_2_3.jar") || file.equals(
+ if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
+ || file.equals(
"http://www.jalview.org/examples/exampleFile_2_7.jar"))
{
file.replace("http:", "https:");
lafSet = setCrossPlatformLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "system":
lafSet = setSystemLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "gtk":
lafSet = setGtkLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "metal":
lafSet = setMetalLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "nimbus":
lafSet = setNimbusLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "quaqua":
lafSet = setQuaquaLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "vaqua":
lafSet = setVaquaLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "mac":
lafSet = setMacLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "none":
break;
default:
- Cache.log.error("Requested laf=" + laf + " not implemented");
+ Console.error("Requested laf=" + laf + " not implemented");
}
if (!lafSet)
{
set = true;
} catch (Exception ex)
{
- Cache.log.error("Unexpected Look and Feel Exception");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Console.error("Unexpected Look and Feel Exception");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
return set;
}
set = true;
} catch (Exception ex)
{
- Cache.log.error("Unexpected Look and Feel Exception");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Console.error("Unexpected Look and Feel Exception");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
return set;
}
if (info.getName() != null && nameStartsWith
? info.getName().toLowerCase(Locale.ROOT)
.startsWith(name.toLowerCase(Locale.ROOT))
- : info.getName().toLowerCase(Locale.ROOT).equals(name.toLowerCase(Locale.ROOT)))
+ : info.getName().toLowerCase(Locale.ROOT)
+ .equals(name.toLowerCase(Locale.ROOT)))
{
className = info.getClassName();
break;
set = true;
} catch (Exception ex)
{
- Cache.log.error("Unexpected Look and Feel Exception");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Console.error("Unexpected Look and Feel Exception");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
return set;
}
@Override
public void run()
{
- Cache.log.debug(
- "Initialising googletracker for usage stats.");
+ Console.debug("Initialising googletracker for usage stats.");
Cache.initGoogleTracker();
- Cache.log.debug("Tracking enabled.");
+ Console.debug("Tracking enabled.");
}
}, new Runnable()
{
@Override
public void run()
{
- Cache.log.debug("Not enabling Google Tracking.");
+ Console.debug("Not enabling Google Tracking.");
}
}, null, true);
desktop.addDialogThread(prompter);
*/
public boolean covers(SequenceI seq)
{
- List<int[]> mappedRanges = null;
+ return covers(seq,false,false);
+ }
+ /**
+ *
+ * @param seq
+ * @param localCover - when true - compare extent of seq's dataset sequence rather than the local extent
+ * @param either - when true coverage is required for either seq or the mapped sequence
+ * @return true if mapping covers full length of given sequence (or the other if either==true)
+ */
+ public boolean covers(SequenceI seq, boolean localCover,boolean either)
+ {
+ List<int[]> mappedRanges = null,otherRanges=null;
MapList mapList = mapping.getMap();
+ int mstart=seq.getStart(),mend=seq.getEnd(),ostart,oend;
+ ;
if (fromSeq == seq || fromSeq == seq.getDatasetSequence())
{
+ if (localCover && fromSeq !=seq)
+ {
+ mstart=fromSeq.getStart();
+ mend=fromSeq.getEnd();
+ }
mappedRanges = mapList.getFromRanges();
+ otherRanges=mapList.getToRanges();
+ ostart=mapping.to.getStart();
+ oend=mapping.to.getEnd();
}
else if (mapping.to == seq || mapping.to == seq.getDatasetSequence())
{
+ if (localCover && mapping.to !=seq)
+ {
+ mstart=mapping.to.getStart();
+ mend=mapping.to.getEnd();
+ }
mappedRanges = mapList.getToRanges();
+ otherRanges=mapList.getFromRanges();
+ ostart=fromSeq.getStart();
+ oend=fromSeq.getEnd();
}
else
{
* (necessary for circular CDS - example EMBL:J03321:AAA91567)
* and mapped length covers (at least) sequence length
*/
- int length = 0;
+ int length = countRange(mappedRanges,mstart,mend);
+
+ if (length != -1)
+ {
+ // add 3 to mapped length to allow for a mapped stop codon
+ if (length + 3 >= (mend - mstart + 1))
+ {
+ return true;
+ }
+ }
+ if (either)
+ {
+ // also check coverage of the other range
+ length = countRange(otherRanges, ostart, oend);
+ if (length != -1)
+ {
+ if (length + 1 >= (oend - ostart + 1))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+ private int countRange(List<int[]> mappedRanges,int mstart,int mend)
+ {
+ int length=0;
for (int[] range : mappedRanges)
{
int from = Math.min(range[0], range[1]);
int to = Math.max(range[0], range[1]);
- if (from < seq.getStart() || to > seq.getEnd())
+ if (from < mstart || to > mend)
{
- return false;
+ return -1;
}
length += (to - from + 1);
}
- // add 1 to mapped length to allow for a mapped stop codon
- if (length + 1 < (seq.getEnd() - seq.getStart() + 1))
- {
- return false;
- }
- return true;
+ return length;
}
/**
* Adds any regions mapped to or from position {@code pos} in sequence
* {@code seq} to the given search results
- *
+ * Note: recommend first using the .covers(,true,true) to ensure mapping covers both sequences
* @param seq
* @param pos
* @param sr
}
for (SequenceToSequenceMapping ssm : mappings)
{
- ssm.markMappedRegion(ds, index, results);
+ if (ssm.covers(seq,true,true)) {
+ ssm.markMappedRegion(ds, index, results);
+ }
}
}
private static final int PDB_ID_LENGTH = 4;
+ /**
+ * property set when id is a 'manufactured' identifier from the structure data's filename
+ */
private static final String FAKED_ID = "faked_pdbid";
+ /**
+ * property set when the id is authoritative, and should be used in preference to any identifiers in the structure data
+ */
+ private static final String AUTHORITATIVE_ID = "authoritative_pdbid";
private String file;
// this shouldn't happen, but could do if the id from the
// file is not the same as the id from the authority that provided
// the file
- if (!newEntry.fakedPDBId())
+ if (!newEntry.fakedPDBId() && !isAuthoritative())
{
return false;
} // otherwise we can update
*/
String key = newProps.nextElement();
Object value = newEntry.getProperty(key);
- if (FAKED_ID.equals(key))
+ if (FAKED_ID.equals(key) || AUTHORITATIVE_ID.equals(key))
{
// we never update the fake ID property
continue;
return true;
}
+ public void setAuthoritative(boolean isAuthoritative)
+ {
+ setProperty(AUTHORITATIVE_ID, Boolean.valueOf(isAuthoritative));
+ }
+
+ /**
+ *
+ * @return true if the identifier should be preferred over any identifiers
+ * embedded in the structure data
+ */
+ public boolean isAuthoritative()
+ {
+ if (_hasProperty(AUTHORITATIVE_ID))
+ {
+ return ((Boolean)getProperty(AUTHORITATIVE_ID));
+ }
+ return false;
+ }
+
/**
* set when Jalview has manufactured the ID using a local filename
* @return
*/
package jalview.ext.ensembl;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.GeneLociI;
import jalview.datamodel.GeneLocus;
chromosome, map);
} catch (NullPointerException | NumberFormatException e)
{
- Cache.log.error("Error looking up gene loci: " + e.getMessage());
+ Console.error("Error looking up gene loci: " + e.getMessage());
e.printStackTrace();
}
return null;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Dna;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
if (upx.size() > 1)
{
- Cache.log.warn(
+ Console.warn(
"Implementation issue - multiple uniprot acc on product sequence.");
}
}
*/
package jalview.ext.htsjdk;
-import jalview.bin.Cache;
-
import java.io.Closeable;
import java.io.File;
import java.io.IOException;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFFileReader;
import htsjdk.variant.vcf.VCFHeader;
+import jalview.bin.Console;
/**
* A thin wrapper for htsjdk classes to read either plain, or compressed, or
}
else
{
- Cache.log.error("File not found: " + filePath);
+ Console.error("File not found: " + filePath);
}
}
import jalview.api.FeatureRenderer;
import jalview.api.FeatureSettingsModelI;
import jalview.api.SequenceRenderer;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.AppJmol;
private String jmolScript(String script)
{
- Cache.log.debug(">>Jmol>> " + script);
+ Console.debug(">>Jmol>> " + script);
String s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
- Cache.log.debug("<<Jmol<< " + s);
+ Console.debug("<<Jmol<< " + s);
return s;
}
import jalview.structure.StructureCommandsBase;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.util.Comparison;
import jalview.util.Platform;
*/
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec)
+ AtomSpecModel atomSpec, AtomSpecType backbone)
{
StringBuilder sb = new StringBuilder(64);
String refModel = refAtoms.getModels().iterator().next();
* command examples don't include modelspec with atoms, getAtomSpec does;
* it works, so leave it as it is for simplicity
*/
- sb.append(getAtomSpec(atomSpec, true)).append("}{");
- sb.append(getAtomSpec(refAtoms, true)).append("}");
+ sb.append(getAtomSpec(atomSpec, backbone)).append("}{");
+ sb.append(getAtomSpec(refAtoms, backbone)).append("}");
sb.append(" ROTATE TRANSLATE ");
sb.append(getCommandSeparator());
/*
* show residues used for superposition as ribbon
*/
- sb.append("select ").append(getAtomSpec(atomSpec, false)).append("|");
- sb.append(getAtomSpec(refAtoms, false)).append(getCommandSeparator())
+ sb.append("select ").append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY)).append("|");
+ sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY)).append(getCommandSeparator())
.append("cartoons");
return Arrays.asList(new StructureCommand(sb.toString()));
* a separate clause in the {@code compare} (superposition) command.
*/
@Override
- public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(128);
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec)
+ AtomSpecModel atomSpec, AtomSpecType specType)
{
+
// https://pymolwiki.org/index.php/Super
List<StructureCommandI> commands = new ArrayList<>();
- String refAtomsAlphaOnly = getAtomSpec(refAtoms, true);
- String atomSpec2AlphaOnly = getAtomSpec(atomSpec, true);
- commands.add(new StructureCommand("super", refAtomsAlphaOnly,
- atomSpec2AlphaOnly));
-
+ String refAtomsAlphaOnly = "("+getAtomSpec(refAtoms, specType)+" and (altloc '' or altloc 'a'))";
+ String atomSpec2AlphaOnly = "("+getAtomSpec(atomSpec, specType)+" and (altloc '' or altloc 'a'))";
+ // pair_fit mobile -> reference
+ // crashes when undo is enabled on 2.5.2 (incentive)
+ commands.add(new StructureCommand("undo_disable"));
+ commands.add(new StructureCommand("pair_fit",
+ atomSpec2AlphaOnly, refAtomsAlphaOnly));
+ commands.add(new StructureCommand("undo_enable"));
+
/*
* and show superposed residues as cartoon
*/
- String refAtomsAll = getAtomSpec(refAtoms, false);
- String atomSpec2All = getAtomSpec(atomSpec, false);
+ String refAtomsAll = getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY);
+ String atomSpec2All = getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY);
commands.add(new StructureCommand("show", "cartoon",
refAtomsAll + " " + atomSpec2All));
* @see https://pymolwiki.org/index.php/Selection_Macros
*/
@Override
- public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(64);
boolean first = true;
}
}
sb.append("/");
- if (alphaOnly)
+ if (specType == AtomSpecType.ALPHA)
{
sb.append("CA");
}
+ if (specType == AtomSpecType.PHOSPHATE)
+ {
+ sb.append("P");
+ }
}
}
return sb.toString();
StringBuilder sb = new StringBuilder(128);
sb.append("p.").append(attributeName).append("='")
.append(attributeValue).append("'");
- String atomSpec = getAtomSpec(atomSpecModel, false);
+ String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
return new StructureCommand("iterate", atomSpec, sb.toString());
}
import java.util.List;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.Preferences;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
int rc = conn.getResponseCode();
if (rc != HttpURLConnection.HTTP_OK)
{
- Cache.log.error(
+ Console.error(
String.format("Error status from %s: %d", rpcUrl, rc));
return result;
}
} catch (SocketException e)
{
// thrown when 'quit' command is sent to PyMol
- Cache.log.warn(String.format("Request to %s returned %s", rpcUrl,
+ Console.warn(String.format("Request to %s returned %s", rpcUrl,
e.toString()));
} catch (Exception e)
{
{
out.close();
}
- if (Cache.log.isTraceEnabled())
+ if (Console.isTraceEnabled())
{
- Cache.log.trace("Sent: " + command.toString());
+ Console.trace("Sent: " + command.toString());
if (result != null)
{
- Cache.log.trace("Received: " + result);
+ Console.trace("Received: " + result);
}
}
}
this.pymolXmlRpcPort = getPortNumber();
if (pymolXmlRpcPort > 0)
{
- Cache.log.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
+ Console.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
}
else
{
error += "Failed to read PyMOL XMLRPC port number";
- Cache.log.error(error);
+ Console.error(error);
pymolProcess.destroy();
pymolProcess = null;
}
}
} catch (Exception e)
{
- Cache.log.error("Failed to get REST port number from " + responses
+ Console.error("Failed to get REST port number from " + responses
+ ": " + e.getMessage());
// logger.error("Failed to get REST port number from " + responses + ": "
// + e.getMessage());
}
if (port == 0)
{
- Cache.log.error("Failed to start PyMOL with XMLRPC, response was: "
+ Console.error("Failed to start PyMOL with XMLRPC, response was: "
+ responses);
}
- Cache.log.error("PyMOL started with XMLRPC on port " + port);
+ Console.info("PyMOL started with XMLRPC on port " + port);
return port;
}
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsBase;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.util.ColorUtils;
/**
StringBuilder sb = new StringBuilder(128);
sb.append("setattr res ").append(attributeName).append(" '")
.append(attributeValue).append("' ");
- sb.append(getAtomSpec(atomSpecModel, false));
+ sb.append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY));
return new StructureCommand(sb.toString());
}
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
- AtomSpecModel spec)
+ AtomSpecModel spec, AtomSpecType backbone)
{
/*
* Form Chimera match command to match spec to ref
* @see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
*/
StringBuilder cmd = new StringBuilder();
- String atomSpecAlphaOnly = getAtomSpec(spec, true);
- String refSpecAlphaOnly = getAtomSpec(ref, true);
+ String atomSpecAlphaOnly = getAtomSpec(spec, backbone);
+ String refSpecAlphaOnly = getAtomSpec(ref, backbone);
cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly);
/*
* show superposed residues as ribbon
*/
- String atomSpec = getAtomSpec(spec, false);
- String refSpec = getAtomSpec(ref, false);
+ String atomSpec = getAtomSpec(spec, AtomSpecType.RESIDUE_ONLY);
+ String refSpec = getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY);
cmd.append("; ribbon ");
cmd.append(atomSpec).append("|").append(refSpec).append("; focus");
* <pre>
*
* @param model
- * @param alphaOnly
+ * @param specType
* @return
* @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
*/
@Override
- public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(128);
boolean firstModel = true;
sb.append("|");
}
firstModel = false;
- appendModel(sb, model, atomSpec, alphaOnly);
+ appendModel(sb, model, atomSpec, specType);
}
return sb.toString();
}
* @param alphaOnly
*/
protected void appendModel(StringBuilder sb, String model,
- AtomSpecModel atomSpec, boolean alphaOnly)
+ AtomSpecModel atomSpec, AtomSpecType specType)
{
sb.append("#").append(model).append(":");
firstPositionForModel = false;
}
}
- if (alphaOnly)
+ if (specType == AtomSpecType.ALPHA)
{
/*
* restrict to alpha carbon, no alternative locations
* (needed to ensuring matching atom counts for superposition)
*/
- // TODO @P instead if RNA - add nucleotide flag to AtomSpecModel?
sb.append("@CA").append(NO_ALTLOCS);
}
+ if (specType == AtomSpecType.PHOSPHATE)
+ {
+ sb.append("@P").append(NO_ALTLOCS);
+ }
}
@Override
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
/**
* Routines for generating ChimeraX commands for Jalview/ChimeraX binding
String attributeValue, AtomSpecModel atomSpecModel)
{
StringBuilder sb = new StringBuilder(128);
- sb.append("setattr ").append(getAtomSpec(atomSpecModel, false));
+ sb.append("setattr ").append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY));
sb.append(" res ").append(attributeName).append(" '")
.append(attributeValue).append("'");
sb.append(" create true");
* @return
*/
@Override
- public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(128);
boolean firstModel = true;
}
firstModel = false;
appendModel(sb, model, atomSpec);
- if (alphaOnly)
+ if (specType == AtomSpecType.ALPHA)
{
- // TODO @P if RNA - add nucleotide flag to AtomSpecModel?
sb.append("@CA");
}
+ if (specType == AtomSpecType.PHOSPHATE)
+ {
+ sb.append("@P");
+ }
}
return sb.toString();
}
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
- AtomSpecModel spec)
+ AtomSpecModel spec, AtomSpecType backbone)
{
/*
* Form ChimeraX match command to match spec to ref
* @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/align.html
*/
StringBuilder cmd = new StringBuilder();
- String atomSpec = getAtomSpec(spec, true);
- String refSpec = getAtomSpec(ref, true);
+ String atomSpec = getAtomSpec(spec, backbone);
+ String refSpec = getAtomSpec(ref, backbone);
cmd.append("align ").append(atomSpec).append(" toAtoms ")
.append(refSpec);
* show superposed residues as ribbon, others as chain
*/
cmd.append("; ribbon ");
- cmd.append(getAtomSpec(spec, false)).append("|");
- cmd.append(getAtomSpec(ref, false)).append("; view");
+ cmd.append(getAtomSpec(spec, AtomSpecType.RESIDUE_ONLY)).append("|");
+ cmd.append(getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY)).append("; view");
return Arrays.asList(new StructureCommand(cmd.toString()));
}
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
if (getResponse)
{
reply = lastReply;
- if (Cache.log.isDebugEnabled()) {
- Cache.log.debug(
+ if (Console.isDebugEnabled()) {
+ Console.debug(
"Response from command ('" + cmd + "') was:\n" + lastReply);
}
}
else
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug("Command executed: " + cmd);
+ Console.debug("Command executed: " + cmd);
}
}
atomSpecs.add(spec);
} catch (IllegalArgumentException e)
{
- Cache.log.error("Failed to parse atomspec: " + atomSpec);
+ Console.error("Failed to parse atomspec: " + atomSpec);
}
}
return atomSpecs;
spec = parseAtomSpec(atomSpec);
} catch (IllegalArgumentException e)
{
- Cache.log.error("Problem parsing atomspec " + atomSpec);
+ Console.error("Problem parsing atomspec " + atomSpec);
continue;
}
import org.biojava.nbio.ontology.io.OboParser;
import org.biojava.nbio.ontology.utils.Annotation;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.io.gff.SequenceOntologyI;
/**
}
}
long elapsed = System.currentTimeMillis() - now;
- Cache.log.info("Loaded Sequence Ontology from " + zipFile + " ("
+ Console.info("Loaded Sequence Ontology from " + zipFile + " ("
+ elapsed + "ms)");
} catch (Exception e)
{
boolean oldTermIsObsolete = isObsolete(replaced);
if (newTermIsObsolete && !oldTermIsObsolete)
{
- Cache.log.debug("Ignoring " + term.getName()
+ Console.debug("Ignoring " + term.getName()
+ " as obsolete and duplicated by "
+ replaced.getName());
term = replaced;
}
else if (!newTermIsObsolete && oldTermIsObsolete)
{
- Cache.log.debug("Ignoring " + replaced.getName()
+ Console.debug("Ignoring " + replaced.getName()
+ " as obsolete and duplicated by " + term.getName());
}
else
{
- Cache.log.debug("Warning: " + term.getName()
+ Console.debug("Warning: " + term.getName()
+ " has replaced " + replaced.getName()
+ " for lookup of '" + description + "'");
}
{
if (!termsNotFound.contains(term))
{
- Cache.log.error("SO term " + term + " invalid");
+ Console.error("SO term " + term + " invalid");
termsNotFound.add(term);
}
}
@Override
public void actionPerformed(ActionEvent e)
{
- jalview.bin.Cache.setProperty(getAutosearchPreference(),
+ Cache.setProperty(getAutosearchPreference(),
Boolean.toString(btn_autosearch.isSelected()));
}
});
import java.util.Map;
import java.util.Objects;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
}
} catch (Exception mfe)
{
- jalview.bin.Cache.log.debug("Exception accessing urls", mfe);
+ Console.debug("Exception accessing urls", mfe);
continue;
}
int colCounter = 0;
import org.json.JSONArray;
import org.json.JSONObject;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
}
} catch (Exception x)
{
- Cache.log.warn(
+ Console.warn(
"Couldn't retrieve 3d-beacons model for uniprot id"
+ searchTerm + " : " + tdbURL,
x);
*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.util.MessageManager;
import jalview.util.Platform;
public void handleQuitRequestWith(
QuitEvent e, QuitResponse r)
{
- boolean confirmQuit = jalview.bin.Cache
+ boolean confirmQuit = Cache
.getDefault(
jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT,
true);
import jalview.api.ViewStyleI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.bin.Jalview;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
// modifyPID.setEnabled(false);
}
- String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+ String sortby = Cache.getDefault("SORT_ALIGNMENT",
"No sort");
if (sortby.equals("Id"))
wrapMenuItem_actionPerformed(null);
}
- if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+ if (Cache.getDefault("SHOW_OVERVIEW", false))
{
this.overviewMenuItem_actionPerformed(null);
}
*/
public String getVersion()
{
- return jalview.bin.Cache.getProperty("VERSION");
+ return Cache.getProperty("VERSION");
}
public FeatureRenderer getFeatureRenderer()
}
else
{
- Cache.log.error(MessageManager
+ Console.error(MessageManager
.formatMessage("label.couldnt_save_file", new Object[]
{ lastFilenameSaved }));
}
BackupFiles backupfiles = null;
if (doBackup)
{
- Cache.log.trace(
+ Console.trace(
"ALIGNFRAME making backupfiles object for " + file);
backupfiles = new BackupFiles(file);
}
{
String tempFilePath = doBackup ? backupfiles.getTempFilePath()
: file;
- Cache.log.trace("ALIGNFRAME setting PrintWriter");
+ Console.trace("ALIGNFRAME setting PrintWriter");
PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
if (backupfiles != null)
{
- Cache.log.trace("ALIGNFRAME about to write to temp file "
+ Console.trace("ALIGNFRAME about to write to temp file "
+ backupfiles.getTempFilePath());
}
out.print(output);
- Cache.log.trace("ALIGNFRAME about to close file");
+ Console.trace("ALIGNFRAME about to close file");
out.close();
- Cache.log.trace("ALIGNFRAME closed file");
+ Console.trace("ALIGNFRAME closed file");
AlignFrame.this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format",
} catch (IOException e)
{
lastSaveSuccessful = false;
- Cache.log.error(
+ Console.error(
"ALIGNFRAME Something happened writing the temp file");
- Cache.log.error(e.getMessage());
- Cache.log.debug(Cache.getStackTraceString(e));
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
} catch (Exception ex)
{
lastSaveSuccessful = false;
- Cache.log.error(
+ Console.error(
"ALIGNFRAME Something unexpected happened writing the temp file");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
if (doBackup)
{
backupfiles.setWriteSuccess(lastSaveSuccessful);
- Cache.log.debug("ALIGNFRAME writing temp file was "
+ Console.debug("ALIGNFRAME writing temp file was "
+ (lastSaveSuccessful ? "" : "NOT ") + "successful");
// do the backup file roll and rename the temp file to actual file
- Cache.log.trace(
+ Console.trace(
"ALIGNFRAME about to rollBackupsAndRenameTempFile");
lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
- Cache.log.debug(
+ Console.debug(
"ALIGNFRAME performed rollBackupsAndRenameTempFile "
+ (lastSaveSuccessful ? "" : "un")
+ "successfully");
public void associatedData_actionPerformed(ActionEvent e)
{
final JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
String tooltip = MessageManager
.getString("label.load_jalview_annotations");
public void run()
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ Cache.setProperty("LAST_DIRECTORY", choice);
loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
}
});
{
if (originalSource != viewport)
{
- Cache.log.warn(
+ Console.warn(
"Implementation worry: mismatch of viewport origin for undo");
}
originalSource.updateHiddenColumns();
if (originalSource != viewport)
{
- Cache.log.warn(
+ Console.warn(
"Implementation worry: mismatch of viewport origin for redo");
}
originalSource.updateHiddenColumns();
{
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.select_newick_like_tree_file"));
}
} catch (Exception e)
{
- Cache.log.debug(
+ Console.debug(
"Exception during web service menu building process.",
e);
}
showProducts.setEnabled(showp);
} catch (Exception e)
{
- Cache.log.warn(
+ Console.warn(
"canShowProducts threw an exception - please report to help@jalview.org",
e);
return false;
al = dna.translateCdna(codeTable);
} catch (Exception ex)
{
- jalview.bin.Cache.log.error(
+ Console.error(
"Exception during translation. Please report this !", ex);
final String msg = MessageManager.getString(
"label.error_when_translating_sequences_submit_bug_report");
}
} catch (Exception x)
{
- Cache.log.debug(
+ Console.debug(
"Exception when processing data source as T-COFFEE score file",
x);
tcf = null;
import jalview.api.FeaturesDisplayedI;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
- if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ if (seqsetid != null)
{
- Cache.log.debug(
+ Console.debug(
"Setting viewport's sequence set id : " + sequenceSetID);
}
- if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ if (viewId != null)
{
- Cache.log.debug("Setting viewport's view id : " + viewId);
+ Console.debug("Setting viewport's view id : " + viewId);
}
init();
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
- if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ if (seqsetid != null)
{
- Cache.log.debug(
+ Console.debug(
"Setting viewport's sequence set id : " + sequenceSetID);
}
- if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ if (viewId != null)
{
- Cache.log.debug("Setting viewport's view id : " + viewId);
+ Console.debug("Setting viewport's view id : " + viewId);
}
if (hiddenColumns != null)
// calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
if (needsUpdate)
{
- Cache.log.debug("trigger update for " + calcId);
+ Console.debug("trigger update for " + calcId);
}
}
try
{
newAlignFrame.setMaximum(
- jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
// could not be validated and it is not clear if it is now being
// called. Log warning here in case it is called and unforeseen
// problems occur
- Cache.log.warn(
+ Console.warn(
"Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
// scroll to start of panel
}
else
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.warn("Closing alignment panel which is already closed.");
+ Console.warn("Closing alignment panel which is already closed.");
}
}
}
import javax.swing.event.InternalFrameEvent;
import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("When trying to open the Jmol viewer!", oomerror);
- Cache.log.debug("File locations are " + filesString);
+ Console.debug("File locations are " + filesString);
} catch (Exception ex)
{
- Cache.log.error("Couldn't open Jmol viewer!", ex);
+ Console.error("Couldn't open Jmol viewer!", ex);
ex.printStackTrace();
return;
}
{
new OOMWarning("When trying to add structures to the Jmol viewer!",
oomerror);
- Cache.log.debug("File locations are " + filesString);
+ Console.debug("File locations are " + filesString);
return;
} catch (Exception ex)
{
- Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ Console.error("Couldn't add files to Jmol viewer!", ex);
ex.printStackTrace();
return;
}
{
try
{
- Cache.log.debug("Waiting around for jmb notify.");
+ Console.debug("Waiting around for jmb notify.");
waitTotal += waitFor;
// Thread.sleep() throws an exception in JS
import jalview.api.AlignmentViewPanel;
import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception e)
{
- Cache.log.error("Failed to launch Jmol-associated url " + url, e);
+ Console.error("Failed to launch Jmol-associated url " + url, e);
// TODO: 2.6 : warn user if browser was not configured.
}
}
package jalview.gui;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
{
if (parent != null)
{
- Cache.log.debug("News window closed.");
+ Console.debug("News window closed.");
jd = null;
parent.showNews(false);
}
public BlogReader(Desktop desktop)
{
- Cache.log.debug("Constructing news reader.");
+ Console.debug("Constructing news reader.");
parent = desktop;
_channelModel = new ChannelListModel();
// Construct our jalview news channel
Channel chan = new Channel();
chan.setURL(
- jalview.bin.Cache.getDefault("JALVIEW_NEWS_RSS",
- jalview.bin.Cache.getDefault("www.jalview.org",
+ Cache.getDefault("JALVIEW_NEWS_RSS",
+ Cache.getDefault("www.jalview.org",
"https://www.jalview.org")
+ "/feeds/desktop/rss"));
loadLastM();
if (setvisible)
{
- Cache.log.debug("Will show jalview news automatically");
+ Console.debug("Will show jalview news automatically");
showNews();
}
- Cache.log.debug("Completed construction of reader.");
+ Console.debug("Completed construction of reader.");
}
MessageManager.getString("label.news_from_jalview"),
bounds.width, bounds.height);
jd.frame.setModalExclusionType(ModalExclusionType.NO_EXCLUDE);
- Cache.log.debug("Displaying news.");
+ Console.debug("Displaying news.");
jd.waitForInput();
}
}
}
if (chan != null && chan.getItems() != null)
{
- Cache.log.debug("Scanning news items: newsnew=" + newsnew
+ Console.debug("Scanning news items: newsnew=" + newsnew
+ " and lastDate is " + lastDate);
for (Item i : (List<Item>) chan.getItems())
{
{
String formatted = Cache
.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", lastDate);
- Cache.log.debug("Saved last read date as " + formatted);
+ Console.debug("Saved last read date as " + formatted);
}
}
}
{
// this tests the detection of new news based on the last read date stored
// in jalview properties
- jalview.bin.Cache.loadProperties(null);
- jalview.bin.Cache.initLogger();
+ Cache.loadProperties(null);
+ Console.initLogger();
// test will advance read date each time
Calendar today = Calendar.getInstance(),
lastread = Calendar.getInstance();
System.out.println("Set last date to " + formattedDate);
if (me.isNewsNew())
{
- Cache.log.debug("There is news to read.");
+ Console.debug("There is news to read.");
}
else
{
- Cache.log.debug("There is no new news.");
+ Console.debug("There is no new news.");
me.xf.setTitle("Testing : Last read is " + me.lastDate);
me.showNews();
me.xf.toFront();
}
- Cache.log.debug("Waiting for closure.");
+ Console.debug("Waiting for closure.");
do
{
try
if (me.isNewsNew())
{
- Cache.log.debug("Still new news after reader displayed.");
+ Console.debug("Still new news after reader displayed.");
}
if (lastread.getTime().before(me.lastDate))
{
- Cache.log.debug("The news was read.");
+ Console.debug("The news was read.");
lastread.setTime(me.lastDate);
}
else
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
initChimera();
} catch (Exception ex)
{
- Cache.log.error("Couldn't open Chimera viewer!", ex);
+ Console.error("Couldn't open Chimera viewer!", ex);
}
}
int num = -1;
oomerror);
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Couldn't open " + pe.getFile() + " in Chimera viewer!",
ex);
} finally
{
- Cache.log.debug("File locations are " + files);
+ Console.debug("File locations are " + files);
}
}
}
import java.io.PipedOutputStream;
import java.io.PrintStream;
+import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
+import javax.swing.border.Border;
+import javax.swing.text.DefaultCaret;
-import org.apache.log4j.Level;
-import org.apache.log4j.SimpleLayout;
-
-import jalview.bin.Cache;
+import jalview.log.JLoggerI.LogLevel;
+import jalview.log.JLoggerLog4j;
+import jalview.log.JalviewAppender;
import jalview.util.ChannelProperties;
import jalview.util.MessageManager;
+import jalview.util.Platform;
/**
* Simple Jalview Java Console. Version 1 - allows viewing of console output
private int MIN_HEIGHT = 250;
- private JComboBox<Level> logLevelCombo = new JComboBox<Level>();
+ private JComboBox<LogLevel> logLevelCombo = new JComboBox<LogLevel>();
- protected Level startingLogLevel = Level.INFO;
+ protected LogLevel startingLogLevel = LogLevel.INFO;
public Console()
{
// textArea = cpt.getTextArea();
textArea = new JTextArea();
textArea.setEditable(false);
+ // autoscroll
+ DefaultCaret caret = (DefaultCaret) textArea.getCaret();
+ caret.setUpdatePolicy(DefaultCaret.ALWAYS_UPDATE);
+ // toggle autoscroll by clicking on the text area
+ Border pausedBorder = BorderFactory.createMatteBorder(2, 2, 2, 2,
+ textArea.getForeground());
+ Border noBorder = BorderFactory.createEmptyBorder(2, 2, 2, 2);
+ JScrollPane scrollPane = new JScrollPane(textArea);
+ scrollPane.setBorder(noBorder);
+ textArea.addMouseListener(new MouseAdapter()
+ {
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getButton() == MouseEvent.BUTTON1)
+ {
+ if (caret.getUpdatePolicy() == DefaultCaret.ALWAYS_UPDATE)
+ {
+ caret.setUpdatePolicy(DefaultCaret.NEVER_UPDATE);
+ scrollPane.setBorder(pausedBorder);
+ }
+ else
+ {
+ caret.setUpdatePolicy(DefaultCaret.ALWAYS_UPDATE);
+ textArea.setCaretPosition(textArea.getDocument().getLength());
+ scrollPane.setBorder(noBorder);
+ }
+ }
+ }
+ });
+
JButton clearButton = new JButton(
MessageManager.getString("action.clear"));
JButton copyToClipboardButton = new JButton(
JLabel logLevelLabel = new JLabel(
MessageManager.getString("label.log_level") + ":");
- // logLevelCombo.addItem(Level.ALL);
- logLevelCombo.addItem(Level.TRACE);
- logLevelCombo.addItem(Level.DEBUG);
- logLevelCombo.addItem(Level.INFO);
- logLevelCombo.addItem(Level.WARN);
- // logLevelCombo.addItem(Level.ERROR);
- // logLevelCombo.addItem(Level.FATAL);
- // logLevelCombo.addItem(Level.OFF);
+ // logLevelCombo.addItem(LogLevel.ALL);
+ logLevelCombo.addItem(LogLevel.TRACE);
+ logLevelCombo.addItem(LogLevel.DEBUG);
+ logLevelCombo.addItem(LogLevel.INFO);
+ logLevelCombo.addItem(LogLevel.WARN);
+ // logLevelCombo.addItem(LogLevel.ERROR);
+ // logLevelCombo.addItem(LogLevel.FATAL);
+ // logLevelCombo.addItem(LogLevel.ERROR);
+ // logLevelCombo.addItem(LogLevel.OFF);
// set startingLogLevel
- startingLogLevel = Cache.log == null ? Level.INFO
- : Cache.log.getLevel();
+ startingLogLevel = jalview.bin.Console.log == null ? LogLevel.INFO
+ : jalview.bin.Console.log.getLevel();
setChosenLogLevelCombo();
logLevelCombo.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- if (Cache.log != null)
+ if (jalview.bin.Console.log != null)
{
- Cache.log.setLevel((Level) logLevelCombo.getSelectedItem());
+ jalview.bin.Console.log.setLevel((LogLevel) logLevelCombo.getSelectedItem());
}
}
// frame = cpt;
frame.getContentPane().setLayout(new BorderLayout());
- frame.getContentPane().add(new JScrollPane(textArea),
- BorderLayout.CENTER);
+ frame.getContentPane().add(scrollPane, BorderLayout.CENTER);
JPanel southPanel = new JPanel();
southPanel.setLayout(new GridBagLayout());
setChosenLogLevelCombo(startingLogLevel);
}
- private void setChosenLogLevelCombo(Level setLogLevel)
+ private void setChosenLogLevelCombo(LogLevel setLogLevel)
{
logLevelCombo.setSelectedItem(setLogLevel);
if (!logLevelCombo.getSelectedItem().equals(setLogLevel))
{
// setLogLevel not (yet) in list
- if (setLogLevel != null && setLogLevel instanceof Level)
+ if (setLogLevel != null && setLogLevel instanceof LogLevel)
{
// add new item to list (might be set via .jalview_properties)
boolean added = false;
for (int i = 0; i < logLevelCombo.getItemCount(); i++)
{
- Level l = (Level) logLevelCombo.getItemAt(i);
- if (l.isGreaterOrEqual(setLogLevel))
+ LogLevel l = (LogLevel) logLevelCombo.getItemAt(i);
+ if (l.compareTo(setLogLevel) >= 0)
{
logLevelCombo.insertItemAt(setLogLevel, i);
added = true;
}
else
{
- logLevelCombo.setSelectedItem(Level.INFO);
+ logLevelCombo.setSelectedItem(LogLevel.INFO);
}
}
}
frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
// desktop.add(frame);
initConsole(false);
- JalviewAppender jappender = new JalviewAppender();
- jappender.setLayout(new SimpleLayout());
- JalviewAppender.setTextArea(textArea);
- org.apache.log4j.Logger.getRootLogger().addAppender(jappender);
+ LogLevel level = (LogLevel) logLevelCombo.getSelectedItem();
+ if (!Platform.isJS())
+ {
+ JalviewAppender jappender = new JalviewAppender(level);
+ JalviewAppender.setTextArea(textArea);
+ jappender.start();
+ if (jalview.bin.Console.log != null && jalview.bin.Console.log instanceof JLoggerLog4j)
+ {
+ JLoggerLog4j.addAppender(jalview.bin.Console.log, jappender);
+ }
+ }
}
public synchronized void stopConsole()
else
{
// reset log level to what it was before
- if (Cache.log != null)
+ if (jalview.bin.Console.log != null)
{
- Cache.log.setLevel(startingLogLevel);
+ jalview.bin.Console.log.setLevel(startingLogLevel);
}
unredirectStreams();
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
new OOMWarning("whilst fetching crossreferences", e);
} catch (Throwable e)
{
- Cache.log.error("Error when finding crossreferences", e);
+ Console.error("Error when finding crossreferences", e);
} finally
{
alignFrame.setProgressBar(MessageManager.formatMessage(
*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.GCutAndPasteHtmlTransfer;
// TODO: JAL-3048 JalviewFileChooser - Save option
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
// TODO: JAL-3048 JalviewFileChooser - Save option
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
try
{
af.setMaximum(
- jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (Exception ex)
{
}
public class Desktop extends jalview.jbgui.GDesktop
implements DropTargetListener, ClipboardOwner, IProgressIndicator, jalview.api.StructureSelectionManagerProvider {
private static final String CITATION;
- static {
- URL bg_logo_url = ChannelProperties.getImageURL("bg_logo." + String.valueOf(SplashScreen.logoSize));
- URL uod_logo_url = ChannelProperties.getImageURL("uod_banner." + String.valueOf(SplashScreen.logoSize));
+ static
+ {
+ URL bg_logo_url = ChannelProperties.getImageURL(
+ "bg_logo." + String.valueOf(SplashScreen.logoSize));
+ URL uod_logo_url = ChannelProperties.getImageURL(
+ "uod_banner." + String.valueOf(SplashScreen.logoSize));
boolean logo = (bg_logo_url != null || uod_logo_url != null);
StringBuilder sb = new StringBuilder();
- sb.append("<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.");
- if (logo) {
+ sb.append(
+ "<br><br>Jalview is free software released under GPLv3.<br><br>Development is managed by The Barton Group, University of Dundee, Scotland, UK.");
+ if (logo)
+ {
sb.append("<br>");
}
- sb.append(bg_logo_url == null ? "" : "<img alt=\"Barton Group logo\" src=\"" + bg_logo_url.toString() + "\">");
+ sb.append(bg_logo_url == null ? ""
+ : "<img alt=\"Barton Group logo\" src=\""
+ + bg_logo_url.toString() + "\">");
sb.append(uod_logo_url == null ? ""
- : " <img alt=\"University of Dundee shield\" src=\"" + uod_logo_url.toString() + "\">");
+ : " <img alt=\"University of Dundee shield\" src=\""
+ + uod_logo_url.toString() + "\">");
sb.append(
- "<br><br>For help, see the FAQ at <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list");
+ "<br><br>For help, see <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and join <a href=\"https://discourse.jalview.org\">discourse.jalview.org</a>");
sb.append("<br><br>If you use Jalview, please cite:"
- + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
- + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
- + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033");
+ + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ + "<br>Bioinformatics <a href=\"https://doi.org/10.1093/bioinformatics/btp033\">doi: 10.1093/bioinformatics/btp033</a>");
CITATION = sb.toString();
}
awtAppClassNameField.setAccessible(true);
awtAppClassNameField.set(xToolkit, title);
} else {
- Cache.log.debug("XToolkit: awtAppClassName not found");
+ jalview.bin.Console.debug("XToolkit: awtAppClassName not found");
}
} catch (Exception e) {
- Cache.debug("Error setting awtAppClassName");
- Cache.trace(Cache.getStackTraceString(e));
+ jalview.bin.Console.debug("Error setting awtAppClassName");
+ jalview.bin.Console.trace(Cache.getStackTraceString(e));
}
}
System.out.println("Cannot set APQHandlers");
// e.printStackTrace();
} catch (Throwable t) {
- Cache.warn("Error setting APQHandlers: " + t.toString());
- Cache.trace(Cache.getStackTraceString(t));
+ jalview.bin.Console.warn("Error setting APQHandlers: " + t.toString());
+ jalview.bin.Console.trace(Cache.getStackTraceString(t));
}
setIconImages(ChannelProperties.getIconList());
new Thread(new Runnable() {
@Override
public void run() {
- Cache.log.debug("Filechooser init thread started.");
+ jalview.bin.Console.debug("Filechooser init thread started.");
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
- Cache.log.debug("Filechooser init thread finished.");
+ jalview.bin.Console.debug("Filechooser init thread finished.");
}
}).start();
// Add the service change listener
@Override
public void propertyChange(PropertyChangeEvent evt) {
- Cache.log.debug("Firing service changed event for " + evt.getNewValue());
+ jalview.bin.Console.debug("Firing service changed event for " + evt.getNewValue());
JalviewServicesChanged(evt);
}
});
new Thread(new Runnable() {
@Override
public void run() {
- Cache.log.debug("Starting news thread.");
+ jalview.bin.Console.debug("Starting news thread.");
jvnews = new BlogReader(me);
showNews.setVisible(true);
- Cache.log.debug("Completed news thread.");
+ jalview.bin.Console.debug("Completed news thread.");
}
}).start();
}
new Thread(new Runnable() {
@Override
public void run() {
- Cache.log.debug("Downloading data from identifiers.org");
+ jalview.bin.Console.debug("Downloading data from identifiers.org");
try {
UrlDownloadClient.download(IdOrgSettings.getUrl(), IdOrgSettings.getDownloadLocation());
} catch (IOException e) {
- Cache.log.debug("Exception downloading identifiers.org data" + e.getMessage());
+ jalview.bin.Console.debug("Exception downloading identifiers.org data" + e.getMessage());
}
}
}).start();
}
void showNews(boolean visible) {
- Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
+ jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news.");
showNews.setSelected(visible);
if (visible && !jvnews.isVisible()) {
new Thread(new Runnable() {
iy = (int) (iy * sh);
ih = (int) (ih * sh);
while (ix >= screenSize.width) {
- Cache.log.debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
+ jalview.bin.Console.debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
ix -= screenSize.width;
}
while (iy >= screenSize.height) {
- Cache.log.debug("Window geometry location recall error: shifting vertical to within screenbounds.");
+ jalview.bin.Console.debug("Window geometry location recall error: shifting vertical to within screenbounds.");
iy -= screenSize.height;
}
- Cache.log.debug("Got last known dimensions for " + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
+ jalview.bin.Console.debug("Got last known dimensions for " + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
+ " height:" + ih);
}
// return dimensions for new instance
frame.requestFocus();
} catch (java.beans.PropertyVetoException ve) {
} catch (java.lang.ClassCastException cex) {
- Cache.log.warn(
+ jalview.bin.Console.warn(
"Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
cex);
}
}
private void storeLastKnownDimensions(String string, Rectangle jc) {
- Cache.log.debug("Storing last known dimensions for " + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+ jalview.bin.Console.debug("Storing last known dimensions for " + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+ " height:" + jc.height);
Cache.setProperty(string + "SCREEN_X", jc.x + "");
@Override
protected void garbageCollect_actionPerformed(ActionEvent e) {
// We simply collect the garbage
- Cache.log.debug("Collecting garbage...");
+ jalview.bin.Console.debug("Collecting garbage...");
System.gc();
- Cache.log.debug("Finished garbage collection.");
+ jalview.bin.Console.debug("Finished garbage collection.");
}
/*
} catch (OutOfMemoryError oom) {
new OOMWarning("Whilst saving current state to " + chosenFile.getName(), oom);
} catch (Exception ex) {
- Cache.log.error("Problems whilst trying to save to " + chosenFile.getName(), ex);
+ jalview.bin.Console.error("Problems whilst trying to save to " + chosenFile.getName(), ex);
JvOptionPane.showMessageDialog(me,
MessageManager.formatMessage("label.error_whilst_saving_current_state_to",
new Object[] { chosenFile.getName() }),
} catch (OutOfMemoryError oom) {
new OOMWarning("Whilst loading project from " + choice, oom);
} catch (Exception ex) {
- Cache.log.error("Problems whilst loading project from " + choice, ex);
+ jalview.bin.Console.error("Problems whilst loading project from " + choice, ex);
JvOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.error_whilst_loading_project_from", new Object[] { choice }),
MessageManager.getString("label.couldnt_load_project"), JvOptionPane.WARNING_MESSAGE);
try {
openGroovyConsole();
} catch (Exception ex) {
- Cache.log.error("Groovy Shell Creation failed.", ex);
+ jalview.bin.Console.error("Groovy Shell Creation failed.", ex);
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_create_groovy_shell"),
});
}
} else {
- Cache.log.error("Errors reported by JABA discovery service. Check web services preferences.\n" + ermsg);
+ jalview.bin.Console.error("Errors reported by JABA discovery service. Check web services preferences.\n" + ermsg);
}
}
}
Desktop.showUrl(url);
} catch (Exception x) {
if (url != null) {
- if (Cache.log != null) {
- Cache.log.error("Couldn't handle string " + url + " as a URL.");
- } else {
- System.err.println("Couldn't handle string " + url + " as a URL.");
- }
+ jalview.bin.Console.error("Couldn't handle string " + url + " as a URL.");
}
// ignore any exceptions due to dud links.
}
try {
SwingUtilities.invokeAndWait(prompter);
} catch (Exception q) {
- Cache.log.warn("Unexpected Exception in dialog thread.", q);
+ jalview.bin.Console.warn("Unexpected Exception in dialog thread.", q);
}
}
});
@Override
public void exportImage(Graphics g) throws Exception {
paintAll(g);
- Cache.log.info("Successfully written snapshot to file " + of.getAbsolutePath());
+ jalview.bin.Console.info("Successfully written snapshot to file " + of.getAbsolutePath());
}
};
String title = "View of desktop";
try {
urlFlavour = new DataFlavor("application/x-java-url; class=java.net.URL");
} catch (ClassNotFoundException cfe) {
- Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe);
+ jalview.bin.Console.debug("Couldn't instantiate the URL dataflavor.", cfe);
}
if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour)) {
if (url != null) {
protocols.add(DataSourceType.URL);
files.add(url.toString());
- Cache.log.debug("Drop handled as URL dataflavor " + files.get(files.size() - 1));
+ jalview.bin.Console.debug("Drop handled as URL dataflavor " + files.get(files.size() - 1));
return;
} else {
if (Platform.isAMacAndNotJS()) {
}
}
} catch (Throwable ex) {
- Cache.log.debug("URL drop handler failed.", ex);
+ jalview.bin.Console.debug("URL drop handler failed.", ex);
}
}
if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) {
// Works on Windows and MacOSX
- Cache.log.debug("Drop handled as javaFileListFlavor");
+ jalview.bin.Console.debug("Drop handled as javaFileListFlavor");
for (Object file : (List) t.getTransferData(DataFlavor.javaFileListFlavor)) {
files.add(file);
protocols.add(DataSourceType.FILE);
boolean added = false;
String data = null;
if (t.isDataFlavorSupported(uriListFlavor)) {
- Cache.log.debug("Drop handled as uriListFlavor");
+ jalview.bin.Console.debug("Drop handled as uriListFlavor");
// This is used by Unix drag system
data = (String) t.getTransferData(uriListFlavor);
}
if (data == null) {
// fallback to text: workaround - on OSX where there's a JVM bug
- Cache.log.debug("standard URIListFlavor failed. Trying text");
+ jalview.bin.Console.debug("standard URIListFlavor failed. Trying text");
// try text fallback
DataFlavor textDf = new DataFlavor("text/plain;class=java.lang.String");
if (t.isDataFlavorSupported(textDf)) {
data = (String) t.getTransferData(textDf);
}
- Cache.log.debug("Plain text drop content returned " + (data == null ? "Null - failed" : data));
+ jalview.bin.Console.debug("Plain text drop content returned " + (data == null ? "Null - failed" : data));
}
if (data != null) {
while (protocols.size() < files.size()) {
- Cache.log.debug("Adding missing FILE protocol for " + files.get(protocols.size()));
+ jalview.bin.Console.debug("Adding missing FILE protocol for " + files.get(protocols.size()));
protocols.add(DataSourceType.FILE);
}
for (java.util.StringTokenizer st = new java.util.StringTokenizer(data, "\r\n"); st.hasMoreTokens();) {
}
}
- if (Cache.log.isDebugEnabled()) {
+ if (jalview.bin.Console.isDebugEnabled()) {
if (data == null || !added) {
if (t.getTransferDataFlavors() != null && t.getTransferDataFlavors().length > 0) {
- Cache.log.debug("Couldn't resolve drop data. Here are the supported flavors:");
+ jalview.bin.Console.debug("Couldn't resolve drop data. Here are the supported flavors:");
for (DataFlavor fl : t.getTransferDataFlavors()) {
- Cache.log.debug("Supported transfer dataflavor: " + fl.toString());
+ jalview.bin.Console.debug("Supported transfer dataflavor: " + fl.toString());
Object df = t.getTransferData(fl);
if (df != null) {
- Cache.log.debug("Retrieves: " + df);
+ jalview.bin.Console.debug("Retrieves: " + df);
} else {
- Cache.log.debug("Retrieved nothing");
+ jalview.bin.Console.debug("Retrieved nothing");
}
}
} else {
- Cache.log.debug("Couldn't resolve dataflavor for drop: " + t.toString());
+ jalview.bin.Console.debug("Couldn't resolve dataflavor for drop: " + t.toString());
}
}
}
}
if (Platform.isWindowsAndNotJS()) {
- Cache.log.debug("Scanning dropped content for Windows Link Files");
+ jalview.bin.Console.debug("Scanning dropped content for Windows Link Files");
// resolve any .lnk files in the file drop
for (int f = 0; f < files.size(); f++) {
Object obj = files.get(f);
File lf = (obj instanceof File ? (File) obj : new File((String) obj));
// process link file to get a URL
- Cache.log.debug("Found potential link file: " + lf);
+ jalview.bin.Console.debug("Found potential link file: " + lf);
WindowsShortcut wscfile = new WindowsShortcut(lf);
String fullname = wscfile.getRealFilename();
protocols.set(f, FormatAdapter.checkProtocol(fullname));
files.set(f, fullname);
- Cache.log.debug("Parsed real filename " + fullname + " to extract protocol: " + protocols.get(f));
+ jalview.bin.Console.debug("Parsed real filename " + fullname + " to extract protocol: " + protocols.get(f));
} catch (Exception ex) {
- Cache.log.error("Couldn't parse " + files.get(f) + " as a link file.", ex);
+ jalview.bin.Console.error("Couldn't parse " + files.get(f) + " as a link file.", ex);
}
}
}
AffineTransform t = gg.getTransform();
double scaleX = t.getScaleX();
double scaleY = t.getScaleY();
- Cache.debug(debugScaleMessage + scaleX + " (X)");
- Cache.debug(debugScaleMessage + scaleY + " (Y)");
+ jalview.bin.Console.debug(debugScaleMessage + scaleX + " (X)");
+ jalview.bin.Console.debug(debugScaleMessage + scaleY + " (Y)");
debugScaleMessageDone = true;
} else {
- Cache.debug("Desktop graphics null");
+ jalview.bin.Console.debug("Desktop graphics null");
}
} catch (Exception e) {
- Cache.debug(Cache.getStackTraceString(e));
+ jalview.bin.Console.debug(Cache.getStackTraceString(e));
}
}
}
JPopupMenu men = new JPopupMenu(MessageManager
.formatMessage("label.settings_for_param", new String[]
{ type }));
- final FeatureColourI featureColour = (FeatureColourI) typeCol;
-
- /*
- * menu option to select (or deselect) variable colour
- */
- final JCheckBoxMenuItem variableColourCB = new JCheckBoxMenuItem(
- MessageManager.getString("label.variable_colour"));
- variableColourCB.setSelected(!featureColour.isSimpleColour());
- men.add(variableColourCB);
-
- /*
- * checkbox action listener doubles up as listener to OK
- * from the variable colour / filters dialog
- */
- variableColourCB.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (e.getSource() == variableColourCB)
- {
- // BH 2018 for JavaScript because this is a checkbox
- men.setVisible(true);
- men.setVisible(false);
- if (featureColour.isSimpleColour())
- {
- /*
- * toggle simple colour to variable colour - show dialog
- */
- FeatureTypeSettings fc = new FeatureTypeSettings(fr, type);
- fc.addActionListener(this);
- }
- else
- {
- /*
- * toggle variable to simple colour - show colour chooser
- */
- String title = MessageManager
- .formatMessage("label.select_colour_for", type);
- ColourChooserListener listener = new ColourChooserListener()
- {
- @Override
- public void colourSelected(Color c)
- {
- table.setValueAt(new FeatureColour(c), rowSelected,
- COLOUR_COLUMN);
- table.validate();
- updateFeatureRenderer(
- ((FeatureTableModel) table.getModel()).getData(),
- false);
- }
- };
- JalviewColourChooser.showColourChooser(FeatureSettings.this,
- title, featureColour.getMaxColour(), listener);
- }
- }
- else
- {
- if (e.getSource() instanceof FeatureTypeSettings)
- {
- /*
- * update after OK in feature colour dialog; the updated
- * colour will have already been set in the FeatureRenderer
- */
- FeatureColourI fci = fr.getFeatureColours().get(type);
- table.setValueAt(fci, rowSelected, COLOUR_COLUMN);
- // BH 2018 setting a table value does not invalidate it.
- // System.out.println("FeatureSettings is valied" +
- // table.validate();
- }
- }
- }
- });
-
- men.addSeparator();
JMenuItem scr = new JMenuItem(
MessageManager.getString("label.sort_by_score"));
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.GraphLine;
import jalview.datamodel.features.FeatureAttributes;
import jalview.datamodel.features.FeatureAttributes.Datatype;
attName = (String) attCombo.getSelectedItem();
} catch (Exception e)
{
- Cache.log.error("Problem casting Combo box entry to String");
+ Console.error("Problem casting Combo box entry to String");
attName = attCombo.getSelectedItem().toString();
}
Condition cond = (Condition) condCombo.getSelectedItem();
*/
package jalview.gui;
+import jalview.bin.Console;
import jalview.util.MessageManager;
import java.awt.Component;
desktop = instance;
if (oomex != null)
{
- if (jalview.bin.Cache.log != null)
- {
- jalview.bin.Cache.log.error("Out of Memory when " + action,
+ Console.error("Out of Memory when " + action,
oomex);
- }
- else
- {
- System.err.println("Out of Memory when " + action);
- oomex.printStackTrace();
- }
}
javax.swing.SwingUtilities.invokeLater(this);
System.gc();
import jalview.api.AlignViewportI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
// JAL-2647 disabled after load from project (until save to project done)
if (getPcaModel().getInputData() == null)
{
- Cache.log.info(
+ Console.info(
"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
urlLink = new UrlLink(link);
} catch (Exception foo)
{
- Cache.log.error("Exception for URLLink '" + link + "'", foo);
+ Console.error("Exception for URLLink '" + link + "'", foo);
continue;
}
if (!urlLink.isValid())
{
- Cache.log.error(urlLink.getInvalidMessage());
+ Console.error(urlLink.getInvalidMessage());
continue;
}
urlLink = new GroupUrlLink(link);
} catch (Exception foo)
{
- Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
+ Console.error("Exception for GroupURLLink '" + link + "'", foo);
continue;
}
if (!urlLink.isValid())
{
- Cache.log.error(urlLink.getInvalidMessage());
+ Console.error(urlLink.getInvalidMessage());
continue;
}
final String label = urlLink.getLabel();
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.bin.MemorySetting;
import jalview.ext.pymol.PymolManager;
import jalview.gui.Help.HelpId;
}
} catch (IllegalArgumentException e)
{
- Cache.log.error("Unknown structure viewer type: " + viewerType
+ Console.error("Unknown structure viewer type: " + viewerType
+ ", defaulting to Jmol");
type = ViewerType.JMOL;
}
}
} catch (IllegalArgumentException x)
{
- Cache.log.error("Failed to set path - unknown viewer type",x);
+ Console.error("Failed to set path - unknown viewer type",x);
}
}
}
proxyType.setSelected(customProxy.getModel(), true);
break;
default:
- Cache.log.warn(
+ Console.warn(
"Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
+ proxyTypeString);
}
if (index == -1)
{
// button no longer enabled if row is not selected
- Cache.log.debug("Edit with no row selected in linkUrlTable");
+ Console.debug("Edit with no row selected in linkUrlTable");
return;
}
if (index == -1)
{
// button no longer enabled if row is not selected
- Cache.log.debug("Delete with no row selected in linkUrlTable");
+ Console.debug("Delete with no row selected in linkUrlTable");
return;
}
else
package jalview.gui;
import jalview.bin.Cache;
+import jalview.bin.Console;
import java.awt.Component;
* @param desktop
* - where the dialog box will be shown
* @param property
- * - boolean property in jalview.bin.Cache
+ * - boolean property in Cache
* @param dialogTitle
* - title of prompt box
* @param dialogText
return;
}
// First - check to see if wee have an old questionnaire/response id pair.
- String lastq = jalview.bin.Cache.getProperty(property);
+ String lastq = Cache.getProperty(property);
if (lastq == null)
{
raiseDialog();
- Cache.log.debug("Got user response.");
+ Console.debug("Got user response.");
}
- lastq = jalview.bin.Cache.getProperty(property);
+ lastq = Cache.getProperty(property);
String extype = "";
Exception e = null;
if (lastq == null)
// report any exceptions
if (e != null)
{
- Cache.log.warn("Unexpected exception when executing the " + extype
+ Console.warn("Unexpected exception when executing the " + extype
+ " runnable for property " + property, e);
}
}
*/
private void raiseDialog()
{
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Prompting user for " + dialogTitle
+ Console.debug("Prompting user for " + dialogTitle
+ " for Cache property " + property);
}
try
JvOptionPane.QUESTION_MESSAGE);
// and finish parsing the result
- jalview.bin.Cache.log.debug("Got response : " + reply);
+ Console.debug("Got response : " + reply);
if (reply == JvOptionPane.YES_OPTION)
{
- jalview.bin.Cache.setProperty(property, "true");
+ Cache.setProperty(property, "true");
}
else if (reply == JvOptionPane.NO_OPTION)
{
if (removeifunset)
{
- jalview.bin.Cache.removeProperty(property);
+ Cache.removeProperty(property);
}
else
{
- jalview.bin.Cache.setProperty(property, "false");
+ Cache.setProperty(property, "false");
}
}
else
{
- jalview.bin.Cache.log.debug("User cancelled setting " + property);
+ Console.debug("User cancelled setting " + property);
return;
}
// verify the property is set for debugging
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("User set property to "
- + jalview.bin.Cache.getProperty(property));
+ Console.debug("User set property to "
+ + Cache.getProperty(property));
}
} catch (Exception e)
{
- jalview.bin.Cache.log.warn(
+ Console.warn(
"Unexpected exception when prompting user for yes/no setting for property "
+ property,
e);
import java.util.Map;
import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.pymol.PymolCommands;
public void highlightAtoms(List<AtomSpec> atoms)
{
/*
- * https://pymolwiki.org/index.php/Label#examples
+ * https://pymolwiki.org/index.php/indicate#examples
*/
StringBuilder sb = new StringBuilder();
for (AtomSpec atom : atoms)
{
// todo promote to StructureCommandsI.showLabel()
- // todo handle CA|P correctly
String modelId = getModelIdForFile(atom.getPdbFile());
- sb.append(String.format(" %s//%s/%d/CA", modelId,
+ sb.append(String.format(" %s//%s/%d/*", modelId,
atom.getChain(),
atom.getPdbResNum()));
}
{
return;
}
- StructureCommandI command = new StructureCommand("label", labelSpec, LABEL_FORMAT);
+ StructureCommandI command = new StructureCommand("indicate", labelSpec);
executeCommand(command, false);
- /*
- * and remove the label(s) previously shown
- */
- if (lastLabelSpec != null)
- {
- command = new StructureCommand("label", lastLabelSpec, "");
- executeCommand(command, false);
- }
-
lastLabelSpec = labelSpec;
}
}
else
{
- Cache.log.error("Failed to launch PyMOL!");
+ Console.error("Failed to launch PyMOL!");
}
return pymol != null;
}
// pdbId.replace('-', 0)
} catch (Exception x)
{
- Cache.log.error("Unxpected encoding exception for '"+pdbId+"'",x);
+ Console.error("Unxpected encoding exception for '"+pdbId+"'",x);
}
cmd.addParameter(pdbId);
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
initPymol();
} catch (Exception ex)
{
- Cache.log.error("Couldn't open PyMOL viewer!", ex);
+ Console.error("Couldn't open PyMOL viewer!", ex);
}
}
int num = -1;
binding.stashFoundChains(pdb, pe.getFile());
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Couldn't open " + pe.getFile() + " in Chimera viewer!",
ex);
} finally
{
- // Cache.log.debug("File locations are " + files);
+ // Cache.debug("File locations are " + files);
}
}
}
boolean opened = binding.openSession(pymolSessionFile);
if (!opened)
{
- Cache.log.error(
+ Console.error(
"An error occurred opening PyMOL session file "
+ pymolSessionFile);
}
}
else if (evt.getKeyChar() == 's')
{
- // Cache.log.warn("DEBUG: Rectangle selection");
+ // Cache.warn("DEBUG: Rectangle selection");
// todo not yet enabled as rectx2, recty2 are always -1
// need to set them in mouseDragged; JAL-1124
// if ((rectx2 != -1) && (recty2 != -1))
import javax.swing.ToolTipManager;
import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
{
if (av.getAlignment() == null)
{
- Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
+ Console.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
+ " ViewId=" + av.getViewId()
+ " 's alignment is NULL! returning immediately.");
return;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
}
} catch (Exception e)
{
- Cache.log.info("Error retrieving " + accession + " from "
+ Console.info("Error retrieving " + accession + " from "
+ proxy.getDbName(), e);
}
return success;
splashText.setVisible(true);
splashText.setSize(new Dimension(750,
- 375 + logoSize + (Platform.isJS() ? 40 : 0)));
+ 425 + logoSize + (Platform.isJS() ? 40 : 0)));
splashText.setBackground(bg);
splashText.setForeground(fg);
splashText.setFont(font);
// StructureChooser
// works
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(
MessageManager.formatMessage("label.select_pdb_file_for",
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
selectedPdbFileName = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
validateSelections();
}
}
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
}
else
{
- Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
+ Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
}
return sview;
}
}
else
{
- Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
+ Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
}
return sview;
}
viewer = new PymolViewer(viewerData, alignPanel, sessionFile, vid);
break;
default:
- Cache.log.error(UNKNOWN_VIEWER_TYPE + type.toString());
+ Console.error(UNKNOWN_VIEWER_TYPE + type.toString());
}
return viewer;
}
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
{
sp.append("'" + alignPanel.getViewName() + "' ");
}
- Cache.log.info("Couldn't align structures with the " + sp.toString()
+ Console.info("Couldn't align structures with the " + sp.toString()
+ "associated alignment panels.", e);
}
return reply;
} else {
if (processingEntry.hasRetrievalUrl())
{
- String safePDBId = java.net.URLEncoder.encode(pdbid,"UTF-8");
+ String safePDBId = java.net.URLEncoder.encode(pdbid,"UTF-8").replace("%","__");
// retrieve from URL to new local tmpfile
File tmpFile = File.createTempFile(safePDBId,
import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import jalview.datamodel.Alignment;
{
// TODO: JAL-3048 save newick file for Jalview-JS
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_tree_as_newick"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ Cache.setProperty("LAST_DIRECTORY",
chooser.getSelectedFile().getParent());
try
AlignmentView originalData = tree.getOriginalData();
if (originalData == null)
{
- jalview.bin.Cache.log.info(
+ Console.info(
"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
*/
package jalview.gui;
+import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.util.MessageManager;
import java.io.BufferedReader;
{
if (url.indexOf("questionnaire.pl") == -1)
{
- jalview.bin.Cache.log.error("'" + url
+ Console.error("'" + url
+ "' is an Invalid URL for the checkForQuestionnaire() method.\n"
+ "This argument is only for questionnaires derived from jalview's questionnaire.pl cgi interface.");
}
private boolean checkresponse(URL qurl) throws Exception
{
- jalview.bin.Cache.log.debug("Checking Response for : " + qurl);
+ Console.debug("Checking Response for : " + qurl);
boolean prompt = false;
// see if we have already responsed to this questionnaire or get a new
// qid/rid pair
try
{
// First - check to see if wee have an old questionnaire/response id pair.
- String lastq = jalview.bin.Cache.getProperty("QUESTIONNAIRE");
+ String lastq = Cache.getProperty("QUESTIONNAIRE");
if (lastq == null)
{
prompt = checkresponse(new URL(url
if (qid != null && rid != null)
{
// Update our local property cache with latest qid and rid
- jalview.bin.Cache.setProperty("QUESTIONNAIRE", qid + ":" + rid);
+ Cache.setProperty("QUESTIONNAIRE", qid + ":" + rid);
}
if (prompt)
{
String qurl = url + (url.indexOf('?') > -1 ? "&" : "?") + "qid="
+ qid + "&rid=" + rid;
- jalview.bin.Cache.log
- .info("Prompting user for questionnaire at " + qurl);
+ Console.info("Prompting user for questionnaire at " + qurl);
int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.getString("label.jalview_new_questionnaire"),
MessageManager.getString("label.jalview_user_survey"),
if (reply == JvOptionPane.YES_OPTION)
{
- jalview.bin.Cache.log.debug("Opening " + qurl);
+ Console.debug("Opening " + qurl);
jalview.util.BrowserLauncher.openURL(qurl);
}
}
} catch (Exception e)
{
- jalview.bin.Cache.log
- .warn("When trying to access questionnaire URL " + url, e);
+ Console.warn("When trying to access questionnaire URL " + url, e);
}
}
package jalview.gui;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
} catch (Exception e)
{
- jalview.bin.Cache.log.error("Couldn't instantiate vamsas client !",
+ Console.error("Couldn't instantiate vamsas client !",
e);
return false;
}
}
} catch (Error e)
{
- Cache.log.warn(
+ Console.warn(
"Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
e);
} catch (Exception e)
{
- Cache.log.warn(
+ Console.warn(
"Probable VAMSAS client incompatibility - carrying on regardless",
e);
}
private ClientHandle getJalviewHandle()
{
return new ClientHandle("jalview.bin.Jalview",
- jalview.bin.Cache.getProperty("VERSION"));
+ Cache.getProperty("VERSION"));
}
/**
addStoreDocumentHandler();
startSession();
inInitialUpdate = true;
- Cache.log.debug(
+ Console.debug(
"Jalview loading the Vamsas Session for the first time.");
dealWithDocumentUpdate(false); // we don't push an update out to the
inInitialUpdate = false;
// document yet.
- Cache.log.debug("... finished update for the first time.");
+ Console.debug("... finished update for the first time.");
}
/**
}
} catch (Exception e)
{
- Cache.log.warn(
+ Console.warn(
"Exception whilst refreshing jalview windows after a vamsas document update.",
e);
}
@Override
public void run()
{
- Cache.log.info("Jalview updating to the Vamsas Session.");
+ Console.info("Jalview updating to the Vamsas Session.");
dealWithDocumentUpdate(true);
- Cache.log.info("Jalview finished updating to the Vamsas Session.");
+ Console.info("Jalview finished updating to the Vamsas Session.");
}
});
{
throw new Error("Jalview not connected to Vamsas session");
}
- Cache.log.info("Jalview disconnecting from the Vamsas Session.");
+ Console.info("Jalview disconnecting from the Vamsas Session.");
try
{
if (joinedSession)
boolean ourprompt = this.promptUser;
this.promptUser = promptUser;
vclient.finalizeClient();
- Cache.log.info("Jalview has left the session.");
+ Console.info("Jalview has left the session.");
this.promptUser = ourprompt; // restore default value
}
else
{
- Cache.log.warn(
+ Console.warn(
"JV Client leaving a session that's its not joined yet.");
}
joinedSession = false;
vobj2jv = null;
} catch (Exception e)
{
- Cache.log.error("Vamsas Session finalization threw exceptions!", e);
+ Console.error("Vamsas Session finalization threw exceptions!", e);
}
}
public void updateJalview(IClientDocument cdoc)
{
- Cache.log.debug("Jalview updating from sesion document ..");
+ Console.debug("Jalview updating from sesion document ..");
ensureJvVamsas();
VamsasAppDatastore vds = new VamsasAppDatastore(cdoc, vobj2jv, jv2vobj,
baseProvEntry(), alRedoState);
vds.updateToJalview();
} catch (Exception e)
{
- Cache.log.error("Failed to update Jalview from vamsas document.", e);
+ Console.error("Failed to update Jalview from vamsas document.", e);
}
try
{
}
} catch (Exception e)
{
- Cache.log.error(
+ Console.error(
"Exception when updating Jalview settings from Appdata.", e);
}
- Cache.log.debug(".. finished updating from sesion document.");
+ Console.debug(".. finished updating from sesion document.");
}
} catch (Exception e)
{
errorsDuringUpdate = true;
- Cache.log.error("Exception synchronizing " + af.getTitle()
+ Console.error("Exception synchronizing " + af.getTitle()
+ " "
+ (af.getViewport().getViewName() == null ? ""
: " view " + af.getViewport().getViewName())
}
} catch (Exception e)
{
- Cache.log.error("Exception synchronizing Views to Document :", e);
+ Console.error("Exception synchronizing Views to Document :", e);
errorsDuringUpdate = true;
}
}
} catch (Exception e)
{
- Cache.log.error("Client Appdata Write exception", e);
+ Console.error("Client Appdata Write exception", e);
errorsDuringAppUpdate = true;
}
vds.clearSkipList();
{
int storedviews = 0;
// called by update handler for document update.
- Cache.log.debug("Updating jalview from changed vamsas document.");
+ Console.debug("Updating jalview from changed vamsas document.");
disableGui(true);
try
{
long time = System.currentTimeMillis();
IClientDocument cdoc = vclient.getClientDocument();
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug("Time taken to get ClientDocument = "
+ Console.debug("Time taken to get ClientDocument = "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
if (fromJalview)
{
storedviews += updateVamsasDocument(cdoc);
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Time taken to update Vamsas Document from jalview\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
cdoc.setVamsasRoots(cdoc.getVamsasRoots());
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug("Time taken to set Document Roots\t\t= "
+ Console.debug("Time taken to set Document Roots\t\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
else
{
updateJalview(cdoc);
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Time taken to update Jalview from vamsas document Roots\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
vclient.updateDocument(cdoc);
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug("Time taken to update Session Document\t= "
+ Console.debug("Time taken to update Session Document\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
recover_objectMappingBackup();
storedviews = 0;
}
- Cache.log.debug("Finished updating from document change.");
+ Console.debug("Finished updating from document change.");
disableGui(false);
return storedviews;
}
@Override
public void propertyChange(PropertyChangeEvent evt)
{
- Cache.log.debug("Dealing with document update event.");
+ Console.debug("Dealing with document update event.");
client.dealWithDocumentUpdate(false);
- Cache.log.debug("finished dealing with event.");
+ Console.debug("finished dealing with event.");
}
});
- Cache.log.debug("Added Jalview handler for vamsas document updates.");
+ Console.debug("Added Jalview handler for vamsas document updates.");
}
private void addStoreDocumentHandler()
{
if (client.promptUser)
{
- Cache.log.debug(
+ Console.debug(
"Asking user if the vamsas session should be stored.");
int reply = JvOptionPane.showInternalConfirmDialog(
Desktop.desktop,
if (reply == JvOptionPane.YES_OPTION)
{
- Cache.log.debug("Prompting for vamsas store filename.");
+ Console.debug("Prompting for vamsas store filename.");
Desktop.instance.vamsasSave_actionPerformed(null);
- Cache.log
- .debug("Finished attempt at storing document.");
+ Console.debug("Finished attempt at storing document.");
}
- Cache.log.debug(
+ Console.debug(
"finished dealing with REQUESTTOCLOSE event.");
}
else
{
- Cache.log.debug(
+ Console.debug(
"Ignoring store document request (promptUser==false)");
}
}
});
- Cache.log.debug("Added Jalview handler for vamsas document updates.");
+ Console.debug("Added Jalview handler for vamsas document updates.");
}
public void disableGui(boolean b)
} catch (Exception e)
{
// Complain to GUI
- Cache.log.error("Failed to join vamsas session.", e);
+ Console.error("Failed to join vamsas session.", e);
vclient = null;
}
try
{
return;
}
- // if (Cache.log.isDebugEnabled())
+ // if (Cache.isDebugEnabled())
// {
- // Cache.log.debug("Received MouseOverMessage "+mm.getVorbaID()+"
+ // Cache.debug("Received MouseOverMessage "+mm.getVorbaID()+"
// "+mm.getPosition());
// }
Object jvobj = vobj2jv.get(mm.getVorbaID());
if (jvobj != null && jvobj instanceof SequenceI)
{
last = mstring;
- // Cache.log.debug("Handling Mouse over "+mm.getVorbaID()+"
+ // Cache.debug("Handling Mouse over "+mm.getVorbaID()+"
// bound to "+jvobj+" at "+mm.getPosition());
// position is character position in aligned sequence
ssm.mouseOverVamsasSequence((SequenceI) jvobj,
if (v != null)
{
// this should really be a trace message.
- // Cache.log.debug("Mouse over " + v.getId() + " bound to "
+ // Cache.debug("Mouse over " + v.getId() + " bound to "
// + seq + " at " + index);
last = seq;
i = index;
{
if (vobj2jv == null)
{
- Cache.log.warn(
+ Console.warn(
"Selection listener still active for dead session.");
// not in a session.
return;
if (sm != null)
{
sm.validate(); // debug
- Cache.log.debug("Selection Message\n" + sm.getRawMessage());
+ Console.debug("Selection Message\n" + sm.getRawMessage());
pm.sendMessage(sm);
}
}
ssm.addSelectionListener(selecter);
} catch (Exception e)
{
- Cache.log.error("Failed to init Vamsas Picking", e);
+ Console.error("Failed to init Vamsas Picking", e);
}
}
}
import compbio.metadata.Preset;
import compbio.metadata.PresetManager;
import compbio.metadata.RunnerConfig;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.OptsAndParamsPage.OptionBox;
import jalview.gui.OptsAndParamsPage.ParamBox;
import jalview.util.MessageManager;
if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
{
final String setname = (String) setName.getSelectedItem();
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug("Item state changed for " + setname
+ Console.debug("Item state changed for " + setname
+ " (handling ? " + !settingDialog + ")");
}
if (settingDialog)
package jalview.gui;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.util.MessageManager;
}
} catch (IOException e)
{
- Cache.log.info("Failed to parse parameter file " + pfile
+ Console.info("Failed to parse parameter file " + pfile
+ " (Check that all JALVIEW_WSPARAMFILES entries are valid!)",
e);
}
{
if (filename != null && !((outfile = new File(filename)).canWrite()))
{
- Cache.log.warn("Can't write to " + filename
+ Console.warn("Can't write to " + filename
+ " - Prompting for new file to write to.");
filename = null;
}
}
if (outfile != null)
{
- String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES",
+ String paramFiles = Cache.getDefault("WS_PARAM_FILES",
filename);
if (paramFiles.indexOf(filename) == -1)
{
parameterSet.setSourceFile(filename);
} catch (Exception e)
{
- Cache.log.error("Couldn't write parameter file to " + outfile, e);
+ Console.error("Couldn't write parameter file to " + outfile, e);
}
}
}
/*
*
- * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ * JalviewFileChooser chooser = new JalviewFileChooser(Cache
* .getProperty("LAST_DIRECTORY"), new String[] { "jc" }, new String[] {
* "Jalview User Colours" }, "Jalview User Colours"); chooser.setFileView(new
* jalview.io.JalviewFileView());
* int value = chooser.showOpenDialog(this);
*
* if (value == JalviewFileChooser.APPROVE_OPTION) { File choice =
- * chooser.getSelectedFile(); jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- * choice.getParent()); String defaultColours = jalview.bin.Cache.getDefault(
+ * chooser.getSelectedFile(); Cache.setProperty("LAST_DIRECTORY",
+ * choice.getParent()); String defaultColours = Cache.getDefault(
* "USER_DEFINED_COLOURS", choice.getPath()); if
* (defaultColours.indexOf(choice.getPath()) == -1) { defaultColours =
* defaultColours.concat("|") .concat(choice.getPath()); } (non-Javadoc)
{
return;
}
- String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES", "");
+ String paramFiles = Cache.getDefault("WS_PARAM_FILES", "");
if (paramFiles.indexOf(filename) > -1)
{
String nparamFiles = new String();
nparamFiles = nparamFiles.concat("|").concat(fl);
}
}
- jalview.bin.Cache.setProperty("WS_PARAM_FILES", nparamFiles);
+ Cache.setProperty("WS_PARAM_FILES", nparamFiles);
}
try
}
} catch (Exception e)
{
- Cache.log.error(
+ Console.error(
"Exception when trying to delete webservice user preset: ",
e);
}
import javax.swing.JTable;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
{
pdbEntry = new PDBEntry();
pdbEntry.setId(pdbIdStr);
+ pdbEntry.setAuthoritative(true);
try
{
pdbEntry.setType(PDBEntry.Type.valueOf(strucFormat));
} catch (Exception q)
{
- Cache.log.warn("Unknown filetype for 3D Beacons Model from: "
+ Console.warn("Unknown filetype for 3D Beacons Model from: "
+ strucFormat + " - " + pdbIdStr + " - " + modelPage);
}
import java.util.TreeMap;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
{
String tempfilename = file.getName();
File tempdir = file.getParentFile();
- Cache.trace(
+ Console.trace(
"BACKUPFILES [file!=null] attempting to create temp file for "
+ tempfilename + " in dir " + tempdir);
temp = File.createTempFile(tempfilename,
TEMP_FILE_EXT + newTempFileSuffix, tempdir);
- Cache.debug(
+ Console.debug(
"BACKUPFILES using temp file " + temp.getAbsolutePath());
}
else
{
- Cache.trace(
+ Console.trace(
"BACKUPFILES [file==null] attempting to create default temp file "
+ DEFAULT_TEMP_FILE + " with extension "
+ TEMP_FILE_EXT);
}
} catch (IOException e)
{
- Cache.error("Could not create temp file to save to (IOException)");
- Cache.error(e.getMessage());
- Cache.debug(Cache.getStackTraceString(e));
+ Console.error("Could not create temp file to save to (IOException)");
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
} catch (Exception e)
{
- Cache.error("Exception creating temp file for saving");
- Cache.debug(Cache.getStackTraceString(e));
+ Console.error("Exception creating temp file for saving");
+ Console.debug(Cache.getStackTraceString(e));
}
this.setTempFile(temp);
}
public static void classInit()
{
- Cache.initLogger();
- Cache.trace("BACKUPFILES classInit");
+ Console.initLogger();
+ Console.trace("BACKUPFILES classInit");
boolean e = Cache.getDefault(ENABLED, !Platform.isJS());
setEnabled(e);
- Cache.trace("BACKUPFILES " + (e ? "enabled" : "disabled"));
+ Console.trace("BACKUPFILES " + (e ? "enabled" : "disabled"));
BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
.getSavedBackupEntry();
- Cache.trace("BACKUPFILES preset scheme " + bfpe.toString());
+ Console.trace("BACKUPFILES preset scheme " + bfpe.toString());
setConfirmDelete(bfpe.confirmDelete);
- Cache.trace("BACKUPFILES confirm delete " + bfpe.confirmDelete);
+ Console.trace("BACKUPFILES confirm delete " + bfpe.confirmDelete);
}
public static void setEnabled(boolean flag)
path = this.getTempFile().getCanonicalPath();
} catch (IOException e)
{
- Cache.error("IOException when getting Canonical Path of temp file '"
+ Console.error("IOException when getting Canonical Path of temp file '"
+ this.getTempFile().getName() + "'");
- Cache.debug(Cache.getStackTraceString(e));
+ Console.debug(Cache.getStackTraceString(e));
}
return path;
}
|| suffix.length() == 0)
{
// nothing to do
- Cache.debug("BACKUPFILES rollBackupFiles nothing to do." + ", "
+ Console.debug("BACKUPFILES rollBackupFiles nothing to do." + ", "
+ "filename: " + (file != null ? file.getName() : "null")
+ ", " + "file exists: " + file.exists() + ", " + "enabled: "
+ enabled + ", " + "max: " + max + ", " + "suffix: '" + suffix
return true;
}
- Cache.trace("BACKUPFILES rollBackupFiles starting");
+ Console.trace("BACKUPFILES rollBackupFiles starting");
String dir = "";
File dirFile;
{
dirFile = file.getParentFile();
dir = dirFile.getCanonicalPath();
- Cache.trace("BACKUPFILES dir: " + dir);
+ Console.trace("BACKUPFILES dir: " + dir);
} catch (Exception e)
{
- Cache.error("Could not get canonical path for file '" + file + "'");
- Cache.error(e.getMessage());
- Cache.debug(Cache.getStackTraceString(e));
+ Console.error("Could not get canonical path for file '" + file + "'");
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
return false;
}
String filename = file.getName();
String basename = filename;
- Cache.trace("BACKUPFILES filename is " + filename);
+ Console.trace("BACKUPFILES filename is " + filename);
boolean ret = true;
// Create/move backups up one
File[] backupFiles = dirFile.listFiles(bff);
int nextIndexNum = 0;
- Cache.trace("BACKUPFILES backupFiles.length: " + backupFiles.length);
+ Console.trace("BACKUPFILES backupFiles.length: " + backupFiles.length);
if (backupFiles.length == 0)
{
// No other backup files. Just need to move existing file to backupfile_1
- Cache.trace(
+ Console.trace(
"BACKUPFILES no existing backup files, setting index to 1");
nextIndexNum = 1;
}
if (reverseOrder)
{
// backup style numbering
- Cache.trace("BACKUPFILES rolling files in reverse order");
+ Console.trace("BACKUPFILES rolling files in reverse order");
int tempMax = noMax ? -1 : max;
// noMax == true means no limits
// no "oldest" file to delete
previousFile = backupfile_n;
fileToBeDeleted = null;
- Cache.trace("BACKUPFILES No oldest file to delete");
+ Console.trace("BACKUPFILES No oldest file to delete");
continue;
}
File replacementFile = backupfile_n;
long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
long replacementFileLMT = replacementFile.lastModified();
- Cache.trace("BACKUPFILES fileToBeDeleted is "
+ Console.trace("BACKUPFILES fileToBeDeleted is "
+ fileToBeDeleted.getAbsolutePath());
- Cache.trace("BACKUPFILES replacementFile is "
+ Console.trace("BACKUPFILES replacementFile is "
+ backupfile_n.getAbsolutePath());
try
.format(fileToBeDeletedLMT);
String replacementFileLMTString = sdf
.format(replacementFileLMT);
- Cache.warn("WARNING! I am set to delete backupfile "
+ Console.warn("WARNING! I am set to delete backupfile "
+ fileToBeDeleted.getName()
+ " has modification time "
+ fileToBeDeletedLMTString
boolean delete = confirmNewerDeleteFile(fileToBeDeleted,
replacementFile, true);
- Cache.trace("BACKUPFILES " + (delete ? "confirmed" : "not")
+ Console.trace("BACKUPFILES " + (delete ? "confirmed" : "not")
+ " deleting file "
+ fileToBeDeleted.getAbsolutePath()
+ " which is newer than "
}
else
{
- Cache.debug("BACKUPFILES moving "
+ Console.debug("BACKUPFILES moving "
+ fileToBeDeleted.getAbsolutePath() + " to "
+ oldestTempFile.getAbsolutePath());
moveFileToFile(fileToBeDeleted, oldestTempFile);
}
else
{
- Cache.debug("BACKUPFILES going to move "
+ Console.debug("BACKUPFILES going to move "
+ fileToBeDeleted.getAbsolutePath() + " to "
+ oldestTempFile.getAbsolutePath());
moveFileToFile(fileToBeDeleted, oldestTempFile);
} catch (Exception e)
{
- Cache.error(
+ Console.error(
"Error occurred, probably making new temp file for '"
+ fileToBeDeleted.getName() + "'");
- Cache.error(Cache.getStackTraceString(e));
+ Console.error(Cache.getStackTraceString(e));
}
// reset
}
bfsb.append(backupFiles[i].getName());
}
- Cache.trace("BACKUPFILES backupFiles: " + bfsb.toString());
+ Console.trace("BACKUPFILES backupFiles: " + bfsb.toString());
// noMax == true means keep all backup files
if ((!noMax) && bfTreeMap.size() >= max)
{
- Cache.trace("BACKUPFILES noMax: " + noMax + ", " + "max: " + max
+ Console.trace("BACKUPFILES noMax: " + noMax + ", " + "max: " + max
+ ", " + "bfTreeMap.size(): " + bfTreeMap.size());
// need to delete some files to keep number of backups to designated
// max.
int numToDelete = suffix.indexOf(NUM_PLACEHOLDER) > -1
? bfTreeMap.size() - max + 1
: 0;
- Cache.trace("BACKUPFILES numToDelete: " + numToDelete);
+ Console.trace("BACKUPFILES numToDelete: " + numToDelete);
// the "replacement" file is the latest backup file being kept (it's
// not replacing though)
File replacementFile = numToDelete < backupFiles.length
File fileToBeDeleted = backupFiles[i];
boolean delete = true;
- Cache.trace("BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
+ Console.trace("BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
boolean newer = false;
if (replacementFile != null)
String replacementFileLMTString = sdf
.format(replacementFileLMT);
- Cache.warn("WARNING! I am set to delete backupfile '"
+ Console.warn("WARNING! I am set to delete backupfile '"
+ fileToBeDeleted.getName()
+ "' has modification time "
+ fileToBeDeletedLMTString
{
// User has confirmed delete -- no need to add it to the list
fileToBeDeleted.delete();
- Cache.debug("BACKUPFILES deleting fileToBeDeleted: "
+ Console.debug("BACKUPFILES deleting fileToBeDeleted: "
+ fileToBeDeleted);
delete = false;
}
else
{
// keeping file, nothing to do!
- Cache.debug("BACKUPFILES keeping fileToBeDeleted: "
+ Console.debug("BACKUPFILES keeping fileToBeDeleted: "
+ fileToBeDeleted);
}
}
if (delete)
{
addDeleteFile(fileToBeDeleted);
- Cache.debug("BACKUPFILES addDeleteFile(fileToBeDeleted): "
+ Console.debug("BACKUPFILES addDeleteFile(fileToBeDeleted): "
+ fileToBeDeleted);
}
String latestBackupFilename = dir + File.separatorChar
+ BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
suffix, digits);
- Cache.trace("BACKUPFILES Moving old file [" + file
+ Console.trace("BACKUPFILES Moving old file [" + file
+ "] to latestBackupFilename [" + latestBackupFilename + "]");
// using boolean '&' instead of '&&' as don't want moveFileToFile attempt to
// be conditional (short-circuit)
ret = ret & moveFileToFile(file, new File(latestBackupFilename));
- Cache.debug("BACKUPFILES moving " + file + " to " + latestBackupFilename
+ Console.debug("BACKUPFILES moving " + file + " to " + latestBackupFilename
+ " was " + (ret ? "" : "NOT ") + "successful");
if (tidyUp)
{
- Cache.debug("BACKUPFILES tidying up files");
+ Console.debug("BACKUPFILES tidying up files");
tidyUpFiles();
}
saveFile = nextTempFile(ftbd.getName(), ftbd.getParentFile());
} catch (Exception e)
{
- Cache.error(
+ Console.error(
"Error when confirming to keep backup file newer than other backup files.");
e.printStackTrace();
}
for (int i = 0; i < deleteFiles.size(); i++)
{
File fileToDelete = deleteFiles.get(i);
- Cache.trace("BACKUPFILES about to delete fileToDelete:"
+ Console.trace("BACKUPFILES about to delete fileToDelete:"
+ fileToDelete);
fileToDelete.delete();
- Cache.warn("deleted '" + fileToDelete.getName() + "'");
+ Console.warn("deleted '" + fileToDelete.getName() + "'");
}
}
dirFile = file.getParentFile();
} catch (Exception e)
{
- Cache.error("Could not get canonical path for file '" + file + "'");
+ Console.error("Could not get canonical path for file '" + file + "'");
return new TreeMap<>();
}
int pos = deleteFiles.indexOf(fileToBeDeleted);
if (pos > -1)
{
- Cache.debug("BACKUPFILES not adding file "
+ Console.debug("BACKUPFILES not adding file "
+ fileToBeDeleted.getAbsolutePath()
+ " to the delete list (already at index" + pos + ")");
return true;
}
else
{
- Cache.debug("BACKUPFILES adding file "
+ Console.debug("BACKUPFILES adding file "
+ fileToBeDeleted.getAbsolutePath() + " to the delete list");
deleteFiles.add(fileToBeDeleted);
}
public static boolean moveFileToFile(File oldFile, File newFile)
{
- Cache.initLogger();
+ Console.initLogger();
boolean ret = false;
Path oldPath = Paths.get(oldFile.getAbsolutePath());
Path newPath = Paths.get(newFile.getAbsolutePath());
try
{
// delete destination file - not usually necessary but Just In Case...
- Cache.trace("BACKUPFILES deleting " + newFile.getAbsolutePath());
+ Console.trace("BACKUPFILES deleting " + newFile.getAbsolutePath());
newFile.delete();
- Cache.trace("BACKUPFILES moving " + oldFile.getAbsolutePath() + " to "
+ Console.trace("BACKUPFILES moving " + oldFile.getAbsolutePath() + " to "
+ newFile.getAbsolutePath());
Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
ret = true;
- Cache.trace("BACKUPFILES move seems to have succeeded");
+ Console.trace("BACKUPFILES move seems to have succeeded");
} catch (IOException e)
{
- Cache.warn("Could not move file '" + oldPath.toString() + "' to '"
+ Console.warn("Could not move file '" + oldPath.toString() + "' to '"
+ newPath.toString() + "'");
- Cache.error(e.getMessage());
- Cache.debug(Cache.getStackTraceString(e));
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
ret = false;
} catch (Exception e)
{
- Cache.error(e.getMessage());
- Cache.debug(Cache.getStackTraceString(e));
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
ret = false;
}
return ret;
import java.util.StringTokenizer;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.util.MessageManager;
public class BackupFilesPresetEntry
confirmDelete = Boolean.valueOf(st.nextToken());
} catch (Exception e)
{
- Cache.log.error("Error parsing backupfiles scheme '" + line + "'");
+ Console.error("Error parsing backupfiles scheme '" + line + "'");
}
return new BackupFilesPresetEntry(suffix, digits, reverse, keepAll,
*/
package jalview.io;
+import jalview.bin.Cache;
import jalview.gui.AlignmentPanel;
import jalview.gui.OOMWarning;
import jalview.json.binding.biojs.BioJSReleasePojo;
public static final String DEFAULT_DIR = System.getProperty("user.home")
+ File.separatorChar + ".biojs_templates" + File.separatorChar;
- public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
+ public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = Cache
.getDefault("biojs_template_directory", DEFAULT_DIR);
- public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache
+ public static final String BJS_TEMPLATE_GIT_REPO = Cache
.getDefault("biojs_template_git_repo",
"https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
import java.util.Map.Entry;
import java.util.TreeMap;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
/**
* Truncates (if necessary) the exon intervals to match 3 times the length of
- * the protein; also accepts 3 bases longer (for stop codon not included in
- * protein)
+ * the protein(including truncation for stop codon included in exon)
*
* @param proteinLength
* @param exon
int exonLength = MappingUtils.getLength(Arrays.asList(exon));
/*
- * if exon length matches protein, or is shorter, or longer by the
- * length of a stop codon (3 bases), then leave it unchanged
+ * if exon length matches protein, or is shorter, then leave it unchanged
*/
- if (expectedCdsLength >= exonLength
- || expectedCdsLength == exonLength - 3)
+ if (expectedCdsLength >= exonLength)
{
return exon;
}
int slashPos = line.indexOf('/');
if (slashPos == -1)
{
- Cache.log.error("Unexpected EMBL line ignored: " + line);
+ Console.error("Unexpected EMBL line ignored: " + line);
line = nextLine();
continue;
}
data.codonStart = Integer.parseInt(featureValue.trim());
} catch (NumberFormatException e)
{
- Cache.log.error("Invalid codon_start in XML for " + this.accession
+ Console.error("Invalid codon_start in XML for " + this.accession
+ ": " + e.getMessage());
}
}
}
else
{
- Cache.log.error("Ignoring CDS feature with no protein_id for "
+ Console.error("Ignoring CDS feature with no protein_id for "
+ sourceDb + ":" + accession);
}
{
if (this.accession == null || this.sequenceString == null)
{
- Cache.log.error("Failed to parse data from EMBL");
+ Console.error("Failed to parse data from EMBL");
return;
}
* workaround until we handle all 'location' formats fully
* e.g. X53828.1:60..1058 or <123..>289
*/
- Cache.log.error(String.format(
+ Console.error(String.format(
"Implementation Notice: EMBLCDS location '%s'not properly supported yet"
+ " - Making up the CDNA region of (%s:%s)... may be incorrect",
data.cdsLocation, sourceDb, this.accession));
if (peptideLength * 3 == completeCodonsLength)
{
// this might occur for CDS sequences where no features are marked
- Cache.log.warn("Assuming no stop codon at end of cDNA fragment");
+ Console.warn("Assuming no stop codon at end of cDNA fragment");
mappedDnaEnd = dna.getEnd();
}
else if ((peptideLength + 1) * 3 == completeCodonsLength)
{
- Cache.log.warn("Assuming stop codon at end of cDNA fragment");
+ Console.warn("Assuming stop codon at end of cDNA fragment");
mappedDnaEnd = dna.getEnd() - 3;
}
return MappingUtils.rangeListToArray(ranges);
} catch (ParseException e)
{
- Cache.log.warn(
+ Console.warn(
String.format("Not parsing inexact CDS location %s in ENA %s",
location, accession));
return new int[] {};
String[] tokens = line.split(WHITESPACE);
if (tokens.length < 2)
{
- Cache.log.error("Ignoring bad EMBL line for " + this.accession
+ Console.error("Ignoring bad EMBL line for " + this.accession
+ ": " + line);
break;
}
import java.io.IOException;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.util.DBRefUtils;
this.length = Integer.valueOf(bits[0]);
} catch (NumberFormatException e)
{
- Cache.log.error("bad length read in flatfile, line: " + line);
+ Console.error("bad length read in flatfile, line: " + line);
}
}
try
{
- alignFrame.setMaximum(jalview.bin.Cache
+ alignFrame.setMaximum(Cache
.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsModelI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.util.MessageManager;
import jalview.util.Platform;
{
if (!input.markSupported())
{
- Cache.log.error(
+ Console.error(
"FileParse.izGzipStream: input stream must support mark/reset");
return false;
}
private void init()
{
- if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+ if (Cache.getDefault("STRUCT_FROM_PDB", true))
{
- annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+ annotFromStructure = Cache.getDefault("ADD_TEMPFACT_ANN",
true);
- localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+ localSecondaryStruct = Cache.getDefault("ADD_SS_ANN",
true);
- serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+ serviceSecondaryStruct = Cache.getDefault("USE_RNAVIEW",
true);
}
else
public boolean isEmbedData()
{
return Boolean.valueOf(
- jalview.bin.Cache.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
+ Cache.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
}
@Override
*/
package jalview.io;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
{
value = r.stringMatched(1);
}
- // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
+ // Cache.debug("from '" + field + "' matched '" + value +
// "'");
try
{
}
else
{
- // jalview.bin.Cache.log.debug(
+ // Cache.debug(
// "Ignoring non-Modeller description: invalid integer-like
// field '" + field + "'");
type = -1; /* invalid field! - throw the FieldSet away */
*/
package jalview.io;
-import java.util.Locale;
-
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
import jalview.util.Format;
import jalview.util.MessageManager;
-// import org.apache.log4j.*;
-
/**
* This class is supposed to parse a Stockholm format file into Jalview There
* are TODOs in this class: we do not know what the database source and version
{
private static final String ANNOTATION = "annotation";
-// private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
-//
-// private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
+ // private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+ //
+ // private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
public static final Regex DETECT_BRACKETS = new Regex(
"(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
- // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using NOT_RNASS first.
+ // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using
+ // NOT_RNASS first.
public static final String RNASS_BRACKETS = "<>[](){}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz";
// use the following regex to decide an annotations (whole) line is NOT an RNA
Regex openparen = new Regex("(<|\\[)", "(");
Regex closeparen = new Regex("(>|\\])", ")");
-// // Detect if file is RNA by looking for bracket types
-// Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
+ // // Detect if file is RNA by looking for bracket types
+ // Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
rend.optimize();
p.optimize();
if (dbr != null)
{
// we could get very clever here - but for now - just try to
- // guess accession type from type of sequence, source of alignment plus
+ // guess accession type from type of sequence, source of alignment
+ // plus
// structure
// of accession
guessDatabaseFor(seqO, dbr, dbsource);
treeName = an.stringMatched(2);
treeString = new StringBuffer();
}
- // TODO: JAL-3532 - this is where GF comments and database references are lost
- // suggest overriding this method for Stockholm files to catch and properly
+ // TODO: JAL-3532 - this is where GF comments and database
+ // references are lost
+ // suggest overriding this method for Stockholm files to catch and
+ // properly
// process CC, DR etc into multivalued properties
setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
}
}
if (dbsource == null)
{
- // make up an origin based on whether the sequence looks like it is nucleotide
+ // make up an origin based on whether the sequence looks like it is
+ // nucleotide
// or protein
dbsource = (seqO.isProtein()) ? "PFAM" : "RFAM";
}
return ref.getSource().toString() + " ; "
+ ref.getAccessionId().toString();
}
+
@Override
public String print(SequenceI[] s, boolean jvSuffix)
{
*/
package jalview.io;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.GraphLine;
Vobject obj = getjv2vObj(seqsetidobj);
if (obj != null && !(obj instanceof Alignment))
{
- Cache.log.warn(
+ Console.warn(
"IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:"
+ seqsetidobj + " to object " + obj);
}
}
else
{
- Cache.log.warn("Unexpected mapping for Jalview String Object ID "
+ Console.warn("Unexpected mapping for Jalview String Object ID "
+ seqsetidobj + " to another jalview dataset object "
+ seqsetidobj);
}
}
}
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Returning null VorbaID binding for jalview object " + jvobj);
}
return null;
if (id == null)
{
id = cdoc.registerObject(vobj);
- Cache.log.debug(
+ Console.debug(
"Registering new object and returning null for getvObj2jv");
return null;
}
if (id == null || vobj.getVorbaId() == null
|| cdoc.getObject(id) != vobj)
{
- Cache.log.error("Failed to get id for "
+ Console.error("Failed to get id for "
+ (vobj.isRegisterable() ? "registerable"
: "unregisterable")
+ " object " + vobj);
if (vobj2jv.containsKey(vobj.getVorbaId())
&& !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
- Cache.log.debug(
+ Console.debug(
"Warning? Overwriting existing vamsas id binding for "
+ vobj.getVorbaId(),
new Exception(MessageManager.getString(
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
{
- Cache.log.debug(
+ Console.debug(
"Warning? Overwriting existing jalview object binding for "
+ jvobj,
new Exception("Overwriting jalview object binding."));
}
/*
- * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
+ * Cache.error("Attempt to make conflicting object binding! "+vobj+" id "
* +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+"
* already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to
* bindjvvobj")); }
*/
// we just update the hash's regardless!
- Cache.log.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
+ Console.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
vobj2jv.put(vobj.getVorbaId(), jvobj);
// JBPNote - better implementing a hybrid invertible hash.
jv2vobj.put(jvobj, vobj.getVorbaId());
DataSet dataset = null;
if (jds == null)
{
- Cache.log.warn("Creating new dataset for an alignment.");
+ Console.warn("Creating new dataset for an alignment.");
jal.setDataset(null);
jds = jal.getDataset();
}
if (dataset == null)
{
- Cache.log.warn("Creating new vamsas dataset for alignment view "
+ Console.warn("Creating new vamsas dataset for alignment view "
+ av.getSequenceSetId());
// we create a new dataset on the default vamsas root.
root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.
if (aa[i].groupRef != null)
{
// TODO: store any group associated annotation references
- Cache.log.warn(
+ Console.warn(
"Group associated sequence annotation is not stored in VAMSAS document.");
continue;
}
// LOCK METHODS)
{
// verify annotation - update (perhaps)
- Cache.log.info(
+ Console.info(
"update alignment sequence annotation. not yet implemented.");
}
else
{
// verify annotation - update (perhaps)
- Cache.log.info(
+ Console.info(
"updated alignment sequence annotation added.");
}
}
}
if (getjv2vObj(jvalsq.getDatasetSequence()) == null)
{
- Cache.log.warn(
+ Console.warn(
"Serious Implementation error - Unbound dataset sequence in alignment: "
+ jvalsq.getDatasetSequence());
}
alseq.setDescription(valseq.getDescription());
modal = true;
}
- if (modal && Cache.log.isDebugEnabled())
+ if (modal && Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Updating apparently edited sequence " + alseq.getName());
}
}
}
else
{
- Cache.log.error(
+ Console.error(
"Invalid dataset sequence id (null) for alignment sequence "
+ valseq.getVorbaId());
}
@Override
public JarInputStream getJarInputStream() throws IOException
{
- jalview.bin.Cache.log.debug(
+ Console.debug(
"Returning client input stream for Jalview from Vamsas Document.");
return new JarInputStream(cappdata.getClientInputStream());
}
@Override
public JarInputStream getJarInputStream() throws IOException
{
- jalview.bin.Cache.log.debug(
+ Console.debug(
"Returning user input stream for Jalview from Vamsas Document.");
return new JarInputStream(cappdata.getUserInputStream());
}
// TODO implement this : af.getNumberOfViews
String seqsetidobj = av.getSequenceSetId();
views = Desktop.getViewports(seqsetidobj);
- Cache.log
- .debug("Found " + (views == null ? " no " : "" + views.length)
+ Console.debug("Found " + (views == null ? " no " : "" + views.length)
+ " views for '" + av.getSequenceSetId() + "'");
if (views.length > 1)
{
} catch (Exception e)
{
// TODO raise GUI warning if user requests it.
- jalview.bin.Cache.log.error(
+ Console.error(
"Couldn't update jalview client application data. Giving up - local settings probably lost.",
e);
}
}
else
{
- jalview.bin.Cache.log.error(
+ Console.error(
"Couldn't access client application data for vamsas session. This is probably a vamsas client bug.");
}
}
int jremain = 0;
if (jdataset == null)
{
- Cache.log.debug("Initialising new jalview dataset fields");
+ Console.debug("Initialising new jalview dataset fields");
newds = true;
dsseqs = new Vector();
}
else
{
- Cache.log.debug("Update jalview dataset from vamsas.");
+ Console.debug("Update jalview dataset from vamsas.");
jremain = jdataset.getHeight();
dsseqs = jdataset.getSequences();
}
dsseqs.set(i, null);
}
jdataset = new jalview.datamodel.Alignment(seqs);
- Cache.log.debug("New vamsas dataset imported into jalview.");
+ Console.debug("New vamsas dataset imported into jalview.");
bindjvvobj(jdataset, dataset);
}
// ////////
// annotations
if (dsSeq == null)
{
- jalview.bin.Cache.log.warn(
+ Console.warn(
"Couldn't resolve jalview sequenceI for dataset object reference "
+ ((Vobject) dataset
.getDataSetAnnotations(dsa)
// JBPNote: we could just add them to all alignments but
// that may complicate cross references in the jalview
// datamodel
- Cache.log.warn(
+ Console.warn(
"Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");
}
}
}
else
{
- Cache.log.warn(
+ Console.warn(
"Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features.");
}
}
// OBJECT LOCK
// METHODS)
{
- Cache.log.info(
+ Console.info(
"UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
// TODO: should at least replace with new one - otherwise
// things will break
dsseqs.set(i, null);
}
jal = new jalview.datamodel.Alignment(seqs);
- Cache.log.debug("New vamsas alignment imported into jalview "
+ Console.debug("New vamsas alignment imported into jalview "
+ alignment.getVorbaId().getId());
jal.setDataset(jdataset);
}
// jan.update(getjAlignmentAnnotation(jal, an[a])); // update
// from another annotation object in place.
- Cache.log.debug(
+ Console.debug(
"update from vamsas alignment annotation to existing jalview alignment annotation.");
if (an[j].getModifiable() == null) // TODO: USE VAMSAS
// LIBRARY OBJECT LOCK
{
// TODO: user defined annotation is totally mutable... - so
// load it up or throw away if locally edited.
- Cache.log.info(
+ Console.info(
"NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
}
// TODO: compare annotation element rows
AlignFrame alignFrame;
if (av == null)
{
- Cache.log.debug("New alignframe for alignment "
+ Console.debug("New alignframe for alignment "
+ alignment.getVorbaId());
// ///////////////////////////////
// construct alignment view
}
// TODO: automatically create meaningful title for a vamsas
// alignment using its provenance.
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
title = title + "(" + alignment.getVorbaId() + ")";
vstree.UpdateSequenceTreeMap(tp);
} catch (RuntimeException e)
{
- Cache.log.warn("update of labels failed.", e);
+ Console.warn("update of labels failed.", e);
}
}
else
{
- Cache.log.warn("Cannot create tree for tree " + t
+ Console.warn("Cannot create tree for tree " + t
+ " in document ("
+ alignment.getTree(t).getVorbaId());
}
if (anot[row][pos] != null)
{
// only time this should happen is if the After flag is set.
- Cache.log.debug("Ignoring duplicate annotation site at " + pos);
+ Console.debug("Ignoring duplicate annotation site at " + pos);
continue;
}
if (anot[1 - row][pos] != null)
else if (glyphs[g].getDict().equals(
uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
{
- Cache.log.debug("ignoring hydrophobicity glyph marker.");
+ Console.debug("ignoring hydrophobicity glyph marker.");
AeContent[HASHPHOB] = true;
char c = (dc = glyphs[g].getContent()).charAt(0);
// dc may get overwritten - but we still set the colour.
}
else
{
- Cache.log.debug(
+ Console.debug(
"IMPLEMENTATION TODO: Ignoring unknown glyph type "
+ glyphs[g].getDict());
}
AeContent[HASVALS] = true;
if (ae[aa].getValueCount() > 1)
{
- Cache.log.warn(
+ Console.warn(
"ignoring additional " + (ae[aa].getValueCount() - 1)
+ " values in annotation element.");
}
}
else
{
- Cache.log.warn("Ignoring out of bound annotation element " + aa
+ Console.warn("Ignoring out of bound annotation element " + aa
+ " in " + annotation.getVorbaId().getId());
}
}
val = Float.valueOf(props[p].getContent());
} catch (Exception e)
{
- Cache.log.warn("Failed to parse threshold property");
+ Console.warn("Failed to parse threshold property");
}
if (val != null)
{
}
if (parsedRangeAnnotation == null)
{
- Cache.log.debug(
+ Console.debug(
"Inserting empty annotation row elements for a whole-alignment annotation.");
}
else
{
if (parsedRangeAnnotation[3] != null)
{
- Cache.log.warn("Ignoring 'After' annotation row in "
+ Console.warn("Ignoring 'After' annotation row in "
+ annotation.getVorbaId());
}
jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) parsedRangeAnnotation[2];
}
if (annotation.getLinkCount() > 0)
{
- Cache.log.warn("Ignoring " + annotation.getLinkCount()
+ Console.warn("Ignoring " + annotation.getLinkCount()
+ "links added to AlignmentAnnotation.");
}
if (annotation.getModifiable() == null
}
} catch (Exception e)
{
- Cache.log.info(
+ Console.info(
"UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
}
return jan;
DataSet dataset = null;
if (jal.getDataset() == null)
{
- Cache.log.warn("Creating new dataset for an alignment.");
+ Console.warn("Creating new dataset for an alignment.");
jal.setDataset(null);
}
dataset = (DataSet) ((Alignment) getjv2vObj(
if (dataset == null)
{
dataset = (DataSet) getjv2vObj(jal.getDataset());
- Cache.log.error(
+ Console.error(
"Can't find the correct dataset for the alignment in this view. Creating new one.");
}
}
else
{
- Cache.log.warn(
+ Console.warn(
"NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR "
+ dmps[smp].getDisplayId(true) + " to "
+ mps[smp].getTo().getName());
*/
package jalview.io.vamsas;
-import jalview.bin.Cache;
-import jalview.io.VamsasAppDatastore;
-import jalview.util.MessageManager;
-
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Vector;
+import jalview.bin.Console;
+import jalview.io.VamsasAppDatastore;
+import jalview.log.JLoggerLog4j;
+import jalview.util.MessageManager;
import uk.ac.vamsas.client.IClientDocument;
import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.client.VorbaId;
/**
* shared log instance
*/
- protected static org.apache.log4j.Logger log = org.apache.log4j.Logger
+ protected static JLoggerLog4j log = JLoggerLog4j
.getLogger(DatastoreItem.class);
/**
{
return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
}
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Returning null VorbaID binding for jalview object " + jvobj);
}
return null;
if (id == null)
{
id = cdoc.registerObject(vobj);
- Cache.log.debug(
+ Console.debug(
"Registering new object and returning null for getvObj2jv");
return null;
}
if (id == null || vobj.getVorbaId() == null
|| cdoc.getObject(id) != vobj)
{
- Cache.log.error("Failed to get id for "
+ Console.error("Failed to get id for "
+ (vobj.isRegisterable() ? "registerable"
: "unregisterable")
+ " object " + vobj);
if (vobj2jv.containsKey(vobj.getVorbaId())
&& !(vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
- Cache.log.debug(
+ Console.debug(
"Warning? Overwriting existing vamsas id binding for "
+ vobj.getVorbaId(),
new Exception(MessageManager.getString(
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
{
- Cache.log.debug(
+ Console.debug(
"Warning? Overwriting existing jalview object binding for "
+ jvobj,
new Exception(MessageManager.getString(
"exception.overwriting_jalview_id_binding")));
}
/*
- * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
+ * Cache.error("Attempt to make conflicting object binding! "+vobj+" id "
* +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+"
* already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to
* bindjvvobj")); }
*/
// we just update the hash's regardless!
- Cache.log.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
+ Console.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
vobj2jv.put(vobj.getVorbaId(), jvobj);
// JBPNote - better implementing a hybrid invertible hash.
jv2vobj.put(jvobj, vobj.getVorbaId());
{
if (this.jvobj != null && this.vobj != null)
{
- Cache.log.debug("updating dsobj registry. ("
- + this.getClass().getName() + ")");
+ Console.debug("updating dsobj registry. (" + this.getClass().getName()
+ + ")");
}
this.jvobj = jvobj;
this.vobj = vobj;
import java.util.Iterator;
import java.util.Map;
+import jalview.log.JLoggerLog4j;
+
public class DatastoreRegistry implements AutoCloseable
{
- protected static org.apache.log4j.Logger log = org.apache.log4j.Logger
+ protected static JLoggerLog4j log = JLoggerLog4j
.getLogger(DatastoreRegistry.class);
/**
*/
package jalview.io.vamsas;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
import jalview.io.VamsasAppDatastore;
}
else
{
- jalview.bin.Cache.log.debug(
+ Console.debug(
"Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
}
// TODO: Jalview ignores all the other maps
if (vobj.getMapCount() > 1)
{
- jalview.bin.Cache.log
- .debug("Ignoring additional mappings on DbRef: "
+ Console.debug("Ignoring additional mappings on DbRef: "
+ jvobj.getSource() + ":" + jvobj.getAccessionId());
}
jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
{
DbRef vobj = (DbRef) this.vobj;
DBRefEntry jvobj = (DBRefEntry) this.jvobj;
- jalview.bin.Cache.log
- .debug("Conflict in dbentry update for " + vobj.getAccessionId()
+ Console.debug("Conflict in dbentry update for " + vobj.getAccessionId()
+ vobj.getSource() + " " + vobj.getVorbaId());
// TODO Auto-generated method stub
// TODO: Jalview ignores all the other maps
if (vobj.getMapCount() > 1)
{
- jalview.bin.Cache.log
- .debug("Ignoring additional mappings on DbRef: "
+ Console.debug("Ignoring additional mappings on DbRef: "
+ jvobj.getSource() + ":" + jvobj.getAccessionId());
}
jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
}
else
{
- jalview.bin.Cache.log.debug(
+ Console.debug(
"Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
}
}
*/
package jalview.io.vamsas;
+import jalview.bin.Console;
import jalview.io.VamsasAppDatastore;
import jalview.util.MessageManager;
{
if (!map.getLocal().hasUnit() || map.getMapped().hasUnit())
{
- jalview.bin.Cache.log
- .warn("using default mapping length of 1:1 for map "
+ Console.warn("using default mapping length of 1:1 for map "
+ (map.isRegistered() ? map.getVorbaId().toString()
: ("<no Id registered> " + map.toString())));
}
*/
package jalview.io.vamsas;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.VamsasAppDatastore;
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
if (dsa.getSeqRefCount() != 1)
{
- Cache.log.warn("Not binding " + dsa.getVorbaId()
+ Console.warn("Not binding " + dsa.getVorbaId()
+ " to Sequence Feature - has multiple dataset sequence references.");
return;
}
if (dsa.getSeqRefCount() != 1)
{
replaceJvObjMapping(feature, null);
- Cache.log.warn(
+ Console.warn(
"Binding of annotation to jalview feature has changed. Removing binding and recreating.");
doSync(); // re-verify bindings.
}
getDSAnnotationFromJalview(dsa, feature);
if (oldref != dsa.hashCode())
{
- Cache.log
- .debug("Updated dataset sequence annotation from feature.");
+ Console.debug("Updated dataset sequence annotation from feature.");
addProvenance(dsa.getProvenance(), "modified");
}
}
{
// conflicting update from document - we cannot map this feature anymore.
replaceJvObjMapping(feature, null);
- Cache.log.warn("annotation (" + dsa.getVorbaId()
+ Console.warn("annotation (" + dsa.getVorbaId()
+ " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
// - consider deleting the feature ?
dsSeq.deleteFeature(feature);
vSeg.setInclusive(true);
if (dsa.getSegCount() > 1)
{
- Cache.log.debug(
+ Console.debug(
"About to destroy complex annotation in vamsas document mapped to sequence feature ("
+ dsa.getVorbaId() + ")");
}
*/
package jalview.io.vamsas;
+import jalview.bin.Console;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
}
if (from != null && sequenceMapping.getLoc() != from)
{
- jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + from
+ Console.warn("Probable IMPLEMENTATION ERROR: " + from
+ " doesn't match the local mapping sequence.");
}
if (ds != null && sequenceMapping.is__stored_in_document()
&& sequenceMapping.getV_parent() != ds)
{
- jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + ds
+ Console.warn("Probable IMPLEMENTATION ERROR: " + ds
+ " doesn't match the parent of the bound sequence mapping object.");
}
}
SequenceType to = (SequenceType) getjv2vObj(jvto);
if (to == null)
{
- jalview.bin.Cache.log.warn(
+ Console.warn(
"FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
return;
}
if (!dnaToProt)
{
- jalview.bin.Cache.log.warn(
+ Console.warn(
"Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
return;
}
// mapping
bindjvvobj(mjvmapping.getMap(), sequenceMapping);
- jalview.bin.Cache.log.debug(
+ Console.debug(
"Successfully created mapping " + sequenceMapping.getVorbaId());
}
// private void update(jalview.util.MapList mjvmapping,
// SequenceMapping sequenceMapping)
{
- jalview.bin.Cache.log
- .error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
+ Console.error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
}
private void update(SequenceMapping sequenceMapping,
jalview.datamodel.Mapping mjvmapping)
{
- jalview.bin.Cache.log
- .error("Not implemented: Update DBRef Mapping from Jalview");
+ Console.error("Not implemented: Update DBRef Mapping from Jalview");
}
private void update(jalview.datamodel.Mapping mjvmapping,
SequenceMapping sequenceMapping)
{
- jalview.bin.Cache.log.error(
+ Console.error(
"Not implemented: Jalview Update Sequence DBRef Mapping");
}
}
if (sdloc == null || sdmap == null)
{
- jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
+ Console.info("Ignoring non sequence-sequence mapping");
return;
}
mobj = this.getvObj2jv(sdloc);
if (from == null || to == null)
{
- jalview.bin.Cache.log.error(
+ Console.error(
"Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
return;
}
{
if (from.getDBRefs() == null && to.getDBRefs() == null)
{
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Not matching conjugate refs for "
+ Console.debug("Not matching conjugate refs for "
+ from.getName() + " and " + to.getName());
}
return;
}
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Matching conjugate refs for "
+ Console.debug("Matching conjugate refs for "
+ from.getName() + " and " + to.getName());
}
List<DBRefEntry> fdb = from.getDBRefs();
boolean fmpnnl = (fmp != null);
// if (fmpnnl && fmp.getTo()!=null)
// {
- // jalview.bin.Cache.log.debug("Not overwriting existing To reference in
+ // Cache.debug("Not overwriting existing To reference in
// "+fe);
// continue;
// }
import jalview.analysis.TreeBuilder;
import jalview.analysis.TreeModel;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
}
} catch (Exception e)
{
- Cache.log.warn("Problems parsing treefile '"
+ Console.warn("Problems parsing treefile '"
+ tree.getNewick(0).getContent() + "'", e);
}
}
@Override
public void conflict()
{
- Cache.log.info(
+ Console.info(
"Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
}
* idata[0] != null) { inputData = (AlignmentView) idata[0]; } ntree =
* getNtree(); title = tree.getNewick(0).getTitle(); if (title == null ||
* title.length() == 0) { title = tree.getTitle(); // hack!!!! } } catch
- * (Exception e) { Cache.log.warn("Problems parsing treefile '" +
+ * (Exception e) { Cache.warn("Problems parsing treefile '" +
* tree.getNewick(0).getContent() + "'", e); }
*/
log.debug("Update the local tree in jalview from the document.");
*/
private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
{
- Cache.log.debug("Making Tree provenance for " + tp.getTitle());
+ Console.debug("Making Tree provenance for " + tp.getTitle());
Provenance prov = new Provenance();
prov.addEntry(new Entry());
prov.getEntry(0).setAction("imported " + tp.getTitle());
vInput.addSeg(visSeg);
}
}
- Cache.log.debug("Finished Tree provenance for " + tp.getTitle());
+ Console.debug("Finished Tree provenance for " + tp.getTitle());
return prov;
}
}
if (alsq.size() < sequences.length)
{
- Cache.log.warn(
+ Console.warn(
"Not recovered all alignment sequences for given set of input sequence CIGARS");
}
return alsq;
if (tp.getTree() == null)
{
- Cache.log.warn(
+ Console.warn(
"Not updating SequenceTreeMap for " + tree.getVorbaId());
return;
}
{
if (tp.getEntry(pe).getInputCount() > 1)
{
- Cache.log.warn(
+ Console.warn(
"Ignoring additional input spec in provenance entry "
+ tp.getEntry(pe).toString());
}
// bidirection alignments yet.
if (to < se[1])
{
- Cache.log.warn("Ignoring invalid segment in InputData spec.");
+ Console.warn("Ignoring invalid segment in InputData spec.");
}
else
{
return new Object[] { new AlignmentView(view), jal };
}
}
- Cache.log.debug(
+ Console.debug(
"Returning null for input data recovery from provenance.");
return null;
}
return true;
} catch (Exception e)
{
- Cache.log.debug("Failed to parse newick tree string", e);
+ Console.debug("Failed to parse newick tree string", e);
}
return false;
}
import jalview.analysis.Dna;
import jalview.api.AlignViewControllerGuiI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLociI;
import jalview.datamodel.Mapping;
VCFHeaderLine headerLine = header.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
if (headerLine == null)
{
- Cache.log.error("VCF reference header not found");
+ Console.error("VCF reference header not found");
return null;
}
String ref = headerLine.getValue();
}
else
{
- Cache.log.error("VCF reference not found: " + ref);
+ Console.error("VCF reference not found: " + ref);
}
return seq;
{
if (reference == null)
{
- Cache.log.error("No VCF ##reference found, defaulting to "
+ Console.error("No VCF ##reference found, defaulting to "
+ DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
}
GeneLociI seqCoords = seq.getGeneLoci();
if (seqCoords == null)
{
- Cache.log.warn(String.format(
+ Console.warn(String.format(
"Can't query VCF for %s as chromosome coordinates not known",
seq.getName()));
return null;
// returned with the Ensembl sequence; todo: support aliases?
if (!vcfSpecies.equalsIgnoreCase(species))
{
- Cache.log.warn("No VCF loaded to " + seq.getName()
+ Console.warn("No VCF loaded to " + seq.getName()
+ " as species not matched");
return null;
}
vcfAssembly);
if (newRange == null)
{
- Cache.log.error(
+ Console.error(
String.format("Failed to map %s:%s:%s:%d:%d to %s", species,
chromosome, seqRef, range[0], range[1],
vcfAssembly));
*/
String msg = String.format("Error reading VCF for %s:%d-%d: %s ",
map.chromosome, vcfStart, vcfEnd,e.getLocalizedMessage());
- Cache.log.error(msg);
+ Console.error(msg);
}
}
VCFInfoHeaderLine infoHeader = header.getInfoHeaderLine(infoId);
if (infoHeader == null)
{
- Cache.log.error("Field " + infoId + " has no INFO header");
+ Console.error("Field " + infoId + " has no INFO header");
return false;
}
VCFHeaderLineType infoType = infoHeader.getType();
if (!badData.contains(token))
{
badData.add(token);
- Cache.log.error(String.format("Invalid VCF data at %s:%d %s=%s",
+ Console.error(String.format("Invalid VCF data at %s:%d %s=%s",
variant.getContig(), variant.getStart(), infoId, value));
}
}
if (seq != last || i != index)
{
// this should really be a trace message.
- // Cache.log.debug("Mouse over " + v.getId() + " bound to "
+ // Cache.debug("Mouse over " + v.getId() + " bound to "
// + seq + " at " + index);
last = seq;
i = index;
+++ /dev/null
-package jalview.javascript.log4j;
-
-import jalview.javascript.log4j.spi.LoggingEvent;
-
-public abstract class Appender
-{
- public abstract void append(LoggingEvent loggingEvent);
-
-}
+++ /dev/null
-package jalview.javascript.log4j;
-
-import jalview.javascript.log4j.spi.LoggingEvent;
-
-public class ConsoleAppender
-{
-
- private String name;
-
- private Layout layout;
-
-
- public ConsoleAppender()
- {
- }
-
- public ConsoleAppender(Layout layout, String name)
- {
- this.layout = layout;
- this.name = name;
- }
-
- public void setLayout(Layout layout)
- {
- this.layout = layout;
- }
-
- public void setName(String name)
- {
- this.name = name;
- }
-
- public void append(LoggingEvent event)
- {
-
- System.out
- .println(event.getLevel() + ": " + event.getRenderedMessage());
-
- }
-
-}
+++ /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.javascript.log4j;
-
-import jalview.javascript.log4j.spi.LoggingEvent;
-import jalview.javascript.log4j.spi.OptionHandler;
-
-import org.apache.log4j.PatternLayout;
-//import org.apache.log4j.TTCCLayout;
-
-public abstract class Layout implements OptionHandler
-{
-
- // Note that the line.separator property can be looked up even by
- // applets.
- public final static String LINE_SEP = System
- .getProperty("line.separator");
-
- public final static int LINE_SEP_LEN = LINE_SEP.length();
-
- /**
- * Implement this method to create your own layout format.
- */
- abstract public String format(LoggingEvent event);
-
- /**
- * Returns the content type output by this layout. The base class returns
- * "text/plain".
- */
- public String getContentType()
- {
- return "text/plain";
- }
-
- /**
- * Returns the header for the layout format. The base class returns
- * <code>null</code>.
- */
- public String getHeader()
- {
- return null;
- }
-
- /**
- * Returns the footer for the layout format. The base class returns
- * <code>null</code>.
- */
- public String getFooter()
- {
- return null;
- }
-
- /**
- * If the layout handles the throwable object contained within
- * {@link LoggingEvent}, then the layout should return <code>false</code>.
- * Otherwise, if the layout ignores throwable object, then the layout should
- * return <code>true</code>. If ignoresThrowable is true, the appender is
- * responsible for rendering the throwable.
- * <p>
- * The {@link SimpleLayout}, {@link TTCCLayout}, {@link PatternLayout} all
- * return <code>true</code>. The {@link org.apache.log4j.xml.XMLLayout}
- * returns <code>false</code>.
- *
- * @since 0.8.4
- */
- abstract public boolean ignoresThrowable();
-
-}
+++ /dev/null
-package jalview.javascript.log4j;
-
-import java.util.Locale;
-
-import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
-import java.io.ObjectStreamException;
-import java.io.Serializable;
-
-/**
- * Defines the minimum set of levels recognized by the system, that is
- * <code>OFF</code>, <code>FATAL</code>, <code>ERROR</code>, <code>WARN</code>,
- * <code>INFO</code>, <code>DEBUG</code> and <code>ALL</code>.
- *
- * <p>
- * The <code>Level</code> class may be subclassed to define a larger level set.
- * </p>
- *
- * @author Ceki Gülcü
- */
-public class Level extends Priority implements Serializable
-{
-
- private static final String ALL_NAME = "ALL";
-
- private static final String TRACE_NAME = "TRACE";
-
- private static final String DEBUG_NAME = "DEBUG";
-
- private static final String INFO_NAME = "INFO";
-
- private static final String WARN_NAME = "WARN";
-
- private static final String ERROR_NAME = "ERROR";
-
- private static final String FATAL_NAME = "FATAL";
-
- private static final String OFF_NAME = "OFF";
-
- /**
- * TRACE level integer value.
- *
- * @since 1.2.12
- */
- public static final int TRACE_INT = 5000;
-
- /**
- * The <code>OFF</code> has the highest possible rank and is intended to turn
- * off logging.
- */
- final static public Level OFF = new Level(OFF_INT, OFF_NAME, 0);
-
- /**
- * The <code>FATAL</code> level designates very severe error events that will
- * presumably lead the application to abort.
- */
- final static public Level FATAL = new Level(FATAL_INT, FATAL_NAME, 0);
-
- /**
- * The <code>ERROR</code> level designates error events that might still allow
- * the application to continue running.
- */
- final static public Level ERROR = new Level(ERROR_INT, ERROR_NAME, 3);
-
- /**
- * The <code>WARN</code> level designates potentially harmful situations.
- */
- final static public Level WARN = new Level(WARN_INT, WARN_NAME, 4);
-
- /**
- * The <code>INFO</code> level designates informational messages that
- * highlight the progress of the application at coarse-grained level.
- */
- final static public Level INFO = new Level(INFO_INT, INFO_NAME, 6);
-
- /**
- * The <code>DEBUG</code> Level designates fine-grained informational events
- * that are most useful to debug an application.
- */
- final static public Level DEBUG = new Level(DEBUG_INT, DEBUG_NAME, 7);
-
- /**
- * The <code>TRACE</code> Level designates finer-grained informational events
- * than the <code>DEBUG</code level.
- *
- * @since 1.2.12
- */
- public static final Level TRACE = new Level(TRACE_INT, TRACE_NAME, 7);
-
- /**
- * The <code>ALL</code> has the lowest possible rank and is intended to turn
- * on all logging.
- */
- final static public Level ALL = new Level(ALL_INT, ALL_NAME, 7);
-
- /**
- * Serialization version id.
- */
- static final long serialVersionUID = 3491141966387921974L;
-
- /**
- * Instantiate a Level object.
- */
- protected Level(int level, String levelStr, int syslogEquivalent)
- {
- super(level, levelStr, syslogEquivalent);
- }
-
- /**
- * Convert the string passed as argument to a level. If the conversion fails,
- * then this method returns {@link #DEBUG}.
- */
- public static Level toLevel(String sArg)
- {
- return toLevel(sArg, Level.DEBUG);
- }
-
- /**
- * Convert an integer passed as argument to a level. If the conversion fails,
- * then this method returns {@link #DEBUG}.
- */
- public static Level toLevel(int val)
- {
- return toLevel(val, Level.DEBUG);
- }
-
- /**
- * Convert an integer passed as argument to a level. If the conversion fails,
- * then this method returns the specified default.
- */
- public static Level toLevel(int val, Level defaultLevel)
- {
- switch (val)
- {
- case ALL_INT:
- return ALL;
- case DEBUG_INT:
- return Level.DEBUG;
- case INFO_INT:
- return Level.INFO;
- case WARN_INT:
- return Level.WARN;
- case ERROR_INT:
- return Level.ERROR;
- case FATAL_INT:
- return Level.FATAL;
- case OFF_INT:
- return OFF;
- case TRACE_INT:
- return Level.TRACE;
- default:
- return defaultLevel;
- }
- }
-
- /**
- * Convert the string passed as argument to a level. If the conversion fails,
- * then this method returns the value of <code>defaultLevel</code>.
- */
- public static Level toLevel(String sArg, Level defaultLevel)
- {
- if (sArg == null)
- {
- return defaultLevel;
- }
- String s = sArg.toUpperCase(Locale.ROOT);
-
- if (s.equals(ALL_NAME))
- {
- return Level.ALL;
- }
- if (s.equals(DEBUG_NAME))
- {
- return Level.DEBUG;
- }
- if (s.equals(INFO_NAME))
- {
- return Level.INFO;
- }
- if (s.equals(WARN_NAME))
- {
- return Level.WARN;
- }
- if (s.equals(ERROR_NAME))
- {
- return Level.ERROR;
- }
- if (s.equals(FATAL_NAME))
- {
- return Level.FATAL;
- }
- if (s.equals(OFF_NAME))
- {
- return Level.OFF;
- }
- if (s.equals(TRACE_NAME))
- {
- return Level.TRACE;
- }
- //
- // For Turkish i problem, see bug 40937
- //
- if (s.equals("\u0130NFO"))
- {
- return Level.INFO;
- }
- return defaultLevel;
- }
-
- /**
- * Custom deserialization of Level.
- *
- * @param s
- * serialization stream.
- * @throws IOException
- * if IO exception.
- * @throws ClassNotFoundException
- * if class not found.
- */
- private void readObject(final ObjectInputStream s)
- throws IOException, ClassNotFoundException
- {
- s.defaultReadObject();
- level = s.readInt();
- syslogEquivalent = s.readInt();
- levelStr = s.readUTF();
- if (levelStr == null)
- {
- levelStr = "";
- }
- }
-
- /**
- * Serialize level.
- *
- * @param s
- * serialization stream.
- * @throws IOException
- * if exception during serialization.
- */
- private void writeObject(final ObjectOutputStream s) throws IOException
- {
- s.defaultWriteObject();
- s.writeInt(level);
- s.writeInt(syslogEquivalent);
- s.writeUTF(levelStr);
- }
-
- /**
- * Resolved deserialized level to one of the stock instances. May be overriden
- * in classes derived from Level.
- *
- * @return resolved object.
- * @throws ObjectStreamException
- * if exception during resolution.
- */
- private Object readResolve() throws ObjectStreamException
- {
- //
- // if the deserizalized object is exactly an instance of Level
- //
- if (getClass() == Level.class)
- {
- return toLevel(level);
- }
- //
- // extension of Level can't substitute stock item
- //
- return this;
- }
-
-}
+++ /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.javascript.log4j;
-
-import jalview.javascript.log4j.spi.LoggingEvent;
-
-import java.util.Hashtable;
-import java.util.Map;
-
-public class Logger
-{
-
- private static Map<String, Logger> registry;
-
- private String name;
-
- private Level level;
-
- private boolean enabled = true;
-
- private boolean isEnabled;
-
- private Appender appender;
-
- private Logger(String name)
- {
- this.name = name;
- }
-
- public static Logger getLogger(String name)
- {
- if (registry == null)
- {
- registry = new Hashtable<>();
- getLogger("root");
- }
- Logger logger = registry.get(name);
- if (logger == null)
- {
- registry.put(name, logger = new Logger(name));
- logger.setLevel(Level.INFO);
- }
- return logger;
- }
-
- public static Logger getRootLogger()
- {
- return getLogger("root");
- }
-
- public void setLevel(Level l)
- {
- this.level = l;
- }
-
- public void addAppender(Appender appender)
- {
- this.appender = appender;
- }
-
- public boolean isDebugEnabled()
- {
- return isEnabled;
- }
-
- public void debug(Object o)
- {
- debug(o, null);
- }
-
- public void debug(Object o, Throwable e)
- {
- switch (level.level)
- {
- case Priority.FATAL_INT:
- case Priority.ERROR_INT:
- case Priority.WARN_INT:
- case Priority.INFO_INT:
- case Priority.DEBUG_INT:
- log(o, e);
- break;
- }
- }
-
- public void info(Object o)
- {
- info(o, null);
- }
-
- public void info(Object o, Throwable e)
- {
- switch (level.level)
- {
- case Priority.FATAL_INT:
- case Priority.ERROR_INT:
- case Priority.WARN_INT:
- case Priority.INFO_INT:
- log(o, e);
- break;
- }
-
- }
-
- public void warn(Object o)
- {
- warn(o, null);
- }
-
- public void warn(Object o, Throwable e)
- {
- switch (level.level)
- {
- case Priority.FATAL_INT:
- case Priority.ERROR_INT:
- case Priority.WARN_INT:
- log(o, e);
- break;
- }
-
- }
-
- public void error(Object o)
- {
- error(o, null);
- }
-
- public void error(Object o, Throwable e)
- {
- switch (level.level)
- {
- case Priority.FATAL_INT:
- case Priority.ERROR_INT:
- log(o, e);
- break;
- }
-
- }
-
- private void log(Object s, Throwable e)
- {
- switch (level.level)
- {
- case Priority.ERROR_INT:
- if (appender == null)
- {
- System.err.println(s);
- return;
- }
- break;
- case Priority.WARN_INT:
- if (appender == null)
- {
- System.err.println(s);
- return;
- }
- break;
- case Priority.INFO_INT:
- if (appender == null)
- {
- System.out.println(s);
- return;
- }
- break;
- case Priority.DEBUG_INT:
- if (appender == null)
- {
- System.out.println(s);
- return;
- }
- break;
- }
- e.printStackTrace();
- appender.append(new LoggingEvent(this, s.toString(), level));
- }
-
-}
+++ /dev/null
-/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements. See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the "License"); you may not use this file except in compliance with
- * the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-// Contributors: Kitching Simon <Simon.Kitching@orange.ch>
-
-package jalview.javascript.log4j;
-
-/**
- <font color="#AA4444">Refrain from using this class directly, use
- the {@link Level} class instead</font>.
-
- @author Ceki Gülcü */
-public class Priority {
-
- transient int level;
- transient String levelStr;
- transient int syslogEquivalent;
-
- public final static int OFF_INT = Integer.MAX_VALUE;
- public final static int FATAL_INT = 50000;
- public final static int ERROR_INT = 40000;
- public final static int WARN_INT = 30000;
- public final static int INFO_INT = 20000;
- public final static int DEBUG_INT = 10000;
- //public final static int FINE_INT = DEBUG_INT;
- public final static int ALL_INT = Integer.MIN_VALUE;
-
- // too twisted for J2S -- Level class initializer initializes Priority, which
- // creates a
- // new Level before Priority is indicated to be a superclass of Level.
- /**
- * @deprecated Use {@link Level#FATAL} instead.
- */
- @Deprecated
- final static public Priority FATAL = null;// new Level(FATAL_INT, "FATAL", 0);
-
- /**
- * @deprecated Use {@link Level#ERROR} instead.
- */
- @Deprecated
- final static public Priority ERROR = null;// new Level(ERROR_INT, "ERROR", 3);
-
- /**
- * @deprecated Use {@link Level#WARN} instead.
- */
- @Deprecated
- final static public Priority WARN = null;// new Level(WARN_INT, "WARN", 4);
-
- /**
- * @deprecated Use {@link Level#INFO} instead.
- */
- @Deprecated
- final static public Priority INFO = null;// new Level(INFO_INT, "INFO", 6);
-
- /**
- * @deprecated Use {@link Level#DEBUG} instead.
- */
- @Deprecated
- final static public Priority DEBUG = null;// new Level(DEBUG_INT, "DEBUG", 7);
-
- /**
- * Default constructor for deserialization.
- */
- protected Priority() {
- level = DEBUG_INT;
- levelStr = "DEBUG";
- syslogEquivalent = 7;
- }
-
- /**
- Instantiate a level object.
- */
- protected
- Priority(int level, String levelStr, int syslogEquivalent) {
- this.level = level;
- this.levelStr = levelStr;
- this.syslogEquivalent = syslogEquivalent;
- }
-
- /**
- Two priorities are equal if their level fields are equal.
- @since 1.2
- */
- @Override
- public
- boolean equals(Object o) {
- if(o instanceof Priority) {
- Priority r = (Priority) o;
- return (this.level == r.level);
- } else {
- return false;
- }
- }
-
- /**
- Return the syslog equivalent of this priority as an integer.
- */
- public
- final
- int getSyslogEquivalent() {
- return syslogEquivalent;
- }
-
-
-
- /**
- Returns <code>true</code> if this level has a higher or equal
- level than the level passed as argument, <code>false</code>
- otherwise.
-
- <p>You should think twice before overriding the default
- implementation of <code>isGreaterOrEqual</code> method.
-
- */
- public
- boolean isGreaterOrEqual(Priority r) {
- return level >= r.level;
- }
-
- // /**
- // Return all possible priorities as an array of Level objects in
- // descending order.
- //
- // @deprecated This method will be removed with no replacement.
- // */
- // public
- // static
- // Priority[] getAllPossiblePriorities() {
- // return new Priority[] {Priority.FATAL, Priority.ERROR, Level.WARN,
- // Priority.INFO, Priority.DEBUG};
- // }
-
-
- /**
- Returns the string representation of this priority.
- */
- @Override
- final
- public
- String toString() {
- return levelStr;
- }
-
- /**
- Returns the integer representation of this level.
- */
- public
- final
- int toInt() {
- return level;
- }
-
- // /**
- // * @deprecated Please use the {@link Level#toLevel(String)} method instead.
- // */
- // public
- // static
- // Priority toPriority(String sArg) {
- // return Level.toLevel(sArg);
- // }
-
- // /**
- // * @deprecated Please use the {@link Level#toLevel(int)} method instead.
- // */
- // public
- // static
- // Priority toPriority(int val) {
- // return toPriority(val, Priority.DEBUG);
- // }
-
- // /**
- // * @deprecated Please use the {@link Level#toLevel(int, Level)} method
- // instead.
- // */
- // public
- // static
- // Priority toPriority(int val, Priority defaultPriority) {
- // return Level.toLevel(val, (Level) defaultPriority);
- // }
- //
- // /**
- // * @deprecated Please use the {@link Level#toLevel(String, Level)} method
- // instead.
- // */
- // public
- // static
- // Priority toPriority(String sArg, Priority defaultPriority) {
- // return Level.toLevel(sArg, (Level) defaultPriority);
- // }
-}
+++ /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.javascript.log4j;
-
-import jalview.javascript.log4j.spi.LoggingEvent;
-
-public class SimpleLayout extends Layout
-{
-
- StringBuffer sbuf = new StringBuffer(128);
-
- @Override
- public void activateOptions()
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public String format(LoggingEvent event)
- {
-
- sbuf.setLength(0);
- sbuf.append(event.getLevel().toString());
- sbuf.append(" - ");
- sbuf.append(event.getRenderedMessage());
- sbuf.append(LINE_SEP);
- return sbuf.toString();
- }
- @Override
- public boolean ignoresThrowable()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
-}
+++ /dev/null
-/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements. See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the "License"); you may not use this file except in compliance with
- * the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package jalview.javascript.log4j;
-
-public abstract class WriterAppender extends Appender
-{
-
-}
+++ /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.javascript.log4j.spi;
-
-import jalview.javascript.log4j.Logger;
-
-public class LoggingEvent
-{
-
- private Object level;
-
- private String msg;
-
- private Logger logger;
-
- public LoggingEvent(Logger logger, String level, Object message)
- {
- this.logger = logger;
- this.level = level;
- this.msg = message.toString();
-
- }
-
- public Object getLevel()
- {
- return level;
- }
-
- public String getRenderedMessage()
- {
- return msg;
- }
-}
+++ /dev/null
-package jalview.javascript.log4j.spi;
-
-public interface OptionHandler
-{
-
- void activateOptions();
-
-}
});
seqLimits.setText(
MessageManager.getString("label.show_sequence_limits"));
- seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+ seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true));
seqLimits.addActionListener(new ActionListener()
{
@Override
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
padGapsMenuitem
- .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+ .setState(Cache.getDefault("PAD_GAPS", false));
padGapsMenuitem.addActionListener(new ActionListener()
{
@Override
autoCalculate.setText(
MessageManager.getString("label.autocalculate_consensus"));
autoCalculate.setState(
- jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ Cache.getDefault("AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
{
@Override
sortByTree.setToolTipText("<html>" + MessageManager.getString(
"label.enable_automatically_sort_alignment_when_open_new_tree"));
sortByTree
- .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
+ .setState(Cache.getDefault("SORT_BY_TREE", false));
sortByTree.addActionListener(new ActionListener()
{
@Override
import javax.swing.table.TableCellRenderer;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.bin.MemorySetting;
import jalview.fts.core.FTSDataColumnPreferences;
import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
}
else
{
- Cache.log.error(
+ Console.error(
"Preset '" + value + "' [key:" + key + "] not implemented");
}
.getSelectedItem();
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Problem casting Combo entry to IntKeyStringValueEntry.");
e = null;
}
e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
continue;
}
i = ((Integer) s.getValue()).intValue();
} catch (Exception e)
{
- Cache.log.error(
+ Console.error(
"Exception casting the initial value of s.getValue()");
}
}
i = (Integer) s.getValue();
} catch (Exception e)
{
- Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
+ Console.error("Failed casting (Integer) JSpinner s.getValue()");
}
return i;
}
*/
package jalview.jbgui;
+import jalview.bin.Cache;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
wsMenuRefreshButs.add(resetWs, null);
wsMenuRefreshButs.add(progressBar, null);
myBorderlayout.setHgap(3);
- if (jalview.bin.Cache.getDefault("ENABLE_RSBS_EDITOR", false))
+ if (Cache.getDefault("ENABLE_RSBS_EDITOR", false))
{
JTabbedPane listPanels = new JTabbedPane();
listPanels.addTab("JABAWS Servers", wsListPanel);
--- /dev/null
+package jalview.log;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import jalview.bin.Console;
+import jalview.util.Platform;
+
+public abstract class JLogger implements JLoggerI
+{
+ protected String name;
+
+ protected LogLevel level;
+
+ private Object logger = null;
+
+ private static Map<String, JLogger> registry = new HashMap<>();
+
+ // implement these abstract methods
+ protected abstract void loggerSetup();
+
+ public abstract boolean loggerExists();
+
+ protected abstract void loggerSetLevel(LogLevel level);
+
+ protected abstract void loggerLogMessage(LogLevel level, String message,
+ Throwable t);
+
+ public static LogLevel toLevel(String levelString)
+ {
+ try
+ {
+ return LogLevel.valueOf(levelString);
+ } catch (IllegalArgumentException e)
+ {
+ Console.error("Could not parse LogLevel '" + levelString + "'", e);
+ return LogLevel.INFO;
+ }
+ }
+
+ public static JLogger getLogger(Class c)
+ {
+ return getLogger(c);
+ }
+
+ public static JLogger getLogger(Class c, LogLevel loglevel)
+ {
+ return getLogger(c.getCanonicalName(), loglevel);
+ }
+
+ public static JLogger getLogger(String name)
+ {
+ return getLogger(name, LogLevel.INFO);
+ }
+
+ public static JLogger getLogger(String name, LogLevel loglevel)
+ {
+ return registry.containsKey(name) ? (JLogger) registry.get(name) : null;
+ }
+
+ protected JLogger()
+ {
+ }
+
+ protected JLogger(String name, LogLevel level)
+ {
+ this.name = name;
+ this.level = level;
+ this.loggerSetup();
+ this.registryStore();
+ }
+
+ protected void registryStore()
+ {
+ registry.put(this.name, this);
+ }
+
+ protected static boolean registryContainsKey(String name)
+ {
+ return registry.containsKey(name);
+ }
+
+ protected static JLogger registryGet(String name)
+ {
+ return registry.get(name);
+ }
+
+ public LogLevel getLevel()
+ {
+ return this.level;
+ }
+
+ public void setLevel(LogLevel level)
+ {
+ this.level = level;
+ if (loggerExists())
+ loggerSetLevel(level);
+ }
+
+ private boolean println(LogLevel loglevel, String message, Throwable t)
+ {
+ if (loglevel.compareTo(this.level) < 0)
+ {
+ return false;
+ }
+ if (!loggerExists() || Platform.isJS())
+ {
+ String logLine = String.format("%s: %s", loglevel.toString(),
+ message);
+ System.out.println(logLine);
+ if (t != null)
+ {
+ if (loglevel.compareTo(LogLevel.DEBUG) <= 0)
+ t.printStackTrace(System.err);
+ else
+ System.err.println(t.getMessage());
+ }
+ return false;
+ }
+ else
+ {
+ loggerLogMessage(loglevel, message, t);
+ return true;
+ }
+ }
+
+ public void trace(String message)
+ {
+ trace(message, null);
+ }
+
+ public void trace(String message, Throwable t)
+ {
+ println(LogLevel.TRACE, message, t);
+ }
+
+ public void debug(String message)
+ {
+ debug(message, null);
+ }
+
+ public void debug(String message, Throwable t)
+ {
+ println(LogLevel.DEBUG, message, t);
+ }
+
+ public void info(String message)
+ {
+ info(message, null);
+ }
+
+ public void info(String message, Throwable t)
+ {
+ println(LogLevel.INFO, message, t);
+ }
+
+ public void warn(String message)
+ {
+ warn(message, null);
+ }
+
+ public void warn(String message, Throwable t)
+ {
+ println(LogLevel.WARN, message, t);
+ }
+
+ public void error(String message)
+ {
+ error(message, null);
+ }
+
+ public void error(String message, Throwable t)
+ {
+ println(LogLevel.ERROR, message, t);
+ }
+
+ public void fatal(String message)
+ {
+ fatal(message, null);
+ }
+
+ public void fatal(String message, Throwable t)
+ {
+ println(LogLevel.FATAL, message, t);
+ }
+
+ public boolean isDebugEnabled()
+ {
+ return level.compareTo(LogLevel.DEBUG) <= 0;
+ }
+
+ public boolean isTraceEnabled()
+ {
+ return level.compareTo(LogLevel.TRACE) <= 0;
+ }
+}
--- /dev/null
+package jalview.log;
+
+public interface JLoggerI
+{
+ public enum LogLevel
+ {
+ ALL, TRACE, DEBUG, INFO, WARN, ERROR, FATAL
+ }
+
+ public LogLevel getLevel();
+
+ public void setLevel(LogLevel level);
+
+ public void trace(String message);
+
+ public void trace(String message, Throwable t);
+
+ public void debug(String message);
+
+ public void debug(String message, Throwable t);
+
+ public void info(String message);
+
+ public void info(String message, Throwable t);
+
+ public void warn(String message);
+
+ public void warn(String message, Throwable t);
+
+ public void error(String message);
+
+ public void error(String message, Throwable t);
+
+ public void fatal(String message);
+
+ public void fatal(String message, Throwable t);
+
+ public boolean isDebugEnabled();
+
+ public boolean isTraceEnabled();
+}
--- /dev/null
+package jalview.log;
+
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.core.Appender;
+
+import jalview.util.Log4j;
+import jalview.util.Platform;
+
+public class JLoggerLog4j extends JLogger implements JLoggerI
+{
+ private Logger logger = null;
+
+ public static JLoggerLog4j getLogger(Class c)
+ {
+ return getLogger(c);
+ }
+
+ public static JLoggerLog4j getLogger(Class c, LogLevel loglevel)
+ {
+ return getLogger(c.getCanonicalName(), loglevel);
+ }
+
+ public static JLoggerLog4j getLogger(String name)
+ {
+ return getLogger(name, LogLevel.INFO);
+ }
+
+ public static JLoggerLog4j getLogger(String name, LogLevel loglevel)
+ {
+ return registryContainsKey(name) ? (JLoggerLog4j) registryGet(name)
+ : new JLoggerLog4j(name, loglevel);
+ }
+
+ private JLoggerLog4j(String name, LogLevel level)
+ {
+ this.name = name;
+ this.level = level;
+ this.loggerSetup();
+ this.registryStore();
+ }
+
+ @Override
+ protected void loggerSetup()
+ {
+ if (!Platform.isJS())
+ this.logger = Log4j.isInit() ? Log4j.getLogger(this.name, this.level)
+ : null;
+ }
+
+ @Override
+ public boolean loggerExists()
+ {
+ return logger != null;
+ }
+
+ @Override
+ protected void loggerSetLevel(JLoggerI.LogLevel level)
+ {
+ if (loggerExists())
+ {
+ Log4j.setLevel(logger, level);
+ }
+ }
+
+ @Override
+ protected void loggerLogMessage(LogLevel level, String message,
+ Throwable t)
+ {
+ if (!loggerExists())
+ return;
+ if (t != null)
+ {
+ switch (level)
+ {
+ case FATAL:
+ logger.fatal(message, t);
+ break;
+ case ERROR:
+ logger.error(message, t);
+ break;
+ case WARN:
+ logger.warn(message, t);
+ break;
+ case INFO:
+ logger.info(message, t);
+ break;
+ case DEBUG:
+ logger.debug(message, t);
+ break;
+ case TRACE:
+ logger.trace(message, t);
+ break;
+ case ALL:
+ logger.trace(message, t);
+ break;
+ }
+ }
+ else
+ {
+ switch (level)
+ {
+ case FATAL:
+ logger.fatal(message);
+ break;
+ case ERROR:
+ logger.error(message);
+ break;
+ case WARN:
+ logger.warn(message);
+ break;
+ case INFO:
+ logger.info(message);
+ break;
+ case DEBUG:
+ logger.debug(message);
+ break;
+ case TRACE:
+ logger.trace(message);
+ break;
+ case ALL:
+ logger.trace(message);
+ break;
+ }
+ }
+ }
+
+ private Logger getLoggerObject()
+ {
+ return this.logger;
+ }
+
+ public synchronized static void addAppender(JLoggerLog4j level,
+ Appender appender)
+ {
+ if (!Platform.isJS())
+ Log4j.addAppender(level.getLoggerObject(), appender);
+ }
+
+ public synchronized static void addAppender(JLoggerLog4j l1,
+ JLoggerLog4j l2, String name)
+ {
+ if (!Platform.isJS())
+ Log4j.addAppender(l1.getLoggerObject(), l2.getLoggerObject(), name);
+ }
+
+}
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.gui;
+package jalview.log;
+
+import java.io.Serializable;
+import java.nio.charset.StandardCharsets;
import javax.swing.JTextArea;
import javax.swing.SwingUtilities;
-import org.apache.log4j.WriterAppender;
-import org.apache.log4j.spi.LoggingEvent;
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.core.Filter;
+import org.apache.logging.log4j.core.Layout;
+import org.apache.logging.log4j.core.LogEvent;
+import org.apache.logging.log4j.core.appender.AbstractAppender;
+import org.apache.logging.log4j.core.config.Property;
+
+import jalview.log.JLoggerI.LogLevel;
+import jalview.util.Log4j;
/**
* From http://textareaappender.zcage.com/ the means to capture the logs, too.
* Simple example of creating a Log4j appender that will write to a JTextArea.
*/
-public class JalviewAppender extends WriterAppender
+public class JalviewAppender extends AbstractAppender
{
+ public final static String NAME = "JalviewAppender";
+
+ public JalviewAppender()
+ {
+ this(LogLevel.INFO);
+ }
+
+ public JalviewAppender(LogLevel loglevel)
+ {
+ super(NAME,
+ Log4j.getThresholdFilter(loglevel == null ? Level.INFO
+ : Log4j.log4jLevel(loglevel)),
+ Log4j.getSimpleLayout(), false, new Property[0]);
+ }
+
+ protected JalviewAppender(String name, Filter filter,
+ Layout<? extends Serializable> layout, boolean ignoreExceptions,
+ Property[] properties)
+ {
+ super(name, filter, layout, ignoreExceptions, properties);
+ // TODO Auto-generated constructor stub
+ }
static private JTextArea jTextArea = null;
/**
* Format and then append the loggingEvent to the stored JTextArea.
*/
- public void append(LoggingEvent loggingEvent)
+ public void append(LogEvent logEvent)
{
- final String message = this.layout.format(loggingEvent);
+ final String message = new String(
+ this.getLayout().toByteArray(logEvent), StandardCharsets.UTF_8);
// Append formatted message to textarea using the Swing Thread.
SwingUtilities.invokeLater(new Runnable()
import jalview.api.analysis.SimilarityParamsI;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
} catch (Exception e)
{
- Cache.log.error("Couln't write Jalview state to " + statefile, e);
+ Console.error("Couln't write Jalview state to " + statefile, e);
// TODO: inform user of the problem - they need to know if their data was
// not saved !
if (errorMessage == null)
System.err.println("error writing date: " + e.toString());
}
object.setVersion(
- jalview.bin.Cache.getDefault("VERSION", "Development Build"));
+ Cache.getDefault("VERSION", "Development Build"));
/**
* rjal is full height alignment, jal is actual alignment with full metadata
}
else
{
- Cache.log.error(
+ Console.error(
"Failed to save viewer state for " + viewerType);
}
}
.getHiddenColumns();
if (hidden == null)
{
- warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
+ Console.warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
}
else
{
object.getPcaViewer().add(viewer);
} catch (Throwable t)
{
- Cache.log.error("Error saving PCA: " + t.getMessage());
+ Console.error("Error saving PCA: " + t.getMessage());
}
}
}
else if (!matchedFile.equals(pdbentry.getFile()))
{
- Cache.log.warn(
+ Console.warn(
"Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+ pdbentry.getFile());
}
calcIdParam.getParameters().replace("|\\n|", "\n"));
} catch (IOException x)
{
- warn("Couldn't parse parameter data for "
+ Console.warn("Couldn't parse parameter data for "
+ calcIdParam.getCalcId(), x);
return false;
}
}
else
{
- warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
+ Console.warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
return false;
}
}
return id.toString();
}
// give up and warn that something has gone wrong
- warn("Cannot find ID for object in external mapping : " + jvobj);
+ Console.warn("Cannot find ID for object in external mapping : " + jvobj);
}
return altCode;
}
mp.setDseqFor(jmpid);
if (!seqRefIds.containsKey(jmpid))
{
- jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+ Console.debug("creatign new DseqFor ID");
seqRefIds.put(jmpid, ps);
}
else
{
- jalview.bin.Cache.log.debug("reusing DseqFor ID");
+ Console.debug("reusing DseqFor ID");
}
// mp.setMappingChoice(mpc);
}
else
{
- warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
+ Console.warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
}
} catch (Exception ex)
{
tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
if (tp == null)
{
- warn("There was a problem recovering stored Newick tree: \n"
+ Console.warn("There was a problem recovering stored Newick tree: \n"
+ tree.getNewick());
continue;
}
else
{
errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
- warn(errorMessage);
+ Console.warn(errorMessage);
}
}
}
} catch (IllegalArgumentException | NullPointerException e)
{
// TODO JAL-3619 show error dialog / offer an alternative viewer
- Cache.log.error("Invalid structure viewer type: " + type);
+ Console.error("Invalid structure viewer type: " + type);
}
}
}
else
{
- warn("Couldn't recover parameters for "
+ Console.warn("Couldn't recover parameters for "
+ calcIdParam.getCalcId());
}
}
String id = object.getViewport().get(0).getSequenceSetId();
if (skipList.containsKey(id))
{
- if (Cache.log != null && Cache.log.isDebugEnabled())
- {
- Cache.log.debug("Skipping seuqence set id " + id);
- }
+ Console.debug("Skipping seuqence set id " + id);
return true;
}
return false;
{
if (ds != null && ds != seqSetDS)
{
- warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
+ Console.warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
+ " - CDS/Protein crossreference data may be lost");
if (xtant_ds != null)
{
// This can only happen if the unique sequence set ID was bound to a
// dataset that did not contain any of the sequences in the view
// currently being restored.
- warn("JAL-3171 SERIOUS! TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed.");
+ Console.warn("JAL-3171 SERIOUS! TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed.");
}
}
ds = seqSetDS;
SequenceI[] dsseqs = new SequenceI[dseqs.size()];
dseqs.copyInto(dsseqs);
ds = new jalview.datamodel.Alignment(dsseqs);
- debug("Created new dataset " + vamsasSet.getDatasetId()
+ Console.debug("Created new dataset " + vamsasSet.getDatasetId()
+ " for alignment " + System.identityHashCode(al));
addDatasetRef(vamsasSet.getDatasetId(), ds);
}
AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
if (prevDS != null && prevDS != ds)
{
- warn("Dataset sequence appears in many datasets: "
+ Console.warn("Dataset sequence appears in many datasets: "
+ restoredSeq.getDsseqid());
// TODO: try to merge!
}
{
if (dataset.getDataset() != null)
{
- warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
+ Console.warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
}
String datasetId = makeHashCode(dataset, null);
if (datasetId == null)
seqRefIds.put(sqid, djs);
}
- jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
+ Console.debug("about to recurse on addDBRefs.");
addDBRefs(djs, ms);
}
private Hashtable jvids2vobj;
- private void warn(String msg)
- {
- warn(msg, null);
- }
-
- private void warn(String msg, Exception e)
- {
- if (Cache.log != null)
- {
- if (e != null)
- {
- Cache.log.warn(msg, e);
- }
- else
- {
- Cache.log.warn(msg);
- }
- }
- else
- {
- System.err.println("Warning: " + msg);
- if (e != null)
- {
- e.printStackTrace();
- }
- }
- }
-
- private void debug(String string)
- {
- debug(string, null);
- }
-
- private void debug(String msg, Exception e)
- {
- if (Cache.log != null)
- {
- if (e != null)
- {
- Cache.log.debug(msg, e);
- }
- else
- {
- Cache.log.debug(msg);
- }
- }
- else
- {
- System.err.println("Warning: " + msg);
- if (e != null)
- {
- e.printStackTrace();
- }
- }
- }
-
/**
* set the object to ID mapping tables used to write/recover objects and XML
* ID strings for the jalview project. If external tables are provided then
if (!jvann.annotationId.equals(anid))
{
// TODO verify that this is the correct behaviour
- this.warn("Overriding Annotation ID for " + anid
+ Console.warn("Overriding Annotation ID for " + anid
+ " from different id : " + jvann.annotationId);
jvann.annotationId = anid;
}
}
else
{
- Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+ Console.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
}
}
}
}
else
{
- warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
+ Console.warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
}
} catch (Exception ex)
{
}
} catch (Exception ex)
{
- Cache.log.error("Error loading PCA: " + ex.toString());
+ Console.error("Error loading PCA: " + ex.toString());
}
}
});
} catch (InvocationTargetException | InterruptedException ex)
{
- warn("Unexpected error when opening " + viewerType
+ Console.warn("Unexpected error when opening " + viewerType
+ " structure viewer", ex);
}
}
}
} catch (IOException e)
{
- Cache.log.error("Error restoring Jmol session: " + e.toString());
+ Console.error("Error restoring Jmol session: " + e.toString());
}
return null;
}
maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
} catch (Exception e)
{
- Cache.log.warn("Couldn't parse out graduated feature color.", e);
+ Console.warn("Couldn't parse out graduated feature color.", e);
}
NoValueColour noCol = colourModel.getNoValueColour();
protected StructureCommandI getColourCommand(AtomSpecModel atomSpecModel,
Color colour)
{
- String atomSpec = getAtomSpec(atomSpecModel, false);
+ String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
return colourResidues(atomSpec, colour);
}
*
* @param refAtoms
* @param atomSpec
+ * @param backbone - superpose based on which kind of atomType
* @return
*/
List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec);
+ AtomSpecModel atomSpec, AtomSpecType backbone);
/**
* Returns a command to open a file of commands at the given path
*/
StructureCommandI saveSession(String filepath);
+ enum AtomSpecType { RESIDUE_ONLY, ALPHA, PHOSPHATE };
/**
* Returns a representation of the atom set represented by the model, in
* viewer syntax format. If {@code alphaOnly} is true, this is restricted to
* Alpha Carbon (peptide) or Phosphorous (rna) only
*
* @param model
- * @param alphaOnly
+ * @param specType
* @return
*/
- String getAtomSpec(AtomSpecModel model, boolean alphaOnly);
+ String getAtomSpec(AtomSpecModel model, AtomSpecType specType);
/**
* Returns the lowest model number used by the structure viewer (likely 0 or
import jalview.analysis.AlignSeq;
import jalview.api.StructureSelectionManagerProvider;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.OrderCommand;
} catch (SiftsException e)
{
isMapUsingSIFTs = false;
- Cache.log.error("SIFTS mapping failed", e);
- Cache.log.error("Falling back on Needleman & Wunsch alignment");
+ Console.error("SIFTS mapping failed", e);
+ Console.error("Falling back on Needleman & Wunsch alignment");
siftsClient = null;
}
} catch (SiftsException e)
{
// fall back to NW alignment
- Cache.log.error(e.getMessage());
+ Console.error(e.getMessage());
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
targetChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
import jalview.api.SequenceRenderer;
import jalview.api.StructureSelectionManagerProvider;
import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.MappedFeatures;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
public String chain = "";
+ /**
+ * is the mapped sequence not protein ?
+ */
public boolean isRna;
/*
protected boolean colourBySequence = true;
+ /**
+ * true if all sequences appear to be nucleotide
+ */
private boolean nucleotide;
private boolean finishedInit = false;
structures[pdbfnum].chain = chain;
}
structures[pdbfnum].pdbId = mapping.getPdbId();
- structures[pdbfnum].isRna = theSequence.getRNA() != null;
+ structures[pdbfnum].isRna = !theSequence.isProtein();
/*
* move on to next pdb file (ignore sequences for other chains
*/
// todo better way to ensure synchronous than setting getReply true!!
executeCommands(commandGenerator.showBackbone(), true, null);
-
+
+ AtomSpecType backbone = structures[refStructure].isRna ? AtomSpecType.PHOSPHATE : AtomSpecType.ALPHA;
/*
* superpose each (other) structure to the reference in turn
*/
{
AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
List<StructureCommandI> commands = commandGenerator
- .superposeStructures(refAtoms, atomSpec);
+ .superposeStructures(refAtoms, atomSpec, backbone);
List<String> replies = executeCommands(commands, true, null);
for (String reply : replies)
{
saveSession(f);
} catch (IOException e)
{
- Cache.log.error(String.format("Error saving %s session: %s", prefix,
+ Console.error(String.format("Error saving %s session: %s", prefix,
e.toString()));
}
package jalview.urls;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.urls.api.UrlProviderI;
import jalview.util.UrlLink;
dataProvider.setUrlData(data);
} catch (IllegalArgumentException ex)
{
- Cache.log.error(ex.getMessage());
+ Console.error(ex.getMessage());
}
}
});
*/
package jalview.util;
+import jalview.bin.Cache;
+
import java.io.File;
import java.io.IOException;
import java.lang.reflect.Constructor;
case OTHER:
default:
- browser = jalview.bin.Cache.getDefault("DEFAULT_BROWSER", "firefox");
+ browser = Cache.getDefault("DEFAULT_BROWSER", "firefox");
break;
}
--- /dev/null
+package jalview.util;
+
+import java.util.Map;
+
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.core.Appender;
+import org.apache.logging.log4j.core.Filter;
+import org.apache.logging.log4j.core.Layout;
+import org.apache.logging.log4j.core.LoggerContext;
+import org.apache.logging.log4j.core.appender.ConsoleAppender;
+import org.apache.logging.log4j.core.config.Configuration;
+import org.apache.logging.log4j.core.config.ConfigurationFactory;
+import org.apache.logging.log4j.core.config.Configurator;
+import org.apache.logging.log4j.core.config.LoggerConfig;
+import org.apache.logging.log4j.core.config.builder.api.AppenderComponentBuilder;
+import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilder;
+import org.apache.logging.log4j.core.config.builder.api.FilterComponentBuilder;
+import org.apache.logging.log4j.core.config.builder.api.LayoutComponentBuilder;
+import org.apache.logging.log4j.core.config.builder.impl.BuiltConfiguration;
+import org.apache.logging.log4j.core.filter.ThresholdFilter;
+import org.apache.logging.log4j.core.layout.PatternLayout;
+
+import jalview.log.JLogger;
+import jalview.log.JalviewAppender;
+
+public class Log4j
+{
+
+ public final static String SIMPLE_PATTERN = "%level - %m%n";
+
+ private static boolean init = false;
+
+ public static boolean isInit()
+ {
+ return init;
+ }
+
+ public static Level log4jLevel(JLogger.LogLevel loglevel)
+ {
+ return Level.toLevel(loglevel.toString());
+ }
+
+ public static void init(JLogger.LogLevel myLevel)
+ {
+ init(log4jLevel(myLevel));
+ }
+
+ public static void init(Level myLevel)
+ {
+ if (init)
+ return;
+ try
+ {
+ // configure the root logger to stderr
+ ConfigurationBuilder<BuiltConfiguration> configBuilder = Log4j
+ .getConfigurationBuilder();
+
+ configBuilder.setStatusLevel(Level.WARN);
+
+ String consoleLoggerName = "STDERR";
+ AppenderComponentBuilder appenderBuilder = configBuilder
+ .newAppender(consoleLoggerName, "Console");
+ appenderBuilder.addAttribute("target",
+ ConsoleAppender.Target.SYSTEM_ERR);
+ appenderBuilder.add(Log4j.getSimpleLayoutBuilder());
+ appenderBuilder.add(Log4j.getThresholdFilterBuilder());
+ configBuilder.add(appenderBuilder);
+
+ configBuilder.add(configBuilder.newRootLogger(myLevel)
+ .add(configBuilder.newAppenderRef(consoleLoggerName)));
+
+ Configurator.initialize(configBuilder.build());
+
+ init = true;
+ } catch (Exception e)
+ {
+ System.err.println("Problems initializing the log4j system\n");
+ e.printStackTrace(System.err);
+ }
+ }
+
+ public static Logger getLogger(String name)
+ {
+ return getLogger(name, Level.INFO);
+ }
+
+ public static Logger getLogger(String name, JLogger.LogLevel loglevel)
+ {
+ return getLogger(name, log4jLevel(loglevel));
+ }
+
+ public static Logger getLogger(String name, Level level)
+ {
+ Logger logger = LogManager.getLogger(name);
+ Log4j.setLevel(logger, level);
+ return logger;
+ }
+
+ public static ConfigurationBuilder<BuiltConfiguration> getConfigurationBuilder()
+ {
+ return ConfigurationFactory.newConfigurationBuilder();
+ }
+
+ public static Layout getSimpleLayout()
+ {
+ return PatternLayout.newBuilder().withPattern(SIMPLE_PATTERN).build();
+ }
+
+ public static LayoutComponentBuilder getSimpleLayoutBuilder()
+ {
+ return getConfigurationBuilder().newLayout("PatternLayout")
+ .addAttribute("pattern", Log4j.SIMPLE_PATTERN);
+ }
+
+ public static Filter getThresholdFilter(Level level)
+ {
+ return ThresholdFilter.createFilter(level, Filter.Result.ACCEPT,
+ Filter.Result.NEUTRAL);
+ }
+
+ public static FilterComponentBuilder getThresholdFilterBuilder()
+ {
+ return getConfigurationBuilder().newFilter("ThresholdFilter",
+ Filter.Result.ACCEPT, Filter.Result.NEUTRAL);
+ }
+
+ public static void setLevel(Logger logger, JLogger.LogLevel loglevel)
+ {
+ setLevel(logger, log4jLevel(loglevel));
+ }
+
+ public static void setLevel(Logger logger, Level level)
+ {
+ if (!Platform.isJS())
+ {
+ LoggerContext context = (LoggerContext) LogManager.getContext(false);
+ Configuration config = context.getConfiguration();
+ LoggerConfig loggerConfig = config.getLoggerConfig(logger.getName());
+ loggerConfig.setLevel(level);
+
+ Map<String, Appender> appenders = config.getAppenders();
+
+ Appender jappender = config.getAppender(JalviewAppender.NAME);
+
+ context.updateLoggers();
+ }
+ }
+
+ public static void setRootLevel(JLogger.LogLevel loglevel)
+ {
+ setRootLevel(log4jLevel(loglevel));
+ }
+
+ public static void setRootLevel(Level level)
+ {
+ setLevel(LogManager.getRootLogger(), level);
+ }
+
+ public static Appender getAppender(String name)
+ {
+ LoggerContext context = (LoggerContext) LogManager.getContext(false);
+ Configuration config = context.getConfiguration();
+ Map<String, Appender> appenders = config.getAppenders();
+ return appenders.get(name);
+ }
+
+ public static void addAppender(Logger logger, Logger logger2,
+ String name2)
+ {
+ LoggerContext context = (LoggerContext) LogManager.getContext(false);
+ Configuration config = context.getConfiguration();
+ LoggerConfig logger2Config = config.getLoggerConfig(logger2.getName());
+ Map<String, Appender> logger2AppendersMap = logger2Config
+ .getAppenders();
+ Appender appender = logger2AppendersMap.get(name2);
+ addAppender(logger, appender);
+ context.updateLoggers();
+ }
+
+ public static void addAppender(Logger logger, Appender appender)
+ {
+ if (appender == null)
+ return;
+ LoggerContext context = (LoggerContext) LogManager.getContext(false);
+ Configuration config = context.getConfiguration();
+ LoggerConfig loggerConfig = config.getLoggerConfig(logger.getName());
+ if (loggerConfig == null)
+ return;
+
+ Level level = loggerConfig.getLevel();
+
+ config.addAppender(appender);
+ loggerConfig.addAppender(appender, null, null);
+
+ context.updateLoggers();
+ }
+
+ public static void addAppenderToRootLogger(Appender appender)
+ {
+ Log4j.addAppender(LogManager.getRootLogger(), appender);
+ }
+}
import java.util.BitSet;
import java.util.List;
-import jalview.bin.Cache;
+import jalview.bin.Console;
/**
* A simple way of bijectively mapping a non-contiguous linear range to another
if (range.length != 2)
{
// throw new IllegalArgumentException(range);
- Cache.log.error("Invalid format for fromRange "
+ Console.error("Invalid format for fromRange "
+ Arrays.toString(range) + " may cause errors");
}
fromLowest = Math.min(fromLowest, Math.min(range[0], range[1]));
if (range.length != 2)
{
// throw new IllegalArgumentException(range);
- Cache.log.error("Invalid format for toRange "
+ Console.error("Invalid format for toRange "
+ Arrays.toString(range) + " may cause errors");
}
toLowest = Math.min(toLowest, Math.min(range[0], range[1]));
import jalview.analysis.AlignmentSorter;
import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Mapping;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
action = action.getUndoAction();
}
// TODO write this
- Cache.log.error("MappingUtils.mapCutOrPaste not yet implemented");
+ Console.error("MappingUtils.mapCutOrPaste not yet implemented");
}
/**
*/
int startResiduePos = selected.findPosition(firstUngappedPos);
int endResiduePos = selected.findPosition(lastUngappedPos);
-
- for (AlignedCodonFrame acf : codonFrames)
+ for (SequenceI seq : mapTo.getAlignment().getSequences())
{
- for (SequenceI seq : mapTo.getAlignment().getSequences())
+ int mappedStartResidue = 0;
+ int mappedEndResidue = 0;
+ for (AlignedCodonFrame acf : codonFrames)
{
- SequenceI peptide = targetIsNucleotide ? selected : seq;
- SequenceI cds = targetIsNucleotide ? seq : selected;
- SequenceToSequenceMapping s2s = acf.getCoveringMapping(cds,
- peptide);
- if (s2s == null)
+ // rather than use acf.getCoveringMapping() we iterate through all
+ // mappings to make sure all CDS are selected for a protein
+ for (SequenceToSequenceMapping map: acf.getMappings())
{
- continue;
- }
- int mappedStartResidue = 0;
- int mappedEndResidue = 0;
- List<AlignedCodonFrame> mapping = Arrays.asList(acf);
- SearchResultsI sr = buildSearchResults(selected, startResiduePos,
- mapping);
- for (SearchResultMatchI m : sr.getResults())
- {
- mappedStartResidue = m.getStart();
- mappedEndResidue = m.getEnd();
- }
- sr = buildSearchResults(selected, endResiduePos, mapping);
- for (SearchResultMatchI m : sr.getResults())
+ if (map.covers(selected) && map.covers(seq))
{
- mappedStartResidue = Math.min(mappedStartResidue, m.getStart());
- mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
- }
+ /*
+ * Found a sequence mapping. Locate the start/end mapped residues.
+ */
+ List<AlignedCodonFrame> mapping = Arrays
+ .asList(new AlignedCodonFrame[]
+ { acf });
+ // locate start
+ SearchResultsI sr = buildSearchResults(selected,
+ startResiduePos, mapping);
+ for (SearchResultMatchI m : sr.getResults())
+ {
+ mappedStartResidue = m.getStart();
+ mappedEndResidue = m.getEnd();
+ }
+ // locate end - allowing for adjustment of start range
+ sr = buildSearchResults(selected, endResiduePos, mapping);
+ for (SearchResultMatchI m : sr.getResults())
+ {
+ mappedStartResidue = Math.min(mappedStartResidue,
+ m.getStart());
+ mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
+ }
- /*
- * Find the mapped aligned columns, save the range. Note findIndex
- * returns a base 1 position, SequenceGroup uses base 0
- */
- int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
- minStartCol = minStartCol == -1 ? mappedStartCol
- : Math.min(minStartCol, mappedStartCol);
- int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
- maxEndCol = maxEndCol == -1 ? mappedEndCol
- : Math.max(maxEndCol, mappedEndCol);
- mappedGroup.addSequence(seq, false);
- break;
- }
+ /*
+ * Find the mapped aligned columns, save the range. Note findIndex
+ * returns a base 1 position, SequenceGroup uses base 0
+ */
+ int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
+ minStartCol = minStartCol == -1 ? mappedStartCol
+ : Math.min(minStartCol, mappedStartCol);
+ int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
+ maxEndCol = maxEndCol == -1 ? mappedEndCol
+ : Math.max(maxEndCol, mappedEndCol);
+ mappedGroup.addSequence(seq, false);
+ break;
+ }
+ }}
}
}
mappedGroup.setStartRes(minStartCol < 0 ? 0 : minStartCol);
{
if (range.length % 2 != 0)
{
- Cache.log.error(
+ Console.error(
"Error unbalance start/end ranges: " + ranges.toString());
return 0;
}
/*
* not coded for [start1, end1, start2, end2, ...]
*/
- Cache.log.error(
+ Console.error(
"MappingUtils.removeEndPositions doesn't handle multiple ranges");
return;
}
/*
* not coded for a reverse strand range (end < start)
*/
- Cache.log.error(
+ Console.error(
"MappingUtils.removeEndPositions doesn't handle reverse strand");
return;
}
import java.util.ResourceBundle.Control;
import java.util.Set;
-import org.apache.log4j.Logger;
+import jalview.log.JLoggerLog4j;
/**
*
{
private static ResourceBundle rb;
- // BH 2018 switched to org.apache.llog4j.Logger
- private static Logger log = Logger
+ private static JLoggerLog4j log = JLoggerLog4j
.getLogger(MessageManager.class.getCanonicalName());
private static Locale loc;
} catch (Exception e)
{
String msg = "I18N missing: " + loc + "\t" + key;
- logWarning(key, msg);
+ logWarning(key, msg);
}
return value;
}
*/
public static String getStringOrReturn(String keyroot, String name)
{
- String smkey = keyroot + name.toLowerCase(Locale.ROOT).replaceAll(" ", "");
+ String smkey = keyroot
+ + name.toLowerCase(Locale.ROOT).replaceAll(" ", "");
try
{
name = rb.getString(smkey);
} catch (Exception x)
{
- String msg = "I18N missing key with root " + keyroot + ": " + loc + "\t"
- + smkey;
- logWarning(smkey, msg);
+ String msg = "I18N missing key with root " + keyroot + ": " + loc
+ + "\t" + smkey;
+ logWarning(smkey, msg);
}
return name;
}
* @param key
* @param msg
*/
- private static void logWarning(String key, String msg)
+ private static void logWarning(String key, String msg)
{
- if (!reportedMissing.contains(key))
- {
+ if (!reportedMissing.contains(key))
+ {
reportedMissing.add(key);
- log.info(msg);
- }
+ log.info(msg);
+ }
}
}
*/
package jalview.ws;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
throw (new Exception(
"Timed out when communicating with server\nTry again later.\n"));
}
- jalview.bin.Cache.log.debug("Job " + j + " Result state "
+ Console.debug("Job " + j + " Result state "
+ jobs[j].getState() + "(ServerError="
+ jobs[j].isServerError() + ")");
} catch (Exception ex)
.formatMessage("info.server_exception", new Object[]
{ WebServiceName, ex.getMessage() }));
// always output the exception's stack trace to the log
- Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+ Console.warn(WebServiceName + " job(" + jobs[j].jobnum
+ ") Server exception.");
// todo: could limit trace to cause if this is a SOAPFaultException.
ex.printStackTrace();
if (jobs[j].allowedServerExceptions > 0)
{
jobs[j].allowedServerExceptions--;
- Cache.log.debug("Sleeping after a server exception.");
+ Console.debug("Sleeping after a server exception.");
try
{
Thread.sleep(5000);
}
else
{
- Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
+ Console.warn("Dropping job " + j + " " + jobs[j].jobId);
jobs[j].subjobComplete = true;
wsInfo.setStatus(jobs[j].jobnum,
WebserviceInfo.STATE_STOPPED_SERVERERROR);
jobs[j].clearResponse(); // may contain out of date result data
wsInfo.setStatus(jobs[j].jobnum,
WebserviceInfo.STATE_STOPPED_ERROR);
- Cache.log.error("Out of memory when retrieving Job " + j
+ Console.error("Out of memory when retrieving Job " + j
+ " id:" + WsUrl + "/" + jobs[j].jobId, er);
new jalview.gui.OOMWarning(
"retrieving result for " + WebServiceName, er);
Thread.sleep(5000);
} catch (InterruptedException e)
{
- Cache.log.debug("Interrupted sleep waiting for next job poll.",
+ Console.debug("Interrupted sleep waiting for next job poll.",
e);
}
// System.out.println("I'm alive "+alTitle);
}
else
{
- Cache.log.debug(
+ Console.debug(
"WebServiceJob poll loop finished with no jobs created.");
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.appendProgressText(
import jalview.analysis.AlignSeq;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
AlignmentI retrieved = null;
try
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug("Querying " + dbsource.getDbName()
+ Console.debug("Querying " + dbsource.getDbName()
+ " with : '" + queryString.toString() + "'");
}
retrieved = dbsource.getSequenceRecords(queryString.toString());
import com.stevesoft.pat.Regex;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
if (al == null)
{
- Cache.log.error(
+ Console.error(
"No record found for '" + dbName + ":" + query + "'");
}
}
import com.stevesoft.pat.Regex;
import jalview.analysis.SequenceIdMatcher;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
return listToArray(ranges);
} catch (ParseException e)
{
- Cache.log.warn(
+ Console.warn(
String.format("Not parsing inexact CDS location %s in ENA %s",
location, accession));
return new int[] {};
import jalview.bin.Cache;
import jalview.datamodel.DBRefSource;
+import jalview.util.Platform;
import com.stevesoft.pat.Regex;
static final String PFAM_BASEURL_KEY = "PFAM_BASEURL";
private static final String DEFAULT_PFAM_BASEURL = "https://pfam.xfam.org";
+ static {
+ Platform.addJ2SDirectDatabaseCall(DEFAULT_PFAM_BASEURL);
+ }
public Pfam()
{
import jalview.bin.Cache;
import jalview.datamodel.DBRefSource;
+import jalview.util.Platform;
import com.stevesoft.pat.Regex;
private static final String DEFAULT_RFAM_BASEURL = "https://rfam.xfam.org";
+ static {
+ Platform.addJ2SDirectDatabaseCall(DEFAULT_RFAM_BASEURL);
+ }
/*
* append to URLs to retrieve as a gzipped file
*/
import java.util.Locale;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.io.DataSourceType;
// TODO: trap HTTP 404 exceptions and return null
String xfamUrl = getURL(queries);
- if (Cache.log != null)
- {
- Cache.log.debug("XFAM URL for retrieval is: " + xfamUrl);
- }
+ Console.debug("XFAM URL for retrieval is: " + xfamUrl);
AlignmentI rcds = new FormatAdapter().readFile(xfamUrl,
DataSourceType.URL, FileFormat.Stockholm);
}
return null;
}
-
+ static {
+ Platform.addJ2SDirectDatabaseCall("https://www.ebi.ac.uk/");
+ }
/**
* Constructs the URL to fetch from
*
*/
package jalview.ws.jws1;
+import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
// timeout
} catch (Exception ex)
{
- jalview.bin.Cache.log.error(
+ Console.error(
"Serious! Service location failed\nfor URL :" + WsURL + "\n",
ex);
static private Vector<URL> getDiscoveryURLS()
{
Vector<URL> urls = new Vector<>();
- String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
+ String RootServiceURLs = Cache.getDefault("DISCOVERY_URLS",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
try
}
else
{
- jalview.bin.Cache.log
- .info("Ignoring duplicate url in DISCOVERY_URLS list");
+ Console.info("Ignoring duplicate url in DISCOVERY_URLS list");
}
} catch (Exception ex)
{
- jalview.bin.Cache.log
- .warn("Problem whilst trying to make a URL from '"
+ Console.warn("Problem whilst trying to make a URL from '"
+ ((url != null) ? url : "<null>") + "'");
- jalview.bin.Cache.log.warn(
+ Console.warn(
"This was probably due to a malformed comma separated list"
+ " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
- jalview.bin.Cache.log.debug("Exception was ", ex);
+ Console.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
- jalview.bin.Cache.log.warn(
+ Console.warn(
"Error parsing comma separated list of urls in DISCOVERY_URLS.",
ex);
}
*/
static public void doDiscovery()
{
- jalview.bin.Cache.log
- .debug("(Re)-Initialising the discovery URL list.");
+ Console.debug("(Re)-Initialising the discovery URL list.");
try
{
- reallyDiscoverServices = jalview.bin.Cache
+ reallyDiscoverServices = Cache
.getDefault("DISCOVERY_START", false);
if (reallyDiscoverServices)
{
}
else
{
- jalview.bin.Cache.log.debug("Setting default services");
+ Console.debug("Setting default services");
services = new Hashtable<>();
// Muscle, Clustal and JPred.
ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
ServiceHandles shs = null;
try
{
- jalview.bin.Cache.log.debug("Discovering services using " + location);
+ Console.debug("Discovering services using " + location);
shs = locateWebService(location).getServices();
} catch (org.apache.axis.AxisFault f)
{
}
else
{
- jalview.bin.Cache.log.warn("No Discovery service at " + location);
- jalview.bin.Cache.log.debug("Axis Fault", f);
+ Console.warn("No Discovery service at " + location);
+ Console.debug("Axis Fault", f);
}
} catch (Exception e)
{
- jalview.bin.Cache.log.warn("No Discovery service at " + location);
- jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
+ Console.warn("No Discovery service at " + location);
+ Console.debug("Discovery Service General Exception", e);
}
if ((shs != null) && shs.getServices().length > 0)
{
{
if (!cat.contains(sh[i]))
{
- jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName()
+ Console.debug("A " + sh[i].getAbstractName()
+ " service called " + sh[i].getName() + " exists at "
+ sh[i].getEndpointURL() + "\n");
if (!sscat.containsKey(sh[i].getAbstractName()))
disc_serv = new java.net.URL(sh[i].getEndpointURL());
if (!ServiceURLList.contains(disc_serv))
{
- jalview.bin.Cache.log.debug(
+ Console.debug(
"Adding new discovery service at " + disc_serv);
ServiceURLList.add(disc_serv);
seenNewDiscovery = true;
}
} catch (Exception e)
{
- jalview.bin.Cache.log
- .debug("Ignoring bad discovery service URL "
+ Console.debug("Ignoring bad discovery service URL "
+ sh[i].getEndpointURL(), e);
}
}
int s_url = 0;
if (ServiceURLList == null)
{
- jalview.bin.Cache.log
- .debug("No service endpoints to use for service discovery.");
+ Console.debug("No service endpoints to use for service discovery.");
return;
}
while (s_url < ServiceURLList.size())
}
else
{
- jalview.bin.Cache.log.warn("No services at "
+ Console.warn("No services at "
+ (ServiceURLList.get(s_url))
+ " - check DISCOVERY_URLS property in .jalview_properties");
}
import java.util.Locale;
import jalview.analysis.AlignSeq;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
Jpred server = locateWebService();
if (server == null)
{
- Cache.log.warn("Couldn't find a Jpred webservice to invoke!");
+ Console.warn("Couldn't find a Jpred webservice to invoke!");
return;
}
SeqCigar[] msf = null;
import jalview.analysis.AlignSeq;
import jalview.analysis.SeqsetUtils;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
JpredResult result = (JpredResult) this.result;
- Cache.log.debug("Parsing output from JNet job.");
+ Console.debug("Parsing output from JNet job.");
// JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt",
// "File");
JPredFile prediction = new JPredFile(result.getPredfile(),
DataSourceType.PASTE);
SequenceI[] preds = prediction.getSeqsAsArray();
- Cache.log.debug("Got prediction profile.");
+ Console.debug("Got prediction profile.");
if ((this.msa != null) && (result.getAligfile() != null))
{
- Cache.log.debug("Getting associated alignment.");
+ Console.debug("Getting associated alignment.");
// we ignore the returned alignment if we only predicted on a single
// sequence
FileFormatI format = new IdentifyFile()
{
job.setSubmitted(true);
job.setSubjobComplete(false);
- Cache.log.info(WsUrl + " Job Id '" + job.getJobId() + "'");
+ Console.info(WsUrl + " Job Id '" + job.getJobId() + "'");
}
}
else
"JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n"
+ e.getMessage() + "\n");
- jalview.bin.Cache.log.warn("Server Exception", e);
+ Console.warn("Server Exception", e);
}
else
{
"info.failed_to_submit_prediction", new String[]
{ e.getMessage(), wsInfo.getProgressText() }));
- jalview.bin.Cache.log
- .debug("Failed Submission of job " + j.getJobnum(), e);
+ Console.debug("Failed Submission of job " + j.getJobnum(), e);
}
j.setAllowedServerExceptions(-1);
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Unexpected exception when processing results for " + altitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
msa = (j.msa != null) ? true : msa;
try
{
- jalview.bin.Cache.log.debug("Parsing output of job " + jn);
+ Console.debug("Parsing output of job " + jn);
jobres = j.getResultSet();
- jalview.bin.Cache.log.debug("Finished parsing output.");
+ Console.debug("Finished parsing output.");
if (jobs.length == 1)
{
res = jobres;
}
} catch (Exception e)
{
- jalview.bin.Cache.log
- .error("JNet Client: JPred Annotation Parse Error", e);
+ Console.error("JNet Client: JPred Annotation Parse Error", e);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.appendProgressText(j.getJobnum(),
}
else
{
- Cache.log.info("Append results onto existing alignment.");
+ Console.info("Append results onto existing alignment.");
}
}
}
package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
{
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
- Cache.log.warn(
+ Console.warn(
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Tried to submit an already submitted job " + j.getJobId());
}
return;
&& jobs[j].hasResults())
{
results++;
- // if (Cache.log.isDebugEnabled())
+ // if (Cache.isDebugEnabled())
// {
// System.out.println("Job lob for job
// "+jobs[j].getJobId()+":"+jobs[j].getJobnum());
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Unexpected exception when processing results for " + alTitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
*/
package jalview.ws.jws1;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
.getSupportedDatabases();
} catch (Exception e)
{
- jalview.bin.Cache.log.warn(
+ Console.warn(
"Database list request failed, so disabling SeqSearch Service client "
+ sh.getName() + " at " + sh.getEndpointURL(),
e);
import jalview.analysis.AlignSeq;
import jalview.api.FeatureColourI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
{
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
- Cache.log.warn(
+ Console.warn(
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
SeqSearchWSJob j = (SeqSearchWSJob) job;
if (j.isSubmitted())
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Tried to submit an already submitted job " + j.getJobId());
}
return;
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Unexpected exception when processing results for " + alTitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
package jalview.ws.jws2;
import jalview.api.FeatureColourI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceFeature;
scores = scoremanager.getAnnotationForSequence(seqId);
} catch (Exception q)
{
- Cache.log
- .info("Couldn't recover disorder prediction for sequence "
+ Console.info("Couldn't recover disorder prediction for sequence "
+ seq.getName() + "(Prediction name was " + seqId
+ ")"
+ "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
import jalview.analysis.SeqsetUtils;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
}
if (collectAnnotationResultsFor(rslt))
{
- jalview.bin.Cache.log.debug("Updating result annotation from Job "
+ Console.debug("Updating result annotation from Job "
+ rslt + " at " + service.getUri());
updateResultAnnotation(true);
ap.adjustAnnotationHeight();
*/
package jalview.ws.jws2;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
else
{
jws2Discoverer.addInvalidServiceUrl(jwsserver);
- Cache.log.warn("Ignoring invalid Jws2 service url " + jwsserver);
+ Console.warn("Ignoring invalid Jws2 service url " + jwsserver);
}
} catch (Exception e)
{
e.printStackTrace();
- Cache.log.warn("Exception when discovering Jws2 services.", e);
+ Console.warn("Exception when discovering Jws2 services.", e);
jws2Discoverer.addInvalidServiceUrl(jwsserver);
} catch (Error e)
{
- Cache.log.error("Exception when discovering Jws2 services.", e);
+ Console.error("Exception when discovering Jws2 services.", e);
jws2Discoverer.addInvalidServiceUrl(jwsserver);
}
running = false;
import compbio.metadata.Argument;
import jalview.api.AlignCalcWorkerI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
if (service != null
&& !fave.getService().hosturl.equals(service.hosturl))
{
- Cache.log.debug("Changing AACon service to " + service.hosturl
+ Console.debug("Changing AACon service to " + service.hosturl
+ " from " + fave.getService().hosturl);
fave.setService(service);
}
if (!service.serviceType.toString()
.equals(compbio.ws.client.Services.AAConWS.toString()))
{
- Cache.log.warn(
+ Console.warn(
"Ignoring invalid preferred service for AACon calculations (service type was "
+ service.serviceType + ")");
service = null;
package jalview.ws.jws2;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
{
try
{
- Cache.log.debug(
+ Console.debug(
"Waiting around for old discovery thread to finish.");
// wait around until old discoverer dies
Thread.sleep(100);
}
}
aborted = false;
- Cache.log.debug("Old discovery thread has finished.");
+ Console.debug("Old discovery thread has finished.");
}
running = true;
}
if (aborted)
{
- Cache.log.debug(
+ Console.debug(
"Aborting " + qrys.size() + " JABAWS discovery threads.");
for (JabaWsServerQuery squery : qrys)
{
}
else
{
- Cache.log.warn("Ignoring duplicate url " + url + " in "
+ Console.warn("Ignoring duplicate url " + url + " in "
+ JWS2HOSTURLS + " list");
}
} catch (MalformedURLException ex)
{
- Cache.log.warn("Problem whilst trying to make a URL from '"
+ Console.warn("Problem whilst trying to make a URL from '"
+ ((url != null) ? url : "<null>") + "'");
- Cache.log.warn(
+ Console.warn(
"This was probably due to a malformed comma separated list"
+ " in the " + JWS2HOSTURLS
+ " entry of $(HOME)/.jalview_properties)");
- Cache.log.debug("Exception was ", ex);
+ Console.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
- Cache.log.warn("Error parsing comma separated list of urls in "
+ Console.warn("Error parsing comma separated list of urls in "
+ JWS2HOSTURLS + " preference.", ex);
}
return urls;
package jalview.ws.jws2;
import jalview.analysis.AlignSeq;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
{
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
- Cache.log.warn(
+ Console.warn(
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Tried to submit an already submitted job " + j.getJobId());
}
return;
} catch (Exception e)
{
- Cache.log.warn(
+ Console.warn(
"Exception when retrieving remaining Job progress data for job "
+ msjob.getJobId() + " on server " + WsUrl);
e.printStackTrace();
}
} while (nunchanged > 0 && nexcept > 0);
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
System.out.println("Job Execution file for job: "
+ msjob.getJobId() + " on server " + WsUrl);
{
// job has failed for some reason - probably due to invalid
// parameters
- Cache.log.debug(
+ Console.debug(
"Results not available for finished job - marking as broken job.",
e);
msjob.jobProgress.append(
msjob.setjobStatus(JobStatus.FAILED);
} catch (Exception e)
{
- Cache.log.error("Couldn't get Alignment for job.", e);
+ Console.error("Couldn't get Alignment for job.", e);
// TODO: Increment count and retry ?
msjob.setjobStatus(JobStatus.UNDEFINED);
}
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Unexpected exception when processing results for " + alTitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
*/
package jalview.ws.rest;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.io.FileParse;
import jalview.io.packed.DataProvider;
import jalview.io.packed.DataProvider.JvDataType;
{
error = true;
errormessage = "Couldn't parse message from web service.";
- Cache.log.warn("Failed to parse MIME multipart content", me);
+ Console.warn("Failed to parse MIME multipart content", me);
en.consumeContent();
}
return new ParsePackedSet().getAlignment(ds,
: en.getContentEncoding().getValue();
if (en.getContentType() != null)
{
- Cache.log.debug("Result Type: " + en.getContentType().toString());
+ Console.debug("Result Type: " + en.getContentType().toString());
}
else
{
- Cache.log.debug("No Result Type Specified.");
+ Console.debug("No Result Type Specified.");
}
if (enc == null || enc.length() < 1)
{
- Cache.log.debug("Assuming 'Default' Result Encoding.");
+ Console.debug("Assuming 'Default' Result Encoding.");
}
else
{
- Cache.log.debug("Result Encoded as : " + enc);
+ Console.debug("Result Encoded as : " + enc);
}
// attempt to identify file and construct an appropriate DataSource
// identifier for it.
: new InputStreamReader(en.getContent());
} catch (UnsupportedEncodingException e)
{
- Cache.log.error("Can't handle encoding '" + enc
+ Console.error("Can't handle encoding '" + enc
+ "' for response from webservice.", e);
en.consumeContent();
error = true;
{
for (RestServiceDescription descr : RestServiceDescription
.parseDescriptions(
- jalview.bin.Cache.getDefault(RSBS_SERVICES,
+ Cache.getDefault(RSBS_SERVICES,
makeShmmrRestClient().service.toString())))
{
services.add(descr.toString());
import java.util.Locale;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+ "</a><br>See Console output for details.";
rj.setAllowedServerExceptions(0);// unrecoverable;
rj.error = true;
- Cache.log.fatal("Unexpected REST Job " + getStage(stg)
+ Console.fatal("Unexpected REST Job " + getStage(stg)
+ "exception for URL " + rj.rsd.postUrl);
throw (he);
} catch (IOException e)
+ "Job. <br>Problematic url was <a href=\""
+ request.getURI() + "\">" + request.getURI()
+ "</a><br>See Console output for details.";
- Cache.log.warn("IO Exception for REST Job " + getStage(stg)
+ Console.warn("IO Exception for REST Job " + getStage(stg)
+ "exception for URL " + rj.rsd.postUrl);
throw (e);
{
case 200:
rj.running = false;
- Cache.log.debug("Processing result set.");
+ Console.debug("Processing result set.");
processResultSet(rj, response, request);
break;
case 202:
{
if (loc.length > 1)
{
- Cache.log.warn("Ignoring additional " + (loc.length - 1)
+ Console.warn("Ignoring additional " + (loc.length - 1)
+ " location(s) provided in response header ( next one is '"
+ loc[1].getValue() + "' )");
}
default:
// Some other response. Probably need to pop up the content in a window.
// TODO: deal with all other HTTP response codes from server.
- Cache.log.warn("Unhandled response status when " + getStage(stg)
+ Console.warn("Unhandled response status when " + getStage(stg)
+ "for " + postUrl + ": " + response.getStatusLine());
rj.error = true;
rj.setAllowedServerExceptions(0);
+ "</a><br/>Filtered response content below:<br/>");
} catch (IOException e)
{
- Cache.log.debug("IOException when consuming unhandled response",
+ Console.debug("IOException when consuming unhandled response",
e);
}
;
{
job.setSubjobComplete(true);
job.setAllowedServerExceptions(-1);
- Cache.log.error("Exception when trying to start Rest Job.", ex);
+ Console.error("Exception when trying to start Rest Job.", ex);
}
}
{
// crazy users will see this message
// TODO: finish this! and remove the message below!
- Cache.log.warn("Rest job result parser is currently INCOMPLETE!");
+ Console.warn("Rest job result parser is currently INCOMPLETE!");
int validres = 0;
for (RestJob rj : (RestJob[]) jobs)
{
String ln = null;
try
{
- Cache.log.debug("Parsing data for job " + rj.getJobId());
+ Console.debug("Parsing data for job " + rj.getJobId());
rj.parseResultSet();
if (rj.hasResults())
{
validres++;
}
- Cache.log.debug("Finished parsing data for job " + rj.getJobId());
+ Console.debug("Finished parsing data for job " + rj.getJobId());
} catch (Error ex)
{
- Cache.log.warn(
+ Console.warn(
"Failed to finish parsing data for job " + rj.getJobId());
ex.printStackTrace();
} catch (Exception ex)
{
- Cache.log.warn(
+ Console.warn(
"Failed to finish parsing data for job " + rj.getJobId());
ex.printStackTrace();
} finally
{
// TODO: decide if multiple multiple alignments returned by
// non-vseparable services are allowed.
- Cache.log.warn(
+ Console.warn(
"dealing with multiple alignment products returned by non-vertically separable service.");
}
// recover reference to last alignment created for this rest frame
}
else
{
- Cache.log.warn(
+ Console.warn(
"Couldn't resolve original sequence for new sequence.");
}
}
grass = groupNames.get(alan[nrj][an].groupRef.getName());
if (grass == null)
{
- Cache.log.error(
+ Console.error(
"Couldn't relocate group referemce for group "
+ alan[nrj][an].groupRef.getName());
}
{
// TODO: process each newick file, lifting over sequence refs to
// current alignment, if necessary.
- Cache.log.error(
+ Console.error(
"Tree recovery from restjob not yet implemented.");
}
}
package jalview.ws.seqfetcher;
import jalview.api.FeatureSettingsModelI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
return true;
}
}
- Cache.log.warn("isFetchable doesn't know about '" + source + "'");
+ Console.warn("isFetchable doesn't know about '" + source + "'");
return false;
}
@Test(groups = { "Functional_Failing" })
public void testFindXrefSequences_withFetch()
{
+ // JBPNote: this fails because pep1 and pep2 do not have DbRefEntrys with mappings
+ // Fix#1 would be to revise the test data so it fits with 2.11.2+ Jalview assumptions
+ // that ENA retrievals yield dbrefs with Mappings
+
SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "Q9ZTS2"));
dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P30419"));
dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P00314"));
final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW");
- pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+ pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2",null,true));
final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG");
- pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
+ pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314",null,true));
/*
* argument false suppresses adding DAS sources
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- private static final int TEST_TIMEOUT = 10500; // Note longer timeout needed
+ private static final int TEST_TIMEOUT = 12500; // Note longer timeout needed
// on
// full test run than on
// individual tests
public void setUpForHeadlessCommandLineInputOperations()
throws IOException
{
- String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo "
+ String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/bin/testProps.jvprops -colour zappo "
+ "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
+ "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
public void setUpForCommandLineInputOperations() throws IOException
{
String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
- Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
- String ln = null;
- int count = 0;
- while ((ln = worker.getErrorReader().readLine()) != null)
+ final Worker worker = getJalviewDesktopRunner(false, cmds,
+ SETUP_TIMEOUT);
+
+
+ // number of lines expected on STDERR when Jalview starts up normally
+ // may need to adjust this if Jalview is excessively noisy ?
+ final int STDERR_SETUPLINES=30;
+
+ // thread monitors stderr - bails after SETUP_TIMEOUT or when
+ // STDERR_SETUPLINES have been read
+ Thread runner = new Thread(new Runnable()
{
- System.out.println(ln);
- successfulCMDs.add(ln);
- if (++count > 25)
+ public void run()
+ {
+ String ln = null;
+ int count = 0;
+ try
+ {
+ while ((ln = worker.getErrorReader().readLine()) != null)
+ {
+ System.out.println(ln);
+ successfulCMDs.add(ln);
+ if (++count > STDERR_SETUPLINES)
+ {
+ break;
+ }
+ }
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Unexpected Exception reading stderr from the Jalview process");
+ e.printStackTrace();
+ }
+ }
+ });
+ long t = System.currentTimeMillis() + SETUP_TIMEOUT;
+ runner.start();
+ while (!runner.isInterrupted() && System.currentTimeMillis() < t)
+ {
+ try
+ {
+ Thread.sleep(500);
+ } catch (InterruptedException e)
{
- break;
}
}
+ runner.interrupt();
if (worker != null && worker.exit == null)
{
worker.interrupt();
@Test(
groups =
- { "Functional", "testben" },
+ { "Functional" },
dataProvider = "headlessModeOutputOperationsData")
public void testHeadlessModeOutputOperations(String harg, String type,
String fileName, boolean withAWT, int expectedMinFileSize,
// headless mode input operations
{ "CMD [-color zappo] executed successfully!",
"Failed command : -color zappo" },
- { "CMD [-props test/jalview/io/testProps.jvprops] executed successfully!",
+ { "CMD [-props test/jalview/bin/testProps.jvprops] executed successfully!",
"Failed command : -props File" },
{ "CMD [-sortbytree] executed successfully!",
"Failed command : -sortbytree" },
VERSION_CHECK=true
LATEST_VERSION=test
+logs.Jalview.level=INFO
PDBEntry case9 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
// different file only
PDBEntry case10 = new PDBEntry("1xyz", "A", null, "a/b/c/File");
-
+
/*
* assertEquals will invoke PDBEntry.equals()
*/
pdb2.setProperty("hello", "moon");
assertTrue(pdb1.updateFrom(pdb2));
assertEquals(pdb1.getProperty("hello"), "moon");
+
+ /*
+ * different id but authoritative
+ */
+ pdb1 = new PDBEntry("af:1xyz", "A", null, "a/b/c/File");
+ pdb2 = new PDBEntry("af-1xyz", "A", null, "a/b/c/File");
+ pdb1.setAuthoritative(true);
+
+ assertTrue(pdb1.isAuthoritative());
+ assertFalse(pdb2.isAuthoritative());
+ // can update pdb1 (authoritative) from pdb2 (non-authoritative)
+ assertTrue(pdb1.updateFrom(pdb2));
+ // but the ID must remain the same
+ assertEquals(pdb1.getId(),"af:1xyz");
+
}
@Test(groups = { "Functional" })
import jalview.schemes.JalviewColourScheme;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
public void testGetAtomSpec()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, false), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "2-4:A/1.1");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1|8:A/1.1");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "2-4:A/1.1|8:A/1.1");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-4:A/1.1|8:A/1.1|5-7:B/1.1");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-7:B/1.1");
model.addRange("2", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1");
model.addRange("2", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1|5-9:C/2.1");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
model.addRange("2", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1|25-35:/5.1");
}
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign);
+ toAlign, AtomSpecType.ALPHA); // doesn't matter for Jmol whether nuc or protein
assertEquals(command.size(), 1);
String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1";
String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1";
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
public class PymolCommandsTest
{
public void testGetAtomSpec()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, false), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, false), "1//A/2-4/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4/");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, false), "1//A/2-4+8/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4+8/");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, false), "1//A/2-4+8/ 1//B/5-7/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4+8/ 1//B/5-7/");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, false), "1//A/2-5+8/ 1//B/5-7/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-5+8/ 1//B/5-7/");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 1//A/2-5+8/ 1//B/5-7/");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-7/");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/ 5///25-35/");
}
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> commands = testee.superposeStructures(ref,
- toAlign);
+ toAlign, AtomSpecType.ALPHA);
assertEquals(commands.size(), 2);
- String refSpecCA = "1//A/12-14/CA 1//B/18+22-23/CA";
- String toAlignSpecCA = "2//B/15-17+20-21/CA 2//C/22/CA";
+ String refSpecCA = "(1//A/12-14/CA 1//B/18+22-23/CA";
+ String toAlignSpecCA = "(2//B/15-17+20-21/CA 2//C/22/CA";
String refSpec = "1//A/12-14/ 1//B/18+22-23/";
String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
-
+ String altLoc = " and (altloc '' or altloc 'a'))";
// super command: separate arguments for regions to align
assertEquals(commands.get(0),
- new StructureCommand("super", refSpecCA, toAlignSpecCA));
+ new StructureCommand("pair_fit", toAlignSpecCA+altLoc, refSpecCA+altLoc));
// show aligned regions: one argument for combined atom specs
assertEquals(commands.get(1), new StructureCommand("show", "cartoon",
refSpec + " " + toAlignSpec));
public void testGetAtomSpec_alphaOnly()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, true), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, true), "1//A/2-4/CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "1//A/2-4/CA");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, true), "1//A/2-4+8/CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "1//A/2-4+8/CA");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"1//A/2-4+8/CA 1//B/5-7/CA");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"1//A/2-5+8/CA 1//B/5-7/CA");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 1//A/2-5+8/CA 1//B/5-7/CA");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-7/CA");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA 5///25-35/CA");
}
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
public class ChimeraCommandsTest
{
public void testGetAtomSpec()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, false), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A,8.A");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A,5-7.B");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A,8.A,5-7.B");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1:2-5.A,8.A,5-7.B");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-5.A,8.A,5-7.B");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B|#1:2-5.A,8.A,5-7.B");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35.");
}
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign);
+ toAlign, AtomSpecType.ALPHA);
// qualifier to restrict match to CA and no altlocs
String carbonAlphas = "@CA&~@.B-Z&~@.2-9";
String refSpec = "#1:12-14.A,18.B,22-23.B";
public void testGetAtomSpec_alphaOnly()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, true), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-4.A@CA&~@.B-Z&~@.2-9");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-4.A,8.A@CA&~@.B-Z&~@.2-9");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-4.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
model.addRange("5", 25, 35, " "); // empty chain code
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9|#5:25-35.@CA&~@.B-Z&~@.2-9");
}
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
public class ChimeraXCommandsTest
{
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign);
+ toAlign,AtomSpecType.ALPHA);
assertEquals(command.size(), 1);
String cmd = command.get(0).getCommand();
String refSpec = "#1/A:12-14/B:18,22-23";
public void testGetAtomSpec()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, false), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY
+ ), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-4");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-4,8");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8/B:5-7");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-4,8/B:5-7");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1/A:2-5,8/B:5-7");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-5,8/B:5-7");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4|#1/A:2-5,8/B:5-7");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-7");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10|#5/:25-35");
}
public void testGetAtomSpec_alphaOnly()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, true), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-4@CA");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-4,8@CA");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8/B:5-7@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-4,8/B:5-7@CA");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, true), "#1/A:2-5,8/B:5-7@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-5,8/B:5-7@CA");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4@CA|#1/A:2-5,8/B:5-7@CA");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-7@CA");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA");
model.addRange("5", 25, 35, " "); // empty chain code
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA|#5/:25-35@CA");
}
*/
package jalview.gui;
-import jalview.bin.Cache;
-
import java.awt.Dimension;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.bin.Console;
+
public class JAL1353bugdemo
{
@Test(groups = { "Functional" }, enabled = false)
public void test()
{
- Cache.initLogger();
+ Console.initLogger();
// final Desktop foo = new Desktop();
final JFrame cfoo = new JFrame("Crash Java");
final JDesktopPane foo = new JDesktopPane();
import org.testng.annotations.Test;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
public void setUp() throws IOException
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.initLogger();
+ Console.initLogger();
String inMenuString = ("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
+ SEQUENCE_ID
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence.DBModList;
@BeforeClass(alwaysRun = true)
public void setUp()
{
- Cache.initLogger();
+ Console.initLogger();
}
/**
{
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1579);
- assertEquals(ranges.get(0)[1], 2934);
+ assertEquals(ranges.get(0)[1], 2931); // excludes stop 2934
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 451);
{
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 2928);
- assertEquals(ranges.get(0)[1], 3992);
+ assertEquals(ranges.get(0)[1], 3989); // excludes stop 3992
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 354);
{
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 4054);
- assertEquals(ranges.get(0)[1], 4848);
+ assertEquals(ranges.get(0)[1], 4845); // excludes stop 4848
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 264);
assertEquals(ranges.get(0)[0], 7022);
assertEquals(ranges.get(0)[1], 7502);
assertEquals(ranges.get(1)[0], 1);
- assertEquals(ranges.get(1)[1], 437);
+ assertEquals(ranges.get(1)[1], 434); // excludes stop at 437
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 305);
// complement(488..1480)
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1480);
- assertEquals(ranges.get(0)[1], 488);
+ assertEquals(ranges.get(0)[1], 491); // // excludes stop at 488
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 330);
// exact length match:
assertSame(exons, EmblFlatFile.adjustForProteinLength(6, exons));
- // match if we assume exons include stop codon not in protein:
- assertSame(exons, EmblFlatFile.adjustForProteinLength(5, exons));
-
+ // patch from JAL-3725 in EmblXmlSource propagated to Flatfile
+ // match if we assume exons include stop codon not in protein:
+ int[] truncated = EmblFlatFile.adjustForProteinLength(5, exons);
+ assertEquals(Arrays.toString(truncated), "[11, 15, 21, 25, 31, 35]");
+
// truncate last exon by 6bp
- int[] truncated = EmblFlatFile.adjustForProteinLength(4, exons);
- assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
+ truncated = EmblFlatFile.adjustForProteinLength(4, exons);
+ assertEquals(Arrays.toString(truncated),"[11, 15, 21, 25, 31, 32]");
// remove last exon and truncate preceding by 1bp (so 3bp in total)
truncated = EmblFlatFile.adjustForProteinLength(3, exons);
- assertEquals("[11, 15, 21, 24]", Arrays.toString(truncated));
+ assertEquals(Arrays.toString(truncated),"[11, 15, 21, 24]");
// exact removal of exon case:
exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
truncated = EmblFlatFile.adjustForProteinLength(4, exons);
- assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
+ assertEquals(Arrays.toString(truncated), "[11, 15, 21, 27]");
// what if exons are too short for protein?
truncated = EmblFlatFile.adjustForProteinLength(7, exons);
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.JvOptionPane;
/**
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- Cache.initLogger();
+ Console.initLogger();
}
/**
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceFeature;
@BeforeClass(alwaysRun = true)
public void setUp()
{
- Cache.initLogger();
+ Console.initLogger();
}
/**
assertTrue(seqString.endsWith("FKQKS"));
map = mapping.getMap();
assertEquals(map.getFromLowest(), 6045);
- assertEquals(map.getFromHighest(), 6788);
+ assertEquals(map.getFromHighest(), 6785); // excludes stop at 6788
assertEquals(map.getToLowest(), 1);
assertEquals(map.getToHighest(), 247);
assertEquals(map.getFromRatio(), 3);
import static org.testng.Assert.assertTrue;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
Cache.setProperty("VCF_FIELDS", ".*");
Cache.setProperty("VEP_FIELDS", ".*");
Cache.setProperty("VCF_ASSEMBLY", "GRCh38=GRCh38");
- Cache.initLogger();
+ Console.initLogger();
}
@BeforeTest(alwaysRun = true)
import jalview.structure.AtomSpec;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import junit.extensions.PA;
Color mColor = new Color(0x82827d);
AtomSpecModel atomSpec = colours.get(mColor);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#0:21.A|#1:21.B");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#0:21.A|#1:21.B");
/*
* H colour is #60609f, seq1.2 mapped to structure 0 residue 22
Color hColor = new Color(0x60609f);
atomSpec = colours.get(hColor);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#0:22.A");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#0:22.A");
/*
* V colour is #ffff00, seq2.2 mapped to structure 1 residue 22
Color vColor = new Color(0xffff00);
atomSpec = colours.get(vColor);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#1:22.B");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#1:22.B");
/*
* hidden columns are Gray (128, 128, 128)
Color gray = new Color(128, 128, 128);
atomSpec = colours.get(gray);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#0:23-25.A|#1:23-25.B");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#0:23-25.A|#1:23-25.B");
/*
* S and G are both coloured #4949b6, structure residues 26-30
Color sgColour = new Color(0x4949b6);
atomSpec = colours.get(sgColour);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false),
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
"#0:26-30.A|#1:26-30.B");
}
}
\ No newline at end of file
--- /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.util;
+
+import static org.testng.Assert.assertNotNull;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.concurrent.TimeUnit;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+import io.github.classgraph.ClassGraph;
+import io.github.classgraph.ScanResult;
+import jalview.bin.Console;
+
+public class Log4jTest
+{
+ private static final int TIMEOUT = 10;
+
+ private static class Worker extends Thread
+ {
+ private final Process process;
+
+ private BufferedReader outputReader;
+
+ private BufferedReader errorReader;
+
+ private boolean exited;
+
+ private Worker(Process process)
+ {
+ this.process = process;
+ }
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ exited = process.waitFor(TIMEOUT, TimeUnit.SECONDS);
+ } catch (InterruptedException ignore)
+ {
+ return;
+ }
+ this.interrupt();
+ this.process.destroy();
+ }
+
+ public BufferedReader getOutputReader()
+ {
+ return outputReader;
+ }
+
+ public void setOutputReader(BufferedReader outputReader)
+ {
+ this.outputReader = outputReader;
+ }
+
+ public BufferedReader getErrorReader()
+ {
+ return errorReader;
+ }
+
+ public void setErrorReader(BufferedReader errorReader)
+ {
+ this.errorReader = errorReader;
+ }
+ }
+
+ private static ClassGraph scanner = null;
+
+ private static String classpath = null;
+
+ private static String java_exe = null;
+
+ public synchronized static String getClassPath()
+ {
+ if (scanner == null)
+ {
+ scanner = new ClassGraph();
+ ScanResult scan = scanner.scan();
+ classpath = scan.getClasspath();
+ java_exe = System.getProperty("java.home") + File.separator + "bin"
+ + File.separator + "java";
+
+ }
+ while (classpath == null)
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException x)
+ {
+
+ }
+ }
+ return classpath;
+ }
+
+ private Worker getJalviewDesktopRunner(String appArgs)
+ {
+ String classpath = getClassPath();
+ String cmd = java_exe + " " + " -classpath " + classpath + " "
+ + " jalview.bin.Jalview " + " "
+ + "-props test/jalview/util/log4jTestProps.jvprops " + appArgs;
+ Process proc = null;
+ Worker worker = null;
+ try
+ {
+ proc = Runtime.getRuntime().exec(cmd);
+ } catch (Throwable e)
+ {
+ e.printStackTrace();
+ }
+ if (proc != null)
+ {
+ BufferedReader outputReader = new BufferedReader(
+ new InputStreamReader(proc.getInputStream()));
+ BufferedReader errorReader = new BufferedReader(
+ new InputStreamReader(proc.getErrorStream()));
+ worker = new Worker(proc);
+ worker.start();
+ worker.setOutputReader(outputReader);
+ worker.setErrorReader(errorReader);
+ }
+ return worker;
+ }
+
+ @BeforeTest(alwaysRun = true)
+ public void initialize()
+ {
+ new Log4jTest();
+ }
+
+ @Test(groups = { "Functional" })
+ public void testLog4j()
+ {
+ String appArgs = " -open examples/uniref50.fa -nosplash -nonews -noquestionnaire -nousagestats -nowebservicediscovery";
+
+ Worker worker = getJalviewDesktopRunner(appArgs);
+ assertNotNull(worker, "worker is null");
+
+ String ln = null;
+ int count = 0;
+ boolean logTestFound = false;
+ try
+ {
+ while ((ln = worker.getErrorReader().readLine()) != null)
+ {
+ if (++count > 500)
+ {
+ break;
+ }
+ if (ln.contains(Console.LOGGING_TEST_MESSAGE))
+ {
+ logTestFound = true;
+ break;
+ }
+ }
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ if (worker != null && worker.exited == false)
+ {
+ worker.interrupt();
+ worker.process.destroy();
+ }
+ if (!logTestFound)
+ {
+ Assert.fail("Did not find Log4j Test message line '"
+ + Console.LOGGING_TEST_MESSAGE + "'");
+ }
+ }
+
+}
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.JvOptionPane;
public class MapListTest
@BeforeClass(alwaysRun = true)
public void setUp()
{
- Cache.initLogger();
+ Console.initLogger();
}
@BeforeClass(alwaysRun = true)
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-import java.awt.Color;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Iterator;
-import java.util.List;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
@BeforeClass(alwaysRun = true)
public void setUp()
{
- Cache.initLogger();
+ Console.initLogger();
}
@BeforeClass(alwaysRun = true)
--- /dev/null
+#---JalviewX Properties File---
+# HiDPI screen
+SCREENGEOMETRY_WIDTH=3840
+SCREENGEOMETRY_HEIGHT=2160
+SCREEN_WIDTH=3000
+SCREEN_HEIGHT=2000
+USAGESTATS=false
+STARTUP_FILE=examples/uniref50.fa
+SHOW_STARTUP_FILE=false
+FONT_STYLE=plain
+FONT_SIZE=10
+ANTI_ALIAS=false
+SHOW_JAVA_CONSOLE=false
+DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
+logs.Jalview.level=DEBUG
import java.util.Locale;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.JvOptionPane;
import jalview.gui.WsJobParameters;
import jalview.util.MessageManager;
public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.initLogger();
+ Console.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
}
import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.JvOptionPane;
public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.initLogger();
+ Console.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
while (disc.isRunning())
import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.JvOptionPane;
public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.initLogger();
+ Console.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
while (disc.isRunning())
import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.JvOptionPane;
import jalview.ws.jabaws.JalviewJabawsTestUtils;
import jalview.ws.jws2.jabaws2.Jws2Instance;
{
serviceTests.add("AAConWS".toLowerCase(Locale.ROOT));
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.initLogger();
+ Console.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
}
RestClient rc = new RestClient(_rc.service, alf, true);
assertNotNull("Couldn't creat RestClient job.", rc);
- jalview.bin.Cache.initLogger();
+ jalview.bin.Console.initLogger();
RestJob rjb = new RestJob(0, new RestJobThread(rc),
rc.av.getAlignment(), null);
rjb.setAlignmentForInputs(rc.service.getInputParams().values(),
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- jalview.bin.Cache.initLogger();
+ jalview.bin.Console.initLogger();
}
/**
git://source.jalview.org / jalview.git / commitdiff