buildTests
buildextclients
buildindices
-castorbinding
clean
compileApplet
distclean
help
init
+jaxb-bindings
linkcheck
makeApplet
makedist
<classpathentry kind="lib" path="lib/saaj.jar"/>
<classpathentry kind="lib" path="lib/wsdl4j.jar"/>
<classpathentry kind="lib" path="lib/xercesImpl.jar"/>
- <classpathentry kind="lib" path="lib/castor-1.1-cycle-xml.jar" sourcepath="C:/Documents and Settings/JimP/workspace-3.3/castor/src/main/java"/>
<classpathentry kind="lib" path="lib/JGoogleAnalytics_0.3.jar" sourcepath="/JGoogleAnalytics/src/main/java"/>
<classpathentry kind="lib" path="lib/vamsas-client.jar"/>
<classpathentry kind="lib" path="lib/commons-logging-1.1.1.jar"/>
<classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
<classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
<classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
- <classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
- <classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
<classpathentry kind="lib" path="lib/jabaws-min-client-2.2.0.jar" sourcepath="/clustengine"/>
<classpathentry kind="lib" path="lib/json_simple-1.1.jar" sourcepath="/Users/jimp/Downloads/json_simple-1.1-all.zip"/>
<classpathentry kind="lib" path="lib/slf4j-api-1.7.7.jar"/>
<classpathentry kind="lib" path="lib/htsjdk-2.12.0.jar"/>
<classpathentry kind="lib" path="lib/groovy-all-2.4.12-indy.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
+ <classpathentry kind="lib" path="lib/intervalstore-v0.4.jar"/>
<classpathentry kind="output" path="classes"/>
</classpath>
-.project
+/*.project
+.classpath
/dist
/clover
/classes
/tests
/test-reports
/test-output
-.externalToolBuilders/Jalview Release indices [Builder].launch
+.externalToolBuilders/*
+.settings/*
/.DS_Store
.DS_Store
/.com.apple.timemachine.supported
/jalviewApplet.jar
/benchmarking/lib
*.class
+/site
min-jaba-client.jar
regex.jar
saaj.jar
-spring-core-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven - TODO: JAL-3035 remove if no longer needed ?
-spring-web-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven - TODO: JAL-3035 remove if no longer needed ?
vamsas-client.jar
wsdl4j.jar
xercesImpl.jar
--- /dev/null
+YEAR=2018
+AUTHORS=J Procter, M Carstairs, B Soares, K Mourao, TC Ofoegbu, AM Waterhouse, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton
+AUTHORFNAMES=Jim Procter, Mungo Carstairs, Ben Soares, Kira Mourao, Tochukwu 'Charles' Ofoegbu, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+
\ No newline at end of file
<delete file="in.jar" />
</target>
+<target name="jaxb-bindings" depends="init" description="Generates JAXB bindings for supported Jalview XML models (needs xjc on the path)">
+ <delete>
+ <fileset dir="${sourceDir}/jalview/xml/binding/jalview">
+ <include name="*.java" />
+ </fileset>
+ </delete>
+ <exec executable="xjc">
+ <arg value="${schemaDir}/jalview.xsd"/>
+ <arg value="-d"/>
+ <arg value="${sourceDir}"/>
+ <arg value="-p"/>
+ <arg value="jalview.xml.binding.jalview"/>
+ </exec>
+ <delete>
+ <fileset dir="${sourceDir}/jalview/xml/binding/embl">
+ <include name="*.java" />
+ </fileset>
+ </delete>
+
+ <exec executable="xjc">
+ <arg value="${schemaDir}/embl.xsd"/>
+ <arg value="-d"/>
+ <arg value="${sourceDir}"/>
+ <arg value="-b"/>
+ <arg value="${schemaDir}/embl_bindings.xml"/>
+ <arg value="-p"/>
+ <arg value="jalview.xml.binding.embl"/>
+ </exec>
+
+ <delete>
+ <fileset dir="${sourceDir}/jalview/xml/binding/uniprot">
+ <include name="*.java" />
+ </fileset>
+ </delete>
+
+ <exec executable="xjc">
+ <arg value="${schemaDir}/uniprot.xsd"/>
+ <arg value="-d"/>
+ <arg value="${sourceDir}"/>
+ <arg value="-p"/>
+ <arg value="jalview.xml.binding.uniprot"/>
+ </exec>
+</target>
+
<target name="sourcedist" description="create jalview source distribution" depends="init">
<delete file="${source.dist.name}" />
<!-- temporary copy of source to update timestamps -->
--- /dev/null
+>BACKUP_FILES/1-6 backupfiles
+AAAARG
import jalview.datamodel.AnnotatedCollectionI
import jalview.datamodel.SequenceI
import jalview.datamodel.SequenceCollectionI
+import jalview.api.AlignViewportI
import jalview.util.Comparison
/*
/*
* to make a new instance for each alignment view
*/
- getInstance: { AnnotatedCollectionI coll, Map<SequenceI, SequenceCollectionI> map -> conserved() },
+ getInstance: { AlignViewportI view, AnnotatedCollectionI coll, Map<SequenceI, SequenceCollectionI> map -> conserved() },
/*
* method only needed if colour scheme has to recalculate
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceCollectionI;
+import jalview.api.AlignViewportI
/*
* Example script that registers two new alignment colour schemes
/*
* to make a new instance for each alignment view
*/
- getInstance: { AnnotatedCollectionI coll, Map<SequenceI, SequenceCollectionI> map -> candy() },
+ getInstance: { AlignViewportI view, AnnotatedCollectionI coll, Map<SequenceI, SequenceCollectionI> map -> candy() },
/*
* method only needed if colour scheme has to recalculate
import jalview.datamodel.AnnotatedCollectionI
import jalview.datamodel.SequenceI
import jalview.datamodel.SequenceCollectionI
+import jalview.api.AlignViewportI
import jalview.util.Comparison
/*
<mapID target="biojson" url="html/features/bioJsonFormat.html" />
<mapID target="pdbfetcher" url="html/features/pdbsequencefetcher.html" />
+ <mapID target="pdbfts" url="html/features/pdbsequencefetcher.html#pdbfts" />
<mapID target="siftsmapping" url="html/features/siftsmapping.html" />
<mapID target="pdbchooser" url="html/features/structurechooser.html" />
<mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
<mapID target="ensemblfetch" url="html/features/ensemblsequencefetcher.html" />
<mapID target="uniprotfetcher" url="html/features/uniprotsequencefetcher.html" />
+ <mapID target="uniprotfts" url="html/features/uniprotsequencefetcher.html#uniprotfts" />
<mapID target="urllinks" url="html/webServices/urllinks.html" />
<mapID target="linksprefs" url="html/features/preferences.html#links" />
<em>Calculating PCAs for aligned sequences</em><br />Jalview can
perform PCA analysis on both proteins and nucleotide sequence
alignments. In both cases, components are generated by an
- eigenvector decomposition of the matrix formed from the sum of
- substitution matrix scores at each aligned position between each
- pair of sequences - computed with one of the available score
- matrices, such as <a href="scorematrices.html#blosum62">BLOSUM62</a>,
+ eigenvector decomposition of the matrix formed from pairwise similarity
+ scores between each pair of sequences. The similarity score model is
+ selected on the <a href="calculations.html">calculations dialog</a>, and
+ may use one of the available score matrices, such as
+ <a href="scorematrices.html#blosum62">BLOSUM62</a>,
<a href="scorematrices.html#pam250">PAM250</a>, or the <a
href="scorematrices.html#simplenucleotide">simple single
- nucleotide substitution matrix</a>. The options available for
- calculation are given in the <strong><em>Change
- Parameters</em></strong> menu.
+ nucleotide substitution matrix</a>, or by sequence percentage identity,
+ or sequence feature similarity.
</p>
<img src="pcaviewer.gif">
<p>
</p>
<p>
<strong><em>Selecting Sequence Leaf Nodes</em></strong><br>
- Selecting sequence ids at the leaves of the tree selects the
+ Selecting sequence IDs at the leaves of the tree selects the
corresponding sequences in the original alignment. These selections
are also reflected in any other analysis windows associated with the
alignment, such as another tree viewer.
</p>
<p>
- <strong><em>Grouping sequences by partitioning the
- tree at a particular distanec</em></strong><br> Clicking anywhere along
+ <strong><em><a name="partitioning">Grouping sequences by partitioning</a> the
+ tree at a particular distance</em></strong><br> Clicking anywhere along
the extent of the tree (but not on a leaf or internal node) defines
a tree 'partition', by cutting every branch of the tree spanning the
depth where the mouse-click occurred. Groups are created containing
sequences at the leaves of each connected sub tree. These groups are
each given a different colour, which are reflected in other windows
- in the same way as if the sequence ids were selected, and can be
+ in the same way as if the sequence IDs were selected, and can be
edited in the same way as user defined sequence groups.
</p>
<p>
identifying specific patterns of conservation and mutation
corresponding to the overall phylogenetic structure, when combined
with the <a href="../colourSchemes/conservation.html">conservation
- based colour scheme</a>.
+ based colour scheme</a>.To distinguish parts of the alignment assigned
+ to different groups, you may also enable the Sequence ID colour
+ scheme via the <a href="../menus/alwcolour.html">Alignment
+ window's Colours menu</a> (<em>Since 2.11</em>).
</p>
<p>
<strong><em>Selecting Subtrees and changing the branch
<p>
<strong>Colour schemes</strong>
</p>
- <p>Jalview allows the user to set a background colour for the
+ <p>Jalview allows the user to set a colour scheme for the
whole alignment view or for each group defined on regions within it.</p>
- <p>To change the background colour, simply select the colour from
+ <p>To change the colour for a view, simply select a new colour scheme from
the "Colour" menu.</p>
<p>To change the colour of a group, right click on any residue
within a group and use the popup menu to define the group colour.</p>
- <p>At the top of the "Colour" menu the tick box
- "Apply Background Colour to all groups". This is ticked by
+ <p>At the top of the "Colour" menu you'll see a tick box
+ "Apply Colour to all groups". This is ticked by
default so that a chosen colour scheme will be applied to all
existing groups. If you wish to maintain the colour scheme for
- defined groups, make sure you deselect this option before changing
- the background colour.</p>
+ defined groups, make sure you deselect this option before selecting
+ a new scheme in the Colour menu.</p>
<p>
The <strong>"Colour→<a
href="../colourSchemes/textcolour.html">Colour Text...</a>"
alt="PDB sequence fetcher (introduced in Jalview 2.9)" />
<p>
- <strong>Searching the PDB Database</strong>
+ <a name="pdbfts"><strong>Searching the PDB Database</strong></a>
</p>
<p>To search the PDB, begin typing in the text box. If the
'autosearch' checkbox is enabled, then the results of your query
sequence alignments and EPS files.
</li>
<li>The <a href="#editing"><strong>"Editing"</strong>
- Preferences</a> tab contains settings affecting the export of
- sequence alignments and EPS files.
+ Preferences</a> tab contains settings affecting behaviour when editing alignments.
</li>
<li>The <a href="../webServices/webServicesPrefs.html"><strong>"Web
Service"</strong> Preferences</a> tab allows you to configure the <a
the backbone atoms in the PDB file will be extracted as annotation
lines shown on the alignment.
<p>
- <em>Default structure viewer</em> - choose JMOL or CHIMERA for
+ <em>Default structure viewer</em> - choose Jmol or CHIMERA for
viewing 3D structures.
<p>
<em>Path to Chimera program</em> - Optional, as Jalview will search
Preferences tab</strong></a>
</p>
<p>
- <em>Default Browser (Unix)</em><br> Its difficult in Java to
+ <em>Default Browser (Unix)</em><br> It's difficult in Java to
detect the default web browser for Unix users. If Jalview can't find
your default web browser, enter the name or full path to your web
browser application.
just those you have configured yourself <em>via</em> the <em>Edit
Links</em> buttons. Press <em>Show all</em> to clear any filters.
</p>
- <p>The links table is prepoulated with persistent URLs for many common
+ <p>The links table is prepopulated with persistent URLs for many common
bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from
the <em>identifiers.org</em> website, and the names and URLs are not
user editable.
allows the user to set a default rendering style for EPS export:
<ul>
<li>"Prompt each time"<br> Choose this to be
- asked select between Lineart and Text each time you make an EPS
+ asked to select between Lineart and Text each time you make an EPS
file.
</li>
<li>"Lineart"<br> EPS files will accurately
ignored if <em>"Automatically set ID width"</em> is set.
</p>
<p>
- <em>Sequence//Start-End Numbering</em><br> The output tab also
+ <em>Sequence/Start-End Numbering</em><br> The output tab also
has a group of checkboxes for each file format. If these are ticked,
then Jalview will write files with the start and end sequence
positions appended to each sequence id:
</p>
<p>
- <strong>Searching the UniProt Database</strong>
+ <a name="uniprotfts"><strong>Searching the UniProt Database</strong></a>
</p>
<p>To search UniProt, simply begin typing in the text box. If the
'autosearch' check box is enabled, then after a short delay (about
</strong> <em>See <a href="../colourSchemes/index.html">colours</a>
for a description of all colour schemes.
</em><br></li>
- <li><strong>By Conservation<br>
+ <li><strong>Sequence ID<br></strong><em>Shades
+ sequences using their Sequence ID colour. Useful when
+ performing <a
+ href="../calculations/treeviewer.html#partitioning">tree
+ based subfamily analysis</a>.
+ </em></li>
+ <li><strong>By Conservation<br>
</strong><em>See <a href="../colourSchemes/conservation.html">Colouring
by Conservation</a>.
</em><br></li>
a description of all colour schemes.
</em><br>
</li>
+ <li><strong>Sequence ID<br></strong><em>Shades
+ sequences using their Sequence ID colour. Useful when performing
+ <a href="../calculations/treeviewer.html#partitioning">tree
+ based subfamily analysis</a>.
+ </em></li>
<li><strong>By Conservation<br>
</strong><em>See <a href="../colourSchemes/conservation.html">Colouring
by Conservation</a>.
<td width="60" nowrap>
<div align="center">
<strong><a name="Jalview.2.11.0">2.11.0</a><br />
- <em>8/09/2018</em></strong>
+ <em>29/01/2019</em></strong>
</div>
</td>
- <td><div align="left">
- <em></em>
- <ul>
- <li>
- <!-- JAL-2865 -->Jalview doesn't hang when closing windows or the overview updates with large alignments.
- </li>
- </ul>
- </div></td>
- <td><div align="left">
- <em></em>
- <ul>
- <li>
- <!-- JAL-3035 -->DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop
- </li>
- </ul>
- </div></td>
+ <td><div align="left">
+ <em>Deprecations</em>
+ <ul>
+ <li>
+ <!-- JAL-3035 -->DAS sequence retrieval and annotation
+ capabilities removed from the Jalview Desktop
+ </li>
+ </ul>
+ <em>Release Processes</em>
+ <ul>
+ <li>Atlassian Bamboo continuous integration server for unattended Test Suite execution</li>
+ <li><!-- JAL-2864 -->Memory test suite to detect leaks in common operations</li>
+ </ul>
+ </div></td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-2865 -->Jalview hangs when closing windows
+ or the overview updates with large alignments.
+ </li>
+ <li>
+ <!-- JAL-2865 -->Tree and PCA calculation fails for selected
+ region if columns were selected by dragging right-to-left
+ and the mouse moved to the left of the first column.
+ </li>
+ <li>
+ <!-- JAL-2846 -->Error message for trying to load in invalid
+ URLs doesn't tell users the invalid URL
+ </li>
+ </ul>
+ <em>Editing</em>
+ <ul>
+ <li>
+ <!-- JAL-2822 -->Start and End should be updated when
+ sequence data at beginning or end of alignment added/removed
+ via 'Edit' sequence
+ </li>
+ <li>
+ <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
+ sequence features correctly when start of sequence is
+ removed (Known defect since 2.10)
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ </ul>
+ <em>New Known Defects</em>
+ <ul>
+ <li>
+ <!-- JAL-3178 -->Nonpositional features lose feature group
+ on export as jalview features file
+ </li>
+ </ul>
+ </div></td>
</tr>
<tr>
<td width="60" nowrap>
--- /dev/null
+# source: IUPAC codes as per http://www.insdc.org/documents/feature_table.html#7.4.1
+DNA
+R AG
+Y TC
+W AT
+S GC
+M AC
+K GT
+H ATC
+B GTC
+V GAC
+D GAT
+N GATC
--- /dev/null
+-- source: ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt (19th March 2018)
+-- SGC3 name edited slightly so as to fit all on one line
+--**************************************************************************
+-- This is the NCBI genetic code table
+-- Initial base data set from Andrzej Elzanowski while at PIR International
+-- Addition of Eubacterial and Alternative Yeast by J.Ostell at NCBI
+-- Base 1-3 of each codon have been added as comments to facilitate
+-- readability at the suggestion of Peter Rice, EMBL
+-- Later additions by Taxonomy Group staff at NCBI
+--
+-- Version 4.2
+-- Added Karyorelict nuclear genetic code 27
+-- Added Condylostoma nuclear genetic code 28
+-- Added Mesodinium nuclear genetic code 29
+-- Added Peritrich nuclear genetic code 30
+-- Added Blastocrithidia nuclear genetic code 31
+--
+-- Version 4.1
+-- Added Pachysolen tannophilus nuclear genetic code 26
+--
+-- Version 4.0
+-- Updated version to reflect numerous undocumented changes:
+-- Corrected start codons for genetic code 25
+-- Name of new genetic code is Candidate Division SR1 and Gracilibacteria
+-- Added candidate division SR1 nuclear genetic code 25
+-- Added GTG as start codon for genetic code 24
+-- Corrected Pterobranchia Mitochondrial genetic code (24)
+-- Added genetic code 24, Pterobranchia Mitochondrial
+-- Genetic code 11 is now Bacterial, Archaeal and Plant Plastid
+-- Fixed capitalization of mitochondrial in codes 22 and 23
+-- Added GTG, ATA, and TTG as alternative start codons to code 13
+--
+-- Version 3.9
+-- Code 14 differs from code 9 only by translating UAA to Tyr rather than
+-- STOP. A recent study (Telford et al, 2000) has found no evidence that
+-- the codon UAA codes for Tyr in the flatworms, but other opinions exist.
+-- There are very few GenBank records that are translated with code 14,
+-- but a test translation shows that retranslating these records with code
+-- 9 can cause premature terminations. Therefore, GenBank will maintain
+-- code 14 until further information becomes available.
+--
+-- Version 3.8
+-- Added GTG start to Echinoderm mitochondrial code, code 9
+--
+-- Version 3.7
+-- Added code 23 Thraustochytrium mitochondrial code
+-- formerly OGMP code 93
+-- submitted by Gertraude Berger, Ph.D.
+--
+-- Version 3.6
+-- Added code 22 TAG-Leu, TCA-stop
+-- found in mitochondrial DNA of Scenedesmus obliquus
+-- submitted by Gertraude Berger, Ph.D.
+-- Organelle Genome Megasequencing Program, Univ Montreal
+--
+-- Version 3.5
+-- Added code 21, Trematode Mitochondrial
+-- (as deduced from: Garey & Wolstenholme,1989; Ohama et al, 1990)
+-- Added code 16, Chlorophycean Mitochondrial
+-- (TAG can translated to Leucine instaed to STOP in chlorophyceans
+-- and fungi)
+--
+-- Version 3.4
+-- Added CTG,TTG as allowed alternate start codons in Standard code.
+-- Prats et al. 1989, Hann et al. 1992
+--
+-- Version 3.3 - 10/13/95
+-- Added alternate intiation codon ATC to code 5
+-- based on complete mitochondrial genome of honeybee
+-- Crozier and Crozier (1993)
+--
+-- Version 3.2 - 6/24/95
+-- Code Comments
+-- 10 Alternative Ciliate Macronuclear renamed to Euplotid Macro...
+-- 15 Blepharisma Macro.. code added
+-- 5 Invertebrate Mito.. GTG allowed as alternate initiator
+-- 11 Eubacterial renamed to Bacterial as most alternate starts
+-- have been found in Archea
+--
+--
+-- Version 3.1 - 1995
+-- Updated as per Andrzej Elzanowski at NCBI
+-- Complete documentation in NCBI toolkit documentation
+-- Note: 2 genetic codes have been deleted
+--
+-- Old id Use id - Notes
+--
+-- id 7 id 4 - Kinetoplast code now merged in code id 4
+-- id 8 id 1 - all plant chloroplast differences due to RNA edit
+--
+--*************************************************************************
+
+Genetic-code-table ::= {
+ {
+ name "Standard" ,
+ name "SGC0" ,
+ id 1 ,
+ ncbieaa "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "---M------**--*----M---------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Vertebrate Mitochondrial" ,
+ name "SGC1" ,
+ id 2 ,
+ ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG",
+ sncbieaa "----------**--------------------MMMM----------**---M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Yeast Mitochondrial" ,
+ name "SGC2" ,
+ id 3 ,
+ ncbieaa "FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------**----------------------MM----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Mold / Protozoan / Coelenterate Mitochondrial; Mycoplasma; Spiroplasma" ,
+ name "SGC3" ,
+ id 4 ,
+ ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "--MM------**-------M------------MMMM---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Invertebrate Mitochondrial" ,
+ name "SGC4" ,
+ id 5 ,
+ ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG",
+ sncbieaa "---M------**--------------------MMMM---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear" ,
+ name "SGC5" ,
+ id 6 ,
+ ncbieaa "FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "--------------*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Echinoderm Mitochondrial; Flatworm Mitochondrial" ,
+ name "SGC8" ,
+ id 9 ,
+ ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
+ sncbieaa "----------**-----------------------M---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Euplotid Nuclear" ,
+ name "SGC9" ,
+ id 10 ,
+ ncbieaa "FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------**-----------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Bacterial, Archaeal and Plant Plastid" ,
+ id 11 ,
+ ncbieaa "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "---M------**--*----M------------MMMM---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Alternative Yeast Nuclear" ,
+ id 12 ,
+ ncbieaa "FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------**--*----M---------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Ascidian Mitochondrial" ,
+ id 13 ,
+ ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG",
+ sncbieaa "---M------**----------------------MM---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Alternative Flatworm Mitochondrial" ,
+ id 14 ,
+ ncbieaa "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
+ sncbieaa "-----------*-----------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Blepharisma Macronuclear" ,
+ id 15 ,
+ ncbieaa "FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------*---*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Chlorophycean Mitochondrial" ,
+ id 16 ,
+ ncbieaa "FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------*---*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Trematode Mitochondrial" ,
+ id 21 ,
+ ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
+ sncbieaa "----------**-----------------------M---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Scenedesmus obliquus Mitochondrial" ,
+ id 22 ,
+ ncbieaa "FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "------*---*---*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Thraustochytrium Mitochondrial" ,
+ id 23 ,
+ ncbieaa "FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "--*-------**--*-----------------M--M---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Pterobranchia Mitochondrial" ,
+ id 24 ,
+ ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG",
+ sncbieaa "---M------**-------M---------------M---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Candidate Division SR1 and Gracilibacteria" ,
+ id 25 ,
+ ncbieaa "FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "---M------**-----------------------M---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Pachysolen tannophilus Nuclear" ,
+ id 26 ,
+ ncbieaa "FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------**--*----M---------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Karyorelict Nuclear" ,
+ id 27 ,
+ ncbieaa "FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "--------------*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Condylostoma Nuclear" ,
+ id 28 ,
+ ncbieaa "FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------**--*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Mesodinium Nuclear" ,
+ id 29 ,
+ ncbieaa "FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "--------------*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Peritrich Nuclear" ,
+ id 30 ,
+ ncbieaa "FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "--------------*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Blastocrithidia Nuclear" ,
+ id 31 ,
+ ncbieaa "FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------**-----------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ }
+}
action.close_all = Close all
action.load_project = Load Project
action.save_project = Save Project
+action.save_project_as = Save Project as...
action.quit = Quit
label.quit_jalview = Quit Jalview?
action.expand_views = Expand Views
action.new_view = New View
action.close = Close
action.add = Add
-action.save_as_default = Save as default
action.save_as = Save as...
action.save = Save
-action.cancel_fetch = Cancel Fetch
action.change_font = Change Font
action.change_font_tree_panel = Change Font (Tree Panel)
action.colour = Colour
action.view_flanking_regions = Show flanking regions
label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment
label.structures_manager = Structures Manager
-label.nickname = Nickname:
label.url = URL
label.url\: = URL:
label.input_file_url = Enter URL or Input File
label.service_action = Service Action:
label.post_url = POST URL:
label.url_suffix = URL Suffix
-label.sequence_source = Sequence Source
label.per_seq = per Sequence
label.result_vertically_separable = Results are vertically separable
label.amend = Amend
label.average_distance_identity = Average Distance Using % Identity
label.neighbour_joining_identity = Neighbour Joining Using % Identity
label.choose_calculation = Choose Calculation
-label.treecalc_title = {0} Using {1}
+label.calc_title = {0} Using {1}
label.tree_calc_av = Average Distance
label.tree_calc_nj = Neighbour Joining
-label.select_score_model = Select score model
label.score_model_pid = % Identity
label.score_model_blosum62 = BLOSUM62
label.score_model_pam250 = PAM 250
label.colourScheme_nucleotide = Nucleotide
label.colourScheme_t-coffee_scores = T-Coffee Scores
label.colourScheme_rna_helices = By RNA Helices
+label.colourScheme_sequence_id = Sequence ID Colour
label.blc = BLC
label.fasta = Fasta
label.msf = MSF
label.channels = Channels
label.channel_title_item_count = {0} ({1})
label.blog_item_published_on_date = {0} {1}
-label.select_das_service_from_table = Select a DAS service from the table to read a full description here.</font></html>
label.session_update = Session Update
label.new_vamsas_session = New Vamsas Session
action.load_vamsas_session = Load Vamsas Session...
label.save_colours = Save Colours
label.load_colours_tooltip = Load feature colours and filters from file
label.save_colours_tooltip = Save feature colours and filters to file
-label.fetch_das_features = Fetch DAS Features
label.selected_database_to_fetch_from = Selected {0} database {1} to fetch from {2}
label.database_param = Database: {0}
label.example = Example
label.no_pdb_id_in_file = No PDB Id in File
label.couldnt_read_pasted_text = Couldn't read the pasted text {0}
label.error_parsing_text = Error parsing text
-label.enter_local_das_source = Enter Nickname & URL of Local DAS Source
-label.you_can_only_edit_or_remove_local_das_sources = You can only edit or remove local DAS Sources!
-label.public_das_source = Public DAS source - not editable
label.input_alignment_from_url = Input Alignment From URL
label.input_alignment = Input Alignment
label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas session.
label.vamsas_document_import_failed = Vamsas Document Import Failed
-label.couldnt_locate = Couldn't locate {0}
+label.couldnt_locate = Could not locate {0}
label.url_not_found = URL not found
label.new_sequence_url_link = New sequence URL link
label.cannot_edit_annotations_in_wrapped_view = Cannot edit annotations in wrapped view
label.error_loading_file = Error loading file
label.problems_opening_file = Encountered problems opening {0}!!
label.file_open_error = File open error
-label.no_das_sources_selected_warn = No das sources were selected.\nPlease select some sources and\ntry again.
-label.no_das_sources_selected_title = No DAS Sources Selected
label.colour_scheme_exists_overwrite = Colour scheme {0} exists.\nContinue saving colour scheme as {1}?"
label.duplicate_scheme_name = Duplicate scheme name
label.jalview_new_questionnaire = There is a new Questionnaire available. Would you like to complete it now ?\n
label.create_sequence_feature = Create Sequence Feature...
label.edit_sequence = Edit Sequence
label.edit_sequences = Edit Sequences
+label.insert_gap = Insert 1 gap
+label.insert_gaps = Insert {0} gaps
+label.delete_gap = Delete 1 gap
+label.delete_gaps = Delete {0} gaps
label.sequence_details = Sequence Details
label.jmol_help = Jmol Help
label.chimera_help = Chimera Help
label.connections = Connections
label.output = Output
label.editing = Editing
-label.das_settings = DAS Settings
label.web_services = Web Services
label.right_click_to_edit_currently_selected_parameter = Right click to edit currently selected parameter.
label.let_jmol_manage_structure_colours = Let Jmol manage structure colours
label.details = Details
label.options = Options
label.parameters = Parameters
-label.available_das_sources = Available DAS Sources
-label.full_details = Full Details
-label.authority = Authority
-label.type = Type
label.proxy_server = Proxy Server
label.file_output = File Output
label.select_input_type = Select input type
label.add_sequences = Add Sequences
label.new_window = New Window
label.split_window = Split Window
-label.refresh_available_sources = Refresh Available Sources
-label.use_registry = Use Registry
-label.add_local_source = Add Local Source
label.set_as_default = Set as Default
label.show_labels = Show labels
action.background_colour = Background Colour...
label.view_and_change_parameters_before_running_calculation = View and change parameters before running calculation
label.view_documentation = View documentation
label.select_return_type = Select return type
-label.translation_of_params = Translation of {0}
+label.translation_of_params = Translation of {0} (Table {1})
label.features_for_params = Features for - {0}
label.annotations_for_params = Annotations for - {0}
label.generating_features_for_params = Generating features for - {0}
label.unable_start_web_service_analysis = Unable to start web service analysis
label.job_couldnt_be_started_check_input = The Job couldn't be started. Please check your input, and the Jalview console for any warning messages.
label.prompt_each_time = Prompt each time
-label.use_source = Use Source
label.couldnt_save_project = Couldn't save project
label.error_whilst_saving_current_state_to = Error whilst saving current state to {0}
label.error_whilst_loading_project_from = Error whilst loading project from {0}
label.save_alignment_to_file = Save Alignment to file
label.save_features_to_file = Save Features to File
label.save_annotation_to_file = Save Annotation to File
-label.no_features_on_alignment = No features found on alignment
label.save_pdb_file = Save PDB File
label.save_text_to_file = Save Text to File
label.save_state = Save State
exception.invocation_target_calling_url = InvocationTargetException while calling openURL: {0}
exception.illegal_access_calling_url = IllegalAccessException while calling openURL: {0}
exception.interrupted_launching_browser = InterruptedException while launching browser: {0}
-exception.das_source_doesnt_support_sequence_command = Source {0} does not support the sequence command.
-exception.invalid_das_source = Invalid das source: {0}
exception.ebiembl_retrieval_failed_on = EBI EMBL XML retrieval failed on {0}:{1}
exception.no_pdb_records_for_chain = No PDB Records for {0} chain {1}
exception.unexpected_handling_rnaml_translation_for_pdb = Unexpected exception when handling RNAML translation of PDB data
status.processing = Processing...
status.refreshing_web_service_menus = Refreshing Web Service Menus
status.collecting_job_results = Collecting job results.
-status.fetching_das_sequence_features = Fetching DAS Sequence Features
-status.no_das_sources_active = No DAS Sources Active
-status.das_feature_fetching_cancelled = DAS Feature Fetching Cancelled
-status.das_feature_fetching_complete = DAS Feature Fetching Complete
status.fetching_db_refs = Fetching db refs
status.loading_cached_pdb_entries = Loading Cached PDB Entries
status.searching_for_pdb_structures = Searching for PDB Structures
warn.urls_no_jaba = URLs without any JABA Services
info.validate_jabaws_server = Validate JabaWS Server ?\n(Look in console output for results)
label.test_server = Test Server?
-info.you_want_jalview_to_find_uniprot_accessions = Do you want Jalview to find\nUniprot Accession ids for given sequence names?
-label.find_uniprot_accession_ids = Find Uniprot Accession Ids
label.new_sequence_fetcher = New Sequence Fetcher
label.additional_sequence_fetcher = Additional Sequence Fetcher
label.select_database_retrieval_source = Select Database Retrieval Source
label.SEQUENCE_ID_for_DB_ACCESSION2 = URL links using '$SEQUENCE_ID$' for DB accessions now use '$DB_ACCESSION$'.
label.do_not_display_again = Do not display this message again
exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one line
-label.filter = Filter text:
action.customfilter = Custom only
action.showall = Show All
label.insert = Insert:
warn.name_cannot_be_duplicate = User-defined URL names must be unique and cannot be MIRIAM ids
label.output_seq_details = Output Sequence Details to list all database references
label.urllinks = Links
-label.default_cache_size = Default Cache Size
action.clear_cached_items = Clear Cached Items
label.togglehidden = Show hidden regions
label.quality_descr = Alignment Quality based on Blosum62 scores
label.graduated_colour = Graduated Colour
label.by_text_of = By text of
label.by_range_of = By range of
-label.filters_tooltip = Click to set or amend filters
label.or = Or
label.and = And
label.sequence_feature_colours = Sequence Feature Colours
label.most_polymer_residues = Most Polymer Residues
label.cached_structures = Cached Structures
label.free_text_search = Free Text Search
+label.backupfiles_confirm_delete = Confirm delete
+label.backupfiles_confirm_delete_old_files = Delete the following older backup files? (see the Backups tab in Preferences for more options)
+label.backupfiles_confirm_save_file = Confirm save file
+label.backupfiles_confirm_save_file_backupfiles_roll_wrong = Something possibly went wrong with the backups of this file.
+label.backupfiles_confirm_save_new_saved_file_ok = The new saved file seems okay.
+label.backupfiles_confirm_save_new_saved_file_not_ok = The new saved file might not be okay.
+label.backups = Backups
+label.backup = Backup
+label.backup_files = Backup Files
+label.enable_backupfiles = Enable backup files
+label.backup_filename_strategy = Backup filename strategy
+label.append_to_filename = Append to filename (%n is replaced by the backup number)
+label.append_to_filename_tooltip = %n in the text will be replaced by the backup number. The text will appear after the filename. See the summary box above.
+label.index_digits = Number of digits to use for the backup number (%n)
+label.summary_of_backups_scheme = Summary of backup scheme
+label.increment_index = Increase appended text numbers - newest file has largest number.
+label.reverse_roll = "Roll" appended text numbers - newest backup file is always number 1.
+label.keep_files = Deleting old backup files
+label.keep_all_backup_files = Do not delete old backup files
+label.keep_only_this_number_of_backup_files = Keep only this number of most recent backup files
+label.autodelete_old_backup_files = Autodelete old backup files:
+label.always_ask = Always ask
+label.auto_delete = Automatically delete
+label.filename = filename
+label.braced_oldest = (oldest)
+label.braced_newest = (most recent)
+label.configuration = Configuration
+label.configure_feature_tooltip = Click to configure variable colour or filters
+label.schemes = Schemes
+label.customise = Customise
+label.default = Default
+label.single_file = Single backup
+label.keep_all_versions = Keep all versions
+label.rolled_backups = Rolled backup files
+label.previously_saved_scheme = Previously saved scheme
+label.no_backup_files = NO BACKUP FILES
+label.include_backup_files = Include backup files
+label.cancel_changes = Cancel changes
+label.warning_confirm_change_reverse = Warning!\nIf you change the increment/decrement of the backup filename number, without changing the suffix or number of digits,\nthis may cause loss of backup files created with the previous backup filename scheme.\nAre you sure you wish to do this?
+label.change_increment_decrement = Change increment/decrement?
+label.was_previous = was {0}
+label.newerdelete_replacement_line = Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted and replaced by apparently older file\n''{1}''\t(modified {3}, size {5}).
+label.confirm_deletion_or_rename = Confirm deletion of ''{0}'' or rename to ''{1}''?
+label.newerdelete_line = Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted but is newer than the oldest remaining backup file\n''{1}''\t(modified {3}, size {5}).
+label.confirm_deletion = Confirm deletion of ''{0}''?
+label.delete = Delete
+label.rename = Rename
+label.keep = Keep
+label.file_info = (modified {0}, size {1})
+label.annotation_name = Annotation Name
+label.annotation_description = Annotation Description
+label.edit_annotation_name_description = Edit Annotation Name/Description
+label.alignment = alignment
+label.pca = PCA
+label.create_image_of = Create {0} image of {1}
+label.click_to_edit = Click to edit, right-click for menu
+label.by_annotation_tooltip = Annotation Colour is configured from the main Colour menu
action.close_all = Cerrar todo
action.load_project = Cargar proyecto
action.save_project = Guardar proyecto
+action.save_project_as = Guardar proyecto como...
action.quit = Salir
label.quit_jalview = Salir Javliew?
action.expand_views = Expandir vistas
action.new_view = Nueva vista
action.close = Cerrar
action.add = Añadir
-action.save_as_default = Guardar como por defecto
action.save_as = Guardar como
action.save = Guardar
-action.cancel_fetch = Cancelar búsqueda
action.change_font = Cambiar Fuente
action.change_font_tree_panel = Cambiar fuente (panel del árbol)
action.colour = Color
action.view_flanking_regions = Mostrar flancos
label.view_flanking_regions = Mostrar los datos de la secuencia a ambos lados de las subsecuencias implicadas en este alineamiento
label.structures_manager = Administrar estructuras
-label.nickname = Sobrenombre:
label.url\: = URL:
label.url = URL
label.input_file_url = Introducir URL en el fichero de entrada
label.service_action = Acción de servicio:
label.post_url = POST URL:
label.url_suffix = URL Sufijo
-label.sequence_source = Fuente de la secuencia
label.per_seq = por secuencia
label.result_vertically_separable = Los resultados son separables verticalmente
label.amend = Modificar
label.average_distance_identity = Distancia Media Usando % de Identidad
label.neighbour_joining_identity = Unir vecinos utilizando % de Identidad
label.choose_calculation = Elegir el cálculo
-label.treecalc_title = {0} utilizando {1}
+label.calc_title = {0} utilizando {1}
label.tree_calc_av = Distancia media
label.tree_calc_nj = Unir vecinos
-label.select_score_model = Selecciones modelo de puntuación
label.score_model_pid = % Identidad
label.score_model_blosum62 = BLOSUM62
label.score_model_pam250 = PAM 250
label.colourScheme_nucleotide = Nucleótido
label.colourScheme_t-coffee_scores = Puntuación del T-Coffee
label.colourScheme_rna_helices = Por hélices de RNA
+label.colourScheme_sequence_id = Color de ID de secuencia
label.blc = BLC
label.fasta = Fasta
label.msf = MSF
label.channels = Canales
label.channel_title_item_count = {0} ({1})
label.blog_item_published_on_date = {0} {1}
-label.select_das_service_from_table = Seleccionar servicio DAS de la tabla para leer una descripción completa aquí.
label.session_update = Actualizar sesión
label.new_vamsas_session = Nueva sesión Vamsas
action.save_vamsas_session = Guardar Sesión Vamsas
label.save_colours = Guardar colores
label.load_colours_tooltip = Cargar colores y filtros desde fichero
label.save_colours_tooltip = Guardar colores y filtros en fichero
-label.fetch_das_features = Recuperar funciones DAS
label.selected_database_to_fetch_from = Seleccionada {0} Base de datos {1} para buscar de {2}
label.database_param = Base de datos: {0}
label.example = Ejemplo
label.no_pdb_id_in_file = No hay un Id PDB en el fichero
label.couldnt_read_pasted_text = No se pudo leer el texto pegado {0}
label.error_parsing_text = Error analizando el texto
-label.enter_local_das_source = Intruduzca el Nickname & URL de la fuente DAS local
-label.you_can_only_edit_or_remove_local_das_sources = Sólo puedes editar o eliminar fuentes DAS locales!
-label.public_das_source = Fuente pública DAS - no editable
label.input_alignment_from_url = Alineamiento de entrada desde URL
label.input_alignment = Alineamiento de entrada
label.couldnt_import_as_vamsas_session = No se pudo importar {0} como una nueva sesión Vamsas.
label.error_loading_file = Error al cargar el fichero
label.problems_opening_file = Encontrados problemas al abrir el fichero {0}!!
label.file_open_error = Error al abrir el fichero
-label.no_das_sources_selected_warn = No han sido seleccionadas fuentes DAS.\nPor favor, seleccione algunas fuentes y\npruebe de nuevo.
-label.no_das_sources_selected_title = No han sido seleccionadas fuentes DAS
label.colour_scheme_exists_overwrite = El esquema de colores {0} ya existe.\nContinuar guardando el esquema de colores como {1}?
label.duplicate_scheme_name = Duplicar nombre de esquema
label.jalview_new_questionnaire = Hay un nuevo cuestionario disponible. Querr\u00EDa completarlo ahora ?\n
label.create_sequence_feature = Crear función de secuencia
label.edit_sequence = Editar secuencia
label.edit_sequences = Editar secuencias
+label.insert_gap = Insertar 1 hueco
+label.insert_gaps = Insertar {0} huecos
+label.delete_gap = Borrar 1 hueco
+label.delete_gaps = Borrar {0} huecos
label.sequence_details = Detalles de la secuencia
label.jmol_help = Ayuda de Jmol
# Todos/Todas is gender-sensitive, but currently only used for feminine (cadena / anotación)!
label.connections = Conexiones
label.output = Salida
label.editing = Edición
-label.das_settings = Configuración DAS
label.web_services = Servicios web
label.right_click_to_edit_currently_selected_parameter = Haga clic en el botón derecho para editar el parámetro seleccionado actualmente.
label.let_jmol_manage_structure_colours = Permitir que Jmol gestione la estructuras cromáticas
label.details = Detalles
label.options = Opciones
label.parameters = Paramétros
-label.available_das_sources = Fuentes DAS disponibles
-label.full_details = Detalles completos
-label.authority = Autoridad
-label.type = Tipo
label.proxy_server = Servidor proxy
label.file_output = Fichero de salida
label.select_input_type = Seleccionar el tipo de entrada
label.sort_alignment_new_tree = Alinear el alineamiento con el nuevo árbol
label.add_sequences = Añadir secuencias
label.new_window = Nueva ventana
-label.refresh_available_sources = Refrescar las fuentes disponibles
-label.use_registry = Utilizar el registro
-label.add_local_source = Añadir fuente local
label.set_as_default = Establecer por defecto
label.show_labels = Mostrar etiquetas
label.associate_nodes_with = Asociar nodos con
label.view_and_change_parameters_before_running_calculation = Ver y cambiar los parámetros antes de lanzar el cálculo
label.view_documentation = Ver documentación
label.select_return_type = Seleccionar el tipo de retorno
-label.translation_of_params = Traducción de {0}
+label.translation_of_params = Traducción de {0} (Tabla {1})
label.features_for_params = Características de - {0}
label.annotations_for_params = Anotaciones de - {0}
label.generating_features_for_params = Generando características de - {0}
label.unable_start_web_service_analysis = No es posible iniciar el servicio web de análisis
label.job_couldnt_be_started_check_input = El trabajo no puede arrancarse. Por favor, compruebe los parámetros de entrada y los mensajes de advertencia de la consola de Jalview.
label.prompt_each_time = Preguntar siempre
-label.use_source = Fuente
label.couldnt_save_project = No es posible guardar el proyecto
label.error_whilst_saving_current_state_to = Error mientras se guardaba el estado a {0}
label.error_whilst_loading_project_from = Error cargando el proyecto desde {0}
label.save_alignment_to_file = Guardar Alineamiento en fichero
label.save_features_to_file = Guardar Características en un fichero
label.save_annotation_to_file = Guardar Anotación en un fichero
-label.no_features_on_alignment = No se han encontrado características en el alineamiento
label.save_pdb_file = Guardar fichero PDB
label.save_text_to_file = Guardar Texto en un fichero
label.save_state = Guardar estado
exception.invocation_target_calling_url = InvocationTargetException mientras se invocaba openURL: {0}
exception.illegal_access_calling_url = IllegalAccessException mientras se invocaba openURL: {0}
exception.interrupted_launching_browser = InterruptedException mientras se lanzaba el navegador: {0}
-exception.das_source_doesnt_support_sequence_command = La fuente {0} no soporta el comando sequence.
-exception.invalid_das_source = Fuente DAS no válida: {0}
exception.ebiembl_retrieval_failed_on = La recuperación de datos EBI EMBL XML ha fallado en {0}:{1}
exception.no_pdb_records_for_chain = No se han encontrado registros {0} para la cadena {1}
exception.unexpected_handling_rnaml_translation_for_pdb = Excepcion inesperada cuando se traducían a RNAML los datos PDB
status.processing = Procesando...
status.refreshing_web_service_menus = Refrescando los menús de servicios web
status.collecting_job_results = Recolectando los resultados de los trabajos.
-status.fetching_das_sequence_features = Recuperando las características DAS de las secuencias
-status.no_das_sources_active = No existe ninguna fuente DAS activa
-status.das_feature_fetching_cancelled = Recuperación de características DAS cancelada
-status.das_feature_fetching_complete = Recuperación de características DAS completada
status.fetching_db_refs = Recuperando db refs
label.font_doesnt_have_letters_defined = La fuente no tiene letras definidas\npor lo que no puede emplease\ncon datos de alineamientos
label.font_too_small = Tamaño de la letra es demasiado pequeña
warn.url_must_contain = La URL de la secuencia debe contener $SEQUENCE_ID$, $DB_ACCESSION$ o un regex
info.validate_jabaws_server = \u00BFValidar el servidor JabaWS?\n(Consulte la consola de salida para obtener los resultados)
label.test_server = ¿Probar servidor?
-info.you_want_jalview_to_find_uniprot_accessions = \u00BFDesea que Jalview encuentre\nUniprot Accession ids para los nombres de secuencias dados?
-label.find_uniprot_accession_ids = Buscar Uniprot Accession Ids
label.new_sequence_fetcher = Añadir recuperador de secuencias
label.additional_sequence_fetcher = Recuperador de secuencia adicional
label.select_database_retrieval_source = Seleccionar fuente de recuperación de bases de datos
label.SEQUENCE_ID_for_DB_ACCESSION2 = URL enlaza usando '$SEQUENCE_ID$' para accesiones DB ahora usar '$DB_ACCESSION$'.
label.do_not_display_again = No mostrar este mensaje de nuevo
exception.url_cannot_have_duplicate_id = {0} no puede ser usada como etiqueta en más de un enlace
-label.filter = Filtrar texto:
action.customfilter = Sólo personalizado
action.showall = Mostrar todo
label.insert = Insertar:
warn.name_cannot_be_duplicate = Los nombres URL definidos por el usuario deben ser únicos y no pueden ser ids de MIRIAM
label.output_seq_details = Seleccionar Detalles de la secuencia para ver todas
label.urllinks = Enlaces
-label.default_cache_size = Tamaño del caché por defecto
action.clear_cached_items = Borrar elementos en caché
label.quality_descr = Calidad de alineamiento basándose en puntuación Blosum62
label.conservation_descr = Conservación del alineamiento total menos de {0}% huecos
label.graduated_colour = Color graduado
label.by_text_of = Por texto de
label.by_range_of = Por rango de
-label.filters_tooltip = Haga clic para configurar o modificar los filtros
label.or = O
label.and = Y
label.sequence_feature_colours = Colores de características de las secuencias
label.most_polymer_residues = Más Residuos de Polímeros
label.cached_structures = Estructuras en Caché
label.free_text_search = Búsqueda de texto libre
+label.backupfiles_confirm_delete = Confirmar borrar
+label.backupfiles_confirm_delete_old_files = ¿Borrar los siguientes archivos? (ver la pestaña 'Copias' de la ventana de Preferencias para más opciones)
+label.backupfiles_confirm_save_file = Confirmar guardar archivo
+label.backupfiles_confirm_save_file_backupfiles_roll_wrong = Posiblemente algo está mal con los archivos de respaldos.
+label.backupfiles_confirm_save_new_saved_file_ok = El nuevo archivo guardado parece estar bien.
+label.backupfiles_confirm_save_new_saved_file_not_ok = El nuevo archivo guardado podría no estar bien.
+label.backups = Respaldos
+label.backup = Respaldo
+label.backup_files = Archivos de respaldos
+label.enable_backupfiles = Habilitar archivos de respaldos
+label.backup_filename_strategy = Estrategia de nombres de archivo de respaldos
+label.append_to_filename = Adjuntar texto (%n es reemplazado por el número de respaldo)
+label.append_to_filename_tooltip = %n en el texto será reemplazado por el número de respaldo. El texto será después del nombre del archivo. Vea el cuadro de resumen arriba.
+label.index_digits = Número de dígitos a utilizar para el número de respaldo.
+label.summary_of_backups_scheme = Resumen del esquema de copias de seguridad
+label.increment_index = Aumente los números de texto adjuntos: el archivo más nuevo tiene el número más grande
+label.reverse_roll = Ciclos de texto adjuntos: el respaldo más reciente es siempre el número 1
+label.keep_files = Borrando los respaldos antiguos
+label.keep_all_backup_files = No borrar respaldos antiguas
+label.keep_only_this_number_of_backup_files = Mantenga solo este número de respaldos más recientes
+label.autodelete_old_backup_files = Borrer automáticamente respaldos antiguos:
+label.always_ask = Pregunta siempre
+label.auto_delete = Borrer automáticamente
+label.filename = nombre_de_archivo
+label.braced_oldest = (mas antiguo)
+label.braced_newest = (mas nuevo)
+label.configuration = Configuración
+label.configure_feature_tooltip = Haga clic para configurar el color o los filtros
+label.schemes = Esquemas
+label.customise = Personalizado
+label.default = Defecto
+label.single_file = Solo uno respaldo
+label.keep_all_versions = Mantener todas las versiones
+label.rolled_backups = Ciclos respaldos
+label.previously_saved_scheme = Esquema previamente guardado
+label.no_backup_files = NO ARCHIVOS DE RESPALDOS
+label.include_backup_files = Incluir archivos de respaldos
+label.cancel_changes = Cancelar cambios
+label.warning_confirm_change_reverse = ¡Advertencia!\nSi cambia el incremento/decremento del número de archivos de respaldos, sin cambiar el sufijo o número de dígitos,\nesto puede causar la pérdida de los archivos de respaldos creados con el esquema anterior de nombre de archivo de respaldos.\n¿Está seguro de que desea hacer esto?
+label.change_increment_decrement = ¿Cambiar de incremento/decremento?
+label.was_previous = era {0}
+label.newerdelete_replacement_line = El archivo de respaldo\n''{0}''\t(modificado {2}, tamaño {4})\nserá borrado y reemplazarse por un archivo aparentemente más antiguo\n''{1}''\t(modificado {3}, tamaño {5}).
+label.confirm_deletion_or_rename = Confirmar borrar ''{0}'', o cambiar el nombre a ''{1}''?
+label.newerdelete_line = El archivo de respaldo\n''{0}''\t(modificado {2}, tamaño {4})\nserá borrado pero es mas nuevo que el archivo de respaldo restante más antiguo\n''{1}''\t(modified {3}, size {5}).
+label.confirm_deletion = Confirmar eliminar ''{0}''?
+label.delete = Borrar
+label.rename = Cambiar
+label.keep = Mantener
+label.file_info = (modificado {0}, tamaño {1})
+label.annotation_name = Nombre de la anotación
+label.annotation_description = Descripción de la anotación
+label.edit_annotation_name_description = Editar el nombre/descripción de la anotación
+label.alignment = alineamiento
+label.pca = ACP
+label.create_image_of = Crear imagen {0} de {1}
+label.click_to_edit = Haga clic para editar, clic en el botón derecho para ver el menú
+label.by_annotation_tooltip = El color de anotación se configura desde el menú principal de colores
</xs:annotation>
</xs:attribute>
<xs:attributeGroup ref="jv:swingwindow" />
+ <xs:attribute name="linkToAllViews" use="optional" default="false" type="xs:boolean" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="PcaViewer" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="sequencePoint" minOccurs="1" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:attribute name="sequenceRef" type="xs:string" />
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="axis" minOccurs="3" maxOccurs="3">
+ <xs:annotation>
+ <xs:documentation>
+ endpoints of X, Y and Z axes in that order
+ </xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="seqPointMin">
+ <xs:complexType>
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="seqPointMax">
+ <xs:complexType>
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="pcaData" type="jv:PcaDataType" />
+ </xs:sequence>
+ <xs:attribute name="title" type="xs:string" />
+ <xs:attribute name="scoreModelName" type="xs:string" />
+ <xs:attribute name="xDim" type="xs:int" />
+ <xs:attribute name="yDim" type="xs:int" />
+ <xs:attribute name="zDim" type="xs:int" />
+ <xs:attribute name="bgColour" type="xs:int" />
+ <xs:attribute name="scaleFactor" type="xs:float" />
+ <xs:attribute name="showLabels" type="xs:boolean" />
+ <xs:attribute name="linkToAllViews" type="xs:boolean" />
+ <xs:attributeGroup ref="jv:SimilarityParams" />
+ <xs:attributeGroup ref="jv:swingwindow" />
</xs:complexType>
</xs:element>
<xs:element name="FeatureSettings" minOccurs="0">
<xs:attribute name="predefinedColours" type="xs:boolean"
use="optional" />
</xs:complexType>
-
+ <xs:attributeGroup name="SimilarityParams">
+ <xs:annotation>
+ <xs:documentation>
+ parameters that condition a similarity score calculation
+ </xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="includeGaps" type="xs:boolean" />
+ <xs:attribute name="matchGaps" type="xs:boolean" />
+ <xs:attribute name="includeGappedColumns" type="xs:boolean" />
+ <xs:attribute name="denominateByShortestLength" type="xs:boolean" />
+ </xs:attributeGroup>
+ <xs:attributeGroup name="position">
+ <xs:attribute name="xPos" type="xs:float" />
+ <xs:attribute name="yPos" type="xs:float" />
+ <xs:attribute name="zPos" type="xs:float" />
+ </xs:attributeGroup>
+ <xs:complexType name="PcaDataType">
+ <xs:annotation>
+ <xs:documentation>
+ The results of a PCA calculation
+ </xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="pairwiseMatrix" type="jv:DoubleMatrix" />
+ <xs:element name="tridiagonalMatrix" type="jv:DoubleMatrix" />
+ <xs:element name="eigenMatrix" type="jv:DoubleMatrix" />
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="DoubleVector">
+ <xs:sequence>
+ <xs:element name="v" type="xs:double" minOccurs="0" maxOccurs="unbounded" />
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="DoubleMatrix">
+ <xs:sequence>
+ <xs:element name="row" type="jv:DoubleVector" minOccurs="0" maxOccurs="unbounded" />
+ <xs:element name="D" minOccurs="0" type="jv:DoubleVector" />
+ <xs:element name="E" minOccurs="0" type="jv:DoubleVector" />
+ </xs:sequence>
+ <xs:attribute name="rows" type="xs:int" />
+ <xs:attribute name="columns" type="xs:int" />
+ </xs:complexType>
</xs:schema>
*/
public class AlignmentUtils
{
-
private static final int CODON_LENGTH = 3;
private static final String SEQUENCE_VARIANT = "sequence_variant:";
- private static final String ID = "ID";
+ /*
+ * the 'id' attribute is provided for variant features fetched from
+ * Ensembl using its REST service with JSON format
+ */
+ public static final String VARIANT_ID = "id";
/**
* A data model to hold the 'normal' base value at a position, and an optional
peptidePos, var.getSource());
StringBuilder attributes = new StringBuilder(32);
- String id = (String) var.variant.getValue(ID);
+ String id = (String) var.variant.getValue(VARIANT_ID);
if (id != null)
{
if (id.startsWith(SEQUENCE_VARIANT))
{
id = id.substring(SEQUENCE_VARIANT.length());
}
- sf.setValue(ID, id);
- attributes.append(ID).append("=").append(id);
+ sf.setValue(VARIANT_ID, id);
+ attributes.append(VARIANT_ID).append("=").append(id);
// TODO handle other species variants JAL-2064
StringBuilder link = new StringBuilder(32);
try
}
/**
+ * Translates cDNA using the specified code table
*
* @return
*/
- public AlignmentI translateCdna()
+ public AlignmentI translateCdna(GeneticCodeI codeTable)
{
AlignedCodonFrame acf = new AlignedCodonFrame();
for (s = 0; s < sSize; s++)
{
SequenceI newseq = translateCodingRegion(selection.get(s),
- seqstring[s], acf, pepseqs);
+ seqstring[s], acf, pepseqs, codeTable);
if (newseq != null)
{
* @param acf
* Definition of global ORF alignment reference frame
* @param proteinSeqs
+ * @param codeTable
* @return sequence ready to be added to alignment.
*/
protected SequenceI translateCodingRegion(SequenceI selection,
String seqstring, AlignedCodonFrame acf,
- List<SequenceI> proteinSeqs)
+ List<SequenceI> proteinSeqs, GeneticCodeI codeTable)
{
List<int[]> skip = new ArrayList<>();
int[] skipint = null;
/*
* Filled up a reading frame...
*/
- AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1],
- cdp[2]);
- String aa = ResidueProperties.codonTranslate(new String(codon));
+ AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1], cdp[2]);
+ String aa = codeTable.translate(new String(codon));
rf = 0;
final String gapString = String.valueOf(gapChar);
if (aa == null)
*/
package jalview.analysis;
+import jalview.api.AlignViewportI;
+import jalview.api.FinderI;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Range;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.VisibleContigsIterator;
import jalview.util.Comparison;
-import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
import com.stevesoft.pat.Regex;
-public class Finder
+/**
+ * Implements the search algorithm for the Find dialog
+ */
+public class Finder implements FinderI
{
- /**
- * Implements the search algorithms for the Find dialog box.
+ /*
+ * matched residue locations
*/
- SearchResultsI searchResults;
+ private SearchResultsI searchResults;
- AlignmentI alignment;
+ /*
+ * sequences matched by id or description
+ */
+ private Vector<SequenceI> idMatches;
- SequenceGroup selection = null;
+ /*
+ * the viewport to search over
+ */
+ private AlignViewportI viewport;
- Vector<SequenceI> idMatch = null;
+ /*
+ * sequence index in alignment to search from
+ */
+ private int sequenceIndex;
- boolean caseSensitive = false;
+ /*
+ * column position in sequence to search from, base 0
+ * - absolute column number including any hidden columns
+ * (position after start of last match for a repeat search)
+ */
+ private int columnIndex;
- private boolean includeDescription = false;
+ /**
+ * Constructor for searching a viewport
+ *
+ * @param av
+ */
+ public Finder(AlignViewportI av)
+ {
+ this.viewport = av;
+ this.sequenceIndex = 0;
+ this.columnIndex = -1;
+ }
- boolean findAll = false;
+ @Override
+ public void findAll(String theSearchString, boolean matchCase,
+ boolean searchDescription)
+ {
+ /*
+ * search from the start
+ */
+ sequenceIndex = 0;
+ columnIndex = -1;
- Regex regex = null;
+ doFind(theSearchString, matchCase, searchDescription, true);
- /**
- * holds last-searched position between calls to find(false)
- */
- int seqIndex = 0, resIndex = -1;
+ /*
+ * reset to start for next search
+ */
+ sequenceIndex = 0;
+ columnIndex = -1;
+ }
- public Finder(AlignmentI alignment, SequenceGroup selection)
+ @Override
+ public void findNext(String theSearchString, boolean matchCase,
+ boolean searchDescription)
{
- this.alignment = alignment;
- this.selection = selection;
+ doFind(theSearchString, matchCase, searchDescription, false);
+
+ if (searchResults.isEmpty() && idMatches.isEmpty())
+ {
+ /*
+ * search failed - reset to start for next search
+ */
+ sequenceIndex = 0;
+ columnIndex = -1;
+ }
}
/**
- * restart search at given sequence and residue on alignment and (optionally)
- * contained in selection
+ * Performs a 'find next' or 'find all'
*
- * @param alignment
- * @param selectionGroup
- * @param seqIndex
- * @param resIndex
+ * @param theSearchString
+ * @param matchCase
+ * @param searchDescription
+ * @param findAll
*/
- public Finder(AlignmentI alignment, SequenceGroup selectionGroup,
- int seqIndex, int resIndex)
+ protected void doFind(String theSearchString, boolean matchCase,
+ boolean searchDescription, boolean findAll)
{
- this(alignment, selectionGroup);
- this.seqIndex = seqIndex;
- this.resIndex = resIndex;
- }
+ String searchString = matchCase ? theSearchString
+ : theSearchString.toUpperCase();
+ Regex searchPattern = new Regex(searchString);
+ searchPattern.setIgnoreCase(!matchCase);
- public boolean find(String searchString)
- {
- boolean hasResults = false;
- if (!caseSensitive)
- {
- searchString = searchString.toUpperCase();
- }
- regex = new Regex(searchString);
- regex.setIgnoreCase(!caseSensitive);
searchResults = new SearchResults();
- idMatch = new Vector<SequenceI>();
- String item = null;
- boolean found = false;
- int end = alignment.getHeight();
+ idMatches = new Vector<>();
- // /////////////////////////////////////////////
-
- if (selection != null)
+ SequenceGroup selection = viewport.getSelectionGroup();
+ if (selection != null && selection.getSize() < 1)
{
- if ((selection.getSize() < 1)
- || ((selection.getEndRes() - selection.getStartRes()) < 2))
- {
- selection = null;
- }
+ selection = null; // ? ignore column-only selection
}
- SearchResultMatchI lastm = null;
- while (!found && (seqIndex < end))
- {
- SequenceI seq = alignment.getSequenceAt(seqIndex);
+ AlignmentI alignment = viewport.getAlignment();
+ int end = alignment.getHeight();
- if ((selection != null && selection.getSize() > 0)
- && !selection.getSequences(null).contains(seq))
+ while (sequenceIndex < end)
+ {
+ SequenceI seq = alignment.getSequenceAt(sequenceIndex);
+ boolean found = findNextMatch(seq, searchString, searchPattern,
+ searchDescription);
+ if (found && !findAll)
{
- seqIndex++;
- resIndex = -1;
-
- continue;
+ return;
}
- if (resIndex < 0)
+ if (!found)
{
- resIndex = 0;
- // test for one off matches - sequence position and sequence ID
- // //// is the searchString a residue number?
- try
- {
- int res = Integer.parseInt(searchString);
- // possibly a residue number - check if valid for seq
- if (seq.getEnd() >= res)
- {
- searchResults.addResult(seq, res, res);
- hasResults = true;
- // resIndex=seq.getLength();
- // seqIndex++;
- if (!findAll)
- {
- found = true;
- break;
- }
- }
- } catch (NumberFormatException ex)
- {
- }
-
- if (regex.search(seq.getName()) && !idMatch.contains(seq))
- {
- idMatch.addElement(seq);
- hasResults = true;
- if (!findAll)
- {
- // stop and return the match
- found = true;
- break;
- }
- }
-
- if (isIncludeDescription() && seq.getDescription() != null
- && regex.search(seq.getDescription())
- && !idMatch.contains(seq))
- {
- idMatch.addElement(seq);
- hasResults = true;
- if (!findAll)
- {
- // stop and return the match
- found = true;
- break;
- }
- }
+ sequenceIndex++;
+ columnIndex = -1;
}
- item = seq.getSequenceAsString();
+ }
+ }
- if ((selection != null)
- && (selection.getEndRes() < alignment.getWidth() - 1))
- {
- item = item.substring(0, selection.getEndRes() + 1);
- }
+ /**
+ * Answers the start-end column range of the visible region of
+ * <code>sequence</code> starting at or after the given <code>column</code>.
+ * If there are no hidden columns, this just returns the remaining width of
+ * the sequence. The range is restricted to the current <code>selection</code>
+ * if there is one. Answers null if there are no visible columns at or after
+ * <code>column</code>.
+ */
+ protected Range getNextVisibleSequenceRegion(SequenceI sequence,
+ int column)
+ {
+ int seqColStart = column;
+ int seqColEnd = sequence.getLength() - 1;
- // /Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
- StringBuilder noGapsSB = new StringBuilder();
- int insertCount = 0;
- List<Integer> spaces = new ArrayList<Integer>();
+ /*
+ * restrict search to (next) visible column region,
+ * in case there are hidden columns
+ */
+ AlignmentI alignment = viewport.getAlignment();
+ VisibleContigsIterator visibleRegions = alignment.getHiddenColumns()
+ .getVisContigsIterator(column, alignment.getWidth(),
+ false);
+ int[] visible = visibleRegions.hasNext() ? visibleRegions.next() : null;
+ if (visible == null)
+ {
+ columnIndex = seqColEnd + 1;
+ return null;
+ }
+ seqColStart = Math.max(seqColStart, visible[0]);
+ seqColEnd = Math.min(seqColEnd, visible[1]);
- for (int j = 0; j < item.length(); j++)
+ /*
+ * restrict search to selected region if there is one
+ */
+ SequenceGroup selection = viewport.getSelectionGroup();
+ if (selection != null)
+ {
+ int selectionStart = selection.getStartRes();
+ int selectionEnd = selection.getEndRes();
+ if (selectionStart > seqColEnd || selectionEnd < seqColStart)
{
- if (!Comparison.isGap(item.charAt(j)))
- {
- noGapsSB.append(item.charAt(j));
- spaces.add(Integer.valueOf(insertCount));
- }
- else
- {
- insertCount++;
- }
+ /*
+ * sequence region doesn't overlap selection region
+ */
+ columnIndex = seqColEnd + 1;
+ return null;
}
+ seqColStart = Math.max(seqColStart, selectionStart);
+ seqColEnd = Math.min(seqColEnd, selectionEnd);
+ }
- String noGaps = noGapsSB.toString();
- for (int r = resIndex; r < noGaps.length(); r++)
- {
+ return new Range(seqColStart, seqColEnd);
+ }
- if (regex.searchFrom(noGaps, r))
- {
- resIndex = regex.matchedFrom();
-
- if ((selection != null && selection.getSize() > 0) && (resIndex
- + spaces.get(resIndex) < selection.getStartRes()))
- {
- continue;
- }
- // if invalid string used, then regex has no matched to/from
- int sres = seq.findPosition(resIndex + spaces.get(resIndex));
- int eres = seq.findPosition(regex.matchedTo() - 1
- + (spaces.get(regex.matchedTo() - 1)));
- // only add result if not contained in previous result
- if (lastm == null || (lastm.getSequence() != seq
- || (!(lastm.getStart() <= sres
- && lastm.getEnd() >= eres))))
- {
- lastm = searchResults.addResult(seq, sres, eres);
- }
- hasResults = true;
- if (!findAll)
- {
- // thats enough, break and display the result
- found = true;
- resIndex++;
-
- break;
- }
-
- r = resIndex;
- }
- else
- {
- break;
- }
- }
+ /**
+ * Finds the next match in the given sequence, starting at column at
+ * <code>columnIndex</code>. Answers true if a match is found, else false. If
+ * a match is found, <code>columnIndex</code> is advanced to the column after
+ * the start of the matched region, ready for a search from the next position.
+ *
+ * @param seq
+ * @param searchString
+ * @param searchPattern
+ * @param matchDescription
+ * @return
+ */
+ protected boolean findNextMatch(SequenceI seq, String searchString,
+ Regex searchPattern, boolean matchDescription)
+ {
+ SequenceGroup selection = viewport.getSelectionGroup();
+ if (selection != null && !selection.contains(seq))
+ {
+ /*
+ * this sequence is not in the selection - advance to next sequence
+ */
+ return false;
+ }
- if (!found)
+ if (columnIndex < 0)
+ {
+ /*
+ * at start of sequence; try find by residue number, in sequence id,
+ * or (optionally) in sequence description
+ */
+ if (doNonMotifSearches(seq, searchString, searchPattern,
+ matchDescription))
{
- seqIndex++;
- resIndex = -1;
+ return true;
}
}
- /**
- * We now search the Id string in the main search loop. for (int id = 0; id
- * < alignment.getHeight(); id++) { if
- * (regex.search(alignment.getSequenceAt(id).getName())) {
- * idMatch.addElement(alignment.getSequenceAt(id)); hasResults = true; } }
+ /*
+ * search for next match in sequence string
*/
- return hasResults;
- }
-
- /**
- * @return the alignment
- */
- public AlignmentI getAlignment()
- {
- return alignment;
+ int end = seq.getLength();
+ while (columnIndex < end)
+ {
+ if (searchNextVisibleRegion(seq, searchPattern))
+ {
+ return true;
+ }
+ }
+ return false;
}
/**
- * @param alignment
- * the alignment to set
+ * Searches the sequence, starting from <code>columnIndex</code>, and adds the
+ * next match (if any) to <code>searchResults</code>. The search is restricted
+ * to the next visible column region, and to the <code>selection</code> region
+ * if there is one. Answers true if a match is added, else false.
+ *
+ * @param seq
+ * @param searchPattern
+ * @return
*/
- public void setAlignment(AlignmentI alignment)
+ protected boolean searchNextVisibleRegion(SequenceI seq, Regex searchPattern)
{
- this.alignment = alignment;
- }
+ Range visible = getNextVisibleSequenceRegion(seq, columnIndex);
+ if (visible == null)
+ {
+ return false;
+ }
+ String seqString = seq.getSequenceAsString(visible.start, visible.end + 1);
+ String noGaps = AlignSeq.extractGaps(Comparison.GapChars, seqString);
- /**
- * @return the caseSensitive
- */
- public boolean isCaseSensitive()
- {
- return caseSensitive;
- }
+ if (searchPattern.search(noGaps))
+ {
+ int sequenceStartPosition = seq.findPosition(visible.start);
+ recordMatch(seq, searchPattern, sequenceStartPosition);
+ return true;
+ }
+ else
+ {
+ /*
+ * no match - advance columnIndex past this visible region
+ * so the next visible region (if any) is searched next
+ */
+ columnIndex = visible.end + 1;
+ }
- /**
- * @param caseSensitive
- * the caseSensitive to set
- */
- public void setCaseSensitive(boolean caseSensitive)
- {
- this.caseSensitive = caseSensitive;
+ return false;
}
/**
- * @return the findAll
+ * Adds the match held in the <code>searchPattern</code> Regex to the
+ * <code>searchResults</code>, unless it is a subregion of the last match
+ * recorded. <code>columnIndex</code> is advanced to the position after the
+ * start of the matched region, ready for the next search. Answers true if a
+ * match was added, else false.
+ *
+ * @param seq
+ * @param searchPattern
+ * @param firstResiduePosition
+ * @return
*/
- public boolean isFindAll()
+ protected boolean recordMatch(SequenceI seq, Regex searchPattern,
+ int firstResiduePosition)
{
- return findAll;
- }
+ /*
+ * get start/end of the match in sequence coordinates
+ */
+ int offset = searchPattern.matchedFrom();
+ int matchStartPosition = firstResiduePosition + offset;
+ int matchEndPosition = matchStartPosition
+ + searchPattern.charsMatched() - 1;
+
+ /*
+ * update columnIndex to next column after the start of the match
+ * (findIndex returns a value base 1, columnIndex is held base 0)
+ */
+ columnIndex = seq.findIndex(matchStartPosition);
- /**
- * @param findAll
- * the findAll to set
- */
- public void setFindAll(boolean findAll)
- {
- this.findAll = findAll;
- }
+ /*
+ * check that this match is not a subset of the previous one (JAL-2302)
+ */
+ List<SearchResultMatchI> matches = searchResults.getResults();
+ SearchResultMatchI lastMatch = matches.isEmpty() ? null
+ : matches.get(matches.size() - 1);
- /**
- * @return the selection
- */
- public jalview.datamodel.SequenceGroup getSelection()
- {
- return selection;
- }
+ if (lastMatch == null || !lastMatch.contains(seq, matchStartPosition,
+ matchEndPosition))
+ {
+ searchResults.addResult(seq, matchStartPosition, matchEndPosition);
+ return true;
+ }
- /**
- * @param selection
- * the selection to set
- */
- public void setSelection(jalview.datamodel.SequenceGroup selection)
- {
- this.selection = selection;
+ return false;
}
/**
- * Returns the (possibly empty) list of matching sequences (when search
- * includes searching sequence names)
+ * Does searches other than for residue patterns. Currently this includes
+ * <ul>
+ * <li>find residue by position (if search string is a number)</li>
+ * <li>match search string to sequence id</li>
+ * <li>match search string to sequence description (optional)</li>
+ * </ul>
+ * Answers true if a match is found, else false.
*
+ * @param seq
+ * @param searchString
+ * @param searchPattern
+ * @param includeDescription
* @return
*/
- public Vector<SequenceI> getIdMatch()
+ protected boolean doNonMotifSearches(SequenceI seq, String searchString,
+ Regex searchPattern, boolean includeDescription)
{
- return idMatch;
- }
+ /*
+ * position sequence search to start of sequence
+ */
+ columnIndex = 0;
- /**
- * @return the regex
- */
- public com.stevesoft.pat.Regex getRegex()
- {
- return regex;
+ if (searchForResidueNumber(seq, searchString))
+ {
+ return true;
+ }
+ if (searchSequenceName(seq, searchPattern))
+ {
+ return true;
+ }
+ if (includeDescription && searchSequenceDescription(seq, searchPattern))
+ {
+ return true;
+ }
+ return false;
}
/**
- * @return the searchResults
+ * Searches for a match with the sequence description, and if found, adds the
+ * sequence to the list of match ids (but not as a duplicate). Answers true if
+ * a match was added, else false.
+ *
+ * @param seq
+ * @param searchPattern
+ * @return
*/
- public SearchResultsI getSearchResults()
+ protected boolean searchSequenceDescription(SequenceI seq, Regex searchPattern)
{
- return searchResults;
+ String desc = seq.getDescription();
+ if (desc != null && searchPattern.search(desc) && !idMatches.contains(seq))
+ {
+ idMatches.addElement(seq);
+ return true;
+ }
+ return false;
}
/**
- * @return the resIndex
+ * Searches for a match with the sequence name, and if found, adds the
+ * sequence to the list of match ids (but not as a duplicate). Answers true if
+ * a match was added, else false.
+ *
+ * @param seq
+ * @param searchPattern
+ * @return
*/
- public int getResIndex()
+ protected boolean searchSequenceName(SequenceI seq, Regex searchPattern)
{
- return resIndex;
+ if (searchPattern.search(seq.getName()) && !idMatches.contains(seq))
+ {
+ idMatches.addElement(seq);
+ return true;
+ }
+ return false;
}
/**
- * @param resIndex
- * the resIndex to set
+ * Tries to interpret the search string as a residue position, and if valid,
+ * adds the position to the search results and returns true, else answers
+ * false
*/
- public void setResIndex(int resIndex)
+ protected boolean searchForResidueNumber(SequenceI seq, String searchString)
{
- this.resIndex = resIndex;
+ try
+ {
+ int res = Integer.parseInt(searchString);
+ if (seq.getStart() <= res && seq.getEnd() >= res)
+ {
+ searchResults.addResult(seq, res, res);
+ return true;
+ }
+ } catch (NumberFormatException ex)
+ {
+ }
+ return false;
}
- /**
- * @return the seqIndex
+ /* (non-Javadoc)
+ * @see jalview.analysis.FinderI#getIdMatch()
*/
- public int getSeqIndex()
+ @Override
+ public Vector<SequenceI> getIdMatches()
{
- return seqIndex;
+ return idMatches;
}
- /**
- * @param seqIndex
- * the seqIndex to set
+ /* (non-Javadoc)
+ * @see jalview.analysis.FinderI#getSearchResults()
*/
- public void setSeqIndex(int seqIndex)
- {
- this.seqIndex = seqIndex;
- }
-
- public boolean isIncludeDescription()
- {
- return includeDescription;
- }
-
- public void setIncludeDescription(boolean includeDescription)
+ @Override
+ public SearchResultsI getSearchResults()
{
- this.includeDescription = includeDescription;
+ return searchResults;
}
}
--- /dev/null
+package jalview.analysis;
+
+public interface GeneticCodeI
+{
+ /**
+ * Answers the single letter amino acid code (e.g. "D") for the given codon
+ * (e.g. "GAC"), or "*" for a stop codon, or null for an unknown input. The
+ * codon is not case-sensitive, the return value is upper case.
+ * <p>
+ * If the codon includes any of the standard ambiguity codes
+ * <ul>
+ * <li>if all possible translations are the same, returns that value</li>
+ * <li>else returns null</li>
+ * </ul>
+ *
+ * @param codon
+ * @return
+ */
+ String translate(String codon);
+
+ /**
+ * Answers the single letter amino acid code (e.g. "D") for the given codon
+ * (e.g. "GAC"), or "*" for a stop codon, or null for an unknown input. The
+ * codon is not case-sensitive, the return value is upper case. If the codon
+ * includes any of the standard ambiguity codes, this method returns null.
+ *
+ * @param codon
+ * @return
+ */
+ String translateCanonical(String codon);
+
+ /**
+ * Answers a unique identifier for the genetic code (using the numbering
+ * system as on NCBI)
+ *
+ * @return
+ */
+ String getId();
+
+ /**
+ * Answers a display name suitable for use in menus, reports etc
+ *
+ * @return
+ */
+ String getName();
+}
--- /dev/null
+package jalview.analysis;
+
+import jalview.bin.Cache;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.Map;
+import java.util.StringTokenizer;
+
+/**
+ * A singleton that provides instances of genetic code translation tables
+ *
+ * @author gmcarstairs
+ * @see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
+ */
+public final class GeneticCodes
+{
+ private static final int CODON_LENGTH = 3;
+
+ private static final String QUOTE = "\"";
+
+ /*
+ * nucleotides as ordered in data file
+ */
+ private static final String NUCS = "TCAG";
+
+ private static final int NUCS_COUNT = NUCS.length();
+
+ private static final int NUCS_COUNT_SQUARED = NUCS_COUNT * NUCS_COUNT;
+
+ private static final int NUCS_COUNT_CUBED = NUCS_COUNT * NUCS_COUNT
+ * NUCS_COUNT;
+
+ private static final String AMBIGUITY_CODES_FILE = "/AmbiguityCodes.dat";
+
+ private static final String RESOURCE_FILE = "/GeneticCodes.dat";
+
+ private static GeneticCodes instance = new GeneticCodes();
+
+ private Map<String, String> ambiguityCodes;
+
+ /*
+ * loaded code tables, with keys in order of loading
+ */
+ private Map<String, GeneticCodeI> codeTables;
+
+ /**
+ * Private constructor enforces singleton
+ */
+ private GeneticCodes()
+ {
+ if (instance == null)
+ {
+ ambiguityCodes = new HashMap<>();
+
+ /*
+ * LinkedHashMap preserves order of addition of entries,
+ * so we can assume the Standard Code Table is the first
+ */
+ codeTables = new LinkedHashMap<>();
+ loadAmbiguityCodes(AMBIGUITY_CODES_FILE);
+ loadCodes(RESOURCE_FILE);
+ }
+ };
+
+ /**
+ * Returns the singleton instance of this class
+ *
+ * @return
+ */
+ public static GeneticCodes getInstance()
+ {
+ return instance;
+ }
+
+ /**
+ * Returns the known code tables, in order of loading.
+ *
+ * @return
+ */
+ public Iterable<GeneticCodeI> getCodeTables()
+ {
+ return codeTables.values();
+ }
+
+ /**
+ * Answers the code table with the given id
+ *
+ * @param id
+ * @return
+ */
+ public GeneticCodeI getCodeTable(String id)
+ {
+ return codeTables.get(id);
+ }
+
+ /**
+ * A convenience method that returns the standard code table (table 1). As
+ * implemented, this has to be the first table defined in the data file.
+ *
+ * @return
+ */
+ public GeneticCodeI getStandardCodeTable()
+ {
+ return codeTables.values().iterator().next();
+ }
+
+ /**
+ * Loads the code tables from a data file
+ */
+ protected void loadCodes(String fileName)
+ {
+ try
+ {
+ InputStream is = getClass().getResourceAsStream(fileName);
+ BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
+
+ /*
+ * skip comments and start of table
+ */
+ String line = "";
+ while (line != null && !line.startsWith("Genetic-code-table"))
+ {
+ line = readLine(dataIn);
+ }
+ line = readLine(dataIn);
+
+ while (line.startsWith("{"))
+ {
+ line = loadOneTable(dataIn);
+ }
+ } catch (IOException | NullPointerException e)
+ {
+ Cache.log.error(
+ "Error reading genetic codes data file: "
+ + e.getMessage());
+ }
+ }
+
+ /**
+ * Reads and saves Nucleotide ambiguity codes from a data file. The file may
+ * include comment lines (starting with #), a header 'DNA', and one line per
+ * ambiguity code, for example:
+ * <p>
+ * R<tab>AG
+ * <p>
+ * means that R is an ambiguity code meaning "A or G"
+ *
+ * @param fileName
+ */
+ protected void loadAmbiguityCodes(String fileName)
+ {
+ try
+ {
+ InputStream is = getClass().getResourceAsStream(fileName);
+ BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
+ String line = "";
+ while (line != null)
+ {
+ line = readLine(dataIn);
+ if (line != null && !"DNA".equals(line.toUpperCase()))
+ {
+ String[] tokens = line.split("\\t");
+ ambiguityCodes.put(tokens[0].toUpperCase(),
+ tokens[1].toUpperCase());
+ }
+ }
+ } catch (IOException e)
+ {
+ Cache.log.error(
+ "Error reading nucleotide ambiguity codes data file: "
+ + e.getMessage());
+ }
+ }
+
+ /**
+ * Reads up to and returns the next non-comment line, trimmed. Comment lines
+ * start with a #. Returns null at end of file.
+ *
+ * @param dataIn
+ * @return
+ * @throws IOException
+ */
+ protected String readLine(BufferedReader dataIn) throws IOException
+ {
+ String line = dataIn.readLine();
+ while (line != null && line.startsWith("#"))
+ {
+ line = readLine(dataIn);
+ }
+ return line == null ? null : line.trim();
+ }
+
+ /**
+ * Reads the lines of the data file describing one translation table, and
+ * creates and stores an instance of GeneticCodeI. Returns the '{' line
+ * starting the next table, or the '}' line at end of all tables. Data format
+ * is
+ *
+ * <pre>
+ * {
+ * name "Vertebrate Mitochondrial" ,
+ * name "SGC1" ,
+ * id 2 ,
+ * ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG",
+ * sncbieaa "----------**--------------------MMMM----------**---M------------"
+ * -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ * -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ * -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ * },
+ * </pre>
+ *
+ * of which we parse the first name, the id, and the ncbieaa translations for
+ * codons as ordered by the Base1/2/3 lines. Note Base1/2/3 are included for
+ * readability and are in a fixed order, these are not parsed. The sncbieaa
+ * line marks alternative start codons, these are not parsed.
+ *
+ * @param dataIn
+ * @return
+ * @throws IOException
+ */
+ protected String loadOneTable(BufferedReader dataIn) throws IOException
+ {
+ String name = null;
+ String id = null;
+ Map<String, String> codons = new HashMap<>();
+
+ String line = readLine(dataIn);
+
+ while (line != null && !line.startsWith("}"))
+ {
+ if (line.startsWith("name") && name == null)
+ {
+ name = line.substring(line.indexOf(QUOTE) + 1,
+ line.lastIndexOf(QUOTE));
+ }
+ else if (line.startsWith("id"))
+ {
+ id = new StringTokenizer(line.substring(2)).nextToken();
+ }
+ else if (line.startsWith("ncbieaa"))
+ {
+ String aminos = line.substring(line.indexOf(QUOTE) + 1,
+ line.lastIndexOf(QUOTE));
+ if (aminos.length() != NUCS_COUNT_CUBED) // 4 * 4 * 4 combinations
+ {
+ Cache.log.error("wrong data length in code table: " + line);
+ }
+ else
+ {
+ for (int i = 0; i < aminos.length(); i++)
+ {
+ String peptide = String.valueOf(aminos.charAt(i));
+ char codon1 = NUCS.charAt(i / NUCS_COUNT_SQUARED);
+ char codon2 = NUCS
+ .charAt((i % NUCS_COUNT_SQUARED) / NUCS_COUNT);
+ char codon3 = NUCS.charAt(i % NUCS_COUNT);
+ String codon = new String(
+ new char[]
+ { codon1, codon2, codon3 });
+ codons.put(codon, peptide);
+ }
+ }
+ }
+ line = readLine(dataIn);
+ }
+
+ registerCodeTable(id, name, codons);
+ return readLine(dataIn);
+ }
+
+ /**
+ * Constructs and registers a GeneticCodeI instance with the codon
+ * translations as defined in the data file. For all instances except the
+ * first, any undeclared translations default to those in the standard code
+ * table.
+ *
+ * @param id
+ * @param name
+ * @param codons
+ */
+ protected void registerCodeTable(final String id, final String name,
+ final Map<String, String> codons)
+ {
+ codeTables.put(id, new GeneticCodeI()
+ {
+ /*
+ * map of ambiguous codons to their 'product'
+ * (null if not all possible translations match)
+ */
+ Map<String, String> ambiguous = new HashMap<>();
+
+ @Override
+ public String translateCanonical(String codon)
+ {
+ return codons.get(codon.toUpperCase());
+ }
+
+ @Override
+ public String translate(String codon)
+ {
+ String upper = codon.toUpperCase();
+ String peptide = translateCanonical(upper);
+
+ /*
+ * if still not translated, check for ambiguity codes
+ */
+ if (peptide == null)
+ {
+ peptide = getAmbiguousTranslation(upper, ambiguous, this);
+ }
+ return peptide;
+ }
+
+ @Override
+ public String getId()
+ {
+ return id;
+ }
+
+ @Override
+ public String getName()
+ {
+ return name;
+ }
+ });
+ }
+
+ /**
+ * Computes all possible translations of a codon including one or more
+ * ambiguity codes, and stores and returns the result (null if not all
+ * translations match). If the codon includes no ambiguity codes, simply
+ * returns null.
+ *
+ * @param codon
+ * @param ambiguous
+ * @param codeTable
+ * @return
+ */
+ protected String getAmbiguousTranslation(String codon,
+ Map<String, String> ambiguous, GeneticCodeI codeTable)
+ {
+ if (codon.length() != CODON_LENGTH)
+ {
+ return null;
+ }
+
+ boolean isAmbiguous = false;
+
+ char[][] expanded = new char[CODON_LENGTH][];
+ for (int i = 0; i < CODON_LENGTH; i++)
+ {
+ String base = String.valueOf(codon.charAt(i));
+ if (ambiguityCodes.containsKey(base))
+ {
+ isAmbiguous = true;
+ base = ambiguityCodes.get(base);
+ }
+ expanded[i] = base.toCharArray();
+ }
+
+ if (!isAmbiguous)
+ {
+ // no ambiguity code involved here
+ return null;
+ }
+
+ /*
+ * generate and translate all permutations of the ambiguous codon
+ * only return the translation if they all agree, else null
+ */
+ String peptide = null;
+ for (char c1 : expanded[0])
+ {
+ for (char c2 : expanded[1])
+ {
+ for (char c3 : expanded[2])
+ {
+ char[] cdn = new char[] { c1, c2, c3 };
+ String possibleCodon = String.valueOf(cdn);
+ String pep = codeTable.translate(possibleCodon);
+ if (pep == null || (peptide != null && !pep.equals(peptide)))
+ {
+ ambiguous.put(codon, null);
+ return null;
+ }
+ peptide = pep;
+ }
+ }
+ }
+
+ /*
+ * all translations of ambiguous codons matched!
+ */
+ ambiguous.put(codon, peptide);
+ return peptide;
+ }
+}
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
+import jalview.datamodel.Point;
import jalview.math.MatrixI;
import java.io.PrintStream;
*/
public class PCA implements Runnable
{
- MatrixI symm;
-
- double[] eigenvalue;
+ /*
+ * inputs
+ */
+ final private AlignmentView seqs;
- MatrixI eigenvector;
+ final private ScoreModelI scoreModel;
- StringBuilder details = new StringBuilder(1024);
+ final private SimilarityParamsI similarityParams;
- final private AlignmentView seqs;
+ /*
+ * outputs
+ */
+ private MatrixI pairwiseScores;
- private ScoreModelI scoreModel;
+ private MatrixI tridiagonal;
- private SimilarityParamsI similarityParams;
+ private MatrixI eigenMatrix;
- public PCA(AlignmentView s, ScoreModelI sm, SimilarityParamsI options)
+ /**
+ * Constructor given the sequences to compute for, the similarity model to
+ * use, and a set of parameters for sequence comparison
+ *
+ * @param sequences
+ * @param sm
+ * @param options
+ */
+ public PCA(AlignmentView sequences, ScoreModelI sm, SimilarityParamsI options)
{
- this.seqs = s;
- this.similarityParams = options;
+ this.seqs = sequences;
this.scoreModel = sm;
-
- details.append("PCA calculation using " + sm.getName()
- + " sequence similarity matrix\n========\n\n");
+ this.similarityParams = options;
}
/**
*/
public double getEigenvalue(int i)
{
- return eigenvector.getD()[i];
+ return eigenMatrix.getD()[i];
}
/**
*
* @return DOCUMENT ME!
*/
- public float[][] getComponents(int l, int n, int mm, float factor)
+ public Point[] getComponents(int l, int n, int mm, float factor)
{
- float[][] out = new float[getHeight()][3];
+ Point[] out = new Point[getHeight()];
for (int i = 0; i < getHeight(); i++)
{
- out[i][0] = (float) component(i, l) * factor;
- out[i][1] = (float) component(i, n) * factor;
- out[i][2] = (float) component(i, mm) * factor;
+ float x = (float) component(i, l) * factor;
+ float y = (float) component(i, n) * factor;
+ float z = (float) component(i, mm) * factor;
+ out[i] = new Point(x, y, z);
}
return out;
{
double out = 0.0;
- for (int i = 0; i < symm.width(); i++)
+ for (int i = 0; i < pairwiseScores.width(); i++)
{
- out += (symm.getValue(row, i) * eigenvector.getValue(i, n));
+ out += (pairwiseScores.getValue(row, i) * eigenMatrix.getValue(i, n));
}
- return out / eigenvector.getD()[n];
+ return out / eigenMatrix.getD()[n];
}
+ /**
+ * Answers a formatted text report of the PCA calculation results (matrices
+ * and eigenvalues) suitable for display
+ *
+ * @return
+ */
public String getDetails()
{
- return details.toString();
+ StringBuilder sb = new StringBuilder(1024);
+ sb.append("PCA calculation using ").append(scoreModel.getName())
+ .append(" sequence similarity matrix\n========\n\n");
+ PrintStream ps = wrapOutputBuffer(sb);
+
+ /*
+ * pairwise similarity scores
+ */
+ sb.append(" --- OrigT * Orig ---- \n");
+ pairwiseScores.print(ps, "%8.2f");
+
+ /*
+ * tridiagonal matrix, with D and E vectors
+ */
+ sb.append(" ---Tridiag transform matrix ---\n");
+ sb.append(" --- D vector ---\n");
+ tridiagonal.printD(ps, "%15.4e");
+ ps.println();
+ sb.append("--- E vector ---\n");
+ tridiagonal.printE(ps, "%15.4e");
+ ps.println();
+
+ /*
+ * eigenvalues matrix, with D vector
+ */
+ sb.append(" --- New diagonalization matrix ---\n");
+ eigenMatrix.print(ps, "%8.2f");
+ sb.append(" --- Eigenvalues ---\n");
+ eigenMatrix.printD(ps, "%15.4e");
+ ps.println();
+
+ return sb.toString();
}
/**
- * DOCUMENT ME!
+ * Performs the PCA calculation
*/
@Override
public void run()
{
+ try
+ {
+ /*
+ * sequence pairwise similarity scores
+ */
+ pairwiseScores = scoreModel.findSimilarities(seqs, similarityParams);
+
+ /*
+ * tridiagonal matrix
+ */
+ tridiagonal = pairwiseScores.copy();
+ tridiagonal.tred();
+
+ /*
+ * the diagonalization matrix
+ */
+ eigenMatrix = tridiagonal.copy();
+ eigenMatrix.tqli();
+ } catch (Exception q)
+ {
+ Cache.log.error("Error computing PCA: " + q.getMessage());
+ q.printStackTrace();
+ }
+ }
+
+ /**
+ * Returns a PrintStream that wraps (appends its output to) the given
+ * StringBuilder
+ *
+ * @param sb
+ * @return
+ */
+ protected PrintStream wrapOutputBuffer(StringBuilder sb)
+ {
PrintStream ps = new PrintStream(System.out)
{
@Override
public void print(String x)
{
- details.append(x);
+ sb.append(x);
}
@Override
public void println()
{
- details.append("\n");
+ sb.append("\n");
}
};
-
- // long now = System.currentTimeMillis();
- try
- {
- eigenvector = scoreModel.findSimilarities(seqs, similarityParams);
-
- details.append(" --- OrigT * Orig ---- \n");
- eigenvector.print(ps, "%8.2f");
-
- symm = eigenvector.copy();
-
- eigenvector.tred();
-
- details.append(" ---Tridiag transform matrix ---\n");
- details.append(" --- D vector ---\n");
- eigenvector.printD(ps, "%15.4e");
- ps.println();
- details.append("--- E vector ---\n");
- eigenvector.printE(ps, "%15.4e");
- ps.println();
-
- // Now produce the diagonalization matrix
- eigenvector.tqli();
- } catch (Exception q)
- {
- q.printStackTrace();
- details.append("\n*** Unexpected exception when performing PCA ***\n"
- + q.getLocalizedMessage());
- details.append(
- "*** Matrices below may not be fully diagonalised. ***\n");
- }
-
- details.append(" --- New diagonalization matrix ---\n");
- eigenvector.print(ps, "%8.2f");
- details.append(" --- Eigenvalues ---\n");
- eigenvector.printD(ps, "%15.4e");
- ps.println();
- /*
- * for (int seq=0;seq<symm.rows;seq++) { ps.print("\"Seq"+seq+"\""); for
- * (int ev=0;ev<symm.rows; ev++) {
- *
- * ps.print(","+component(seq, ev)); } ps.println(); }
- */
- // System.out.println(("PCA.run() took "
- // + (System.currentTimeMillis() - now) + "ms"));
+ return ps;
}
/**
public int getHeight()
{
// TODO can any of seqs[] be null?
- return seqs.getSequences().length;
+ return pairwiseScores.height();// seqs.getSequences().length;
+ }
+
+ /**
+ * Answers the sequence pairwise similarity scores which were the first step
+ * of the PCA calculation
+ *
+ * @return
+ */
+ public MatrixI getPairwiseScores()
+ {
+ return pairwiseScores;
+ }
+
+ public void setPairwiseScores(MatrixI m)
+ {
+ pairwiseScores = m;
+ }
+
+ public MatrixI getEigenmatrix()
+ {
+ return eigenMatrix;
+ }
+
+ public void setEigenmatrix(MatrixI m)
+ {
+ eigenMatrix = m;
+ }
+
+ public MatrixI getTridiagonal()
+ {
+ return tridiagonal;
+ }
+
+ public void setTridiagonal(MatrixI tridiagonal)
+ {
+ this.tridiagonal = tridiagonal;
}
}
protected MatrixI findSimilarities(String[] seqs,
SimilarityParamsI options)
{
- // TODO reuse code in ScoreMatrix instead somehow
- double[][] values = new double[seqs.length][];
+ /*
+ * calculation is symmetric so just compute lower diagonal
+ */
+ double[][] values = new double[seqs.length][seqs.length];
for (int row = 0; row < seqs.length; row++)
{
- values[row] = new double[seqs.length];
- for (int col = 0; col < seqs.length; col++)
+ for (int col = row; col < seqs.length; col++)
{
double total = computePID(seqs[row], seqs[col], options);
values[row][col] = total;
+ values[col][row] = total;
}
}
return new Matrix(values);
private float maxValue;
+ private boolean symmetric;
+
/**
* Constructor given a name, symbol alphabet, and matrix of scores for pairs
* of symbols. The matrix should be square and of the same size as the
findMinMax();
+ symmetric = checkSymmetry();
+
/*
* crude heuristic for now...
*/
}
/**
+ * Answers true if the matrix is symmetric, else false. Usually, substitution
+ * matrices are symmetric, which allows calculations to be short cut.
+ *
+ * @return
+ */
+ private boolean checkSymmetry()
+ {
+ for (int i = 0; i < matrix.length; i++)
+ {
+ for (int j = i; j < matrix.length; j++)
+ {
+ if (matrix[i][j] != matrix[j][i])
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
+
+ /**
* Record the minimum and maximum score values
*/
protected void findMinMax()
protected MatrixI findSimilarities(String[] seqs,
SimilarityParamsI params)
{
- double[][] values = new double[seqs.length][];
+ double[][] values = new double[seqs.length][seqs.length];
for (int row = 0; row < seqs.length; row++)
{
- values[row] = new double[seqs.length];
- for (int col = 0; col < seqs.length; col++)
+ for (int col = symmetric ? row : 0; col < seqs.length; col++)
{
double total = computeSimilarity(seqs[row], seqs[col], params);
values[row][col] = total;
+ if (symmetric)
+ {
+ values[col][row] = total;
+ }
}
}
return new Matrix(values);
{
return this;
}
+
+ public boolean isSymmetric()
+ {
+ return symmetric;
+ }
}
private final ScoreMatrix DNA;
- private static ScoreModels instance = new ScoreModels();
+ private static ScoreModels instance;
private Map<String, ScoreModelI> models;
+ /**
+ * Answers the singleton instance of this class, with lazy initialisation
+ * (built-in score models are loaded on the first call to this method)
+ *
+ * @return
+ */
public static ScoreModels getInstance()
{
+ if (instance == null)
+ {
+ instance = new ScoreModels();
+ }
return instance;
}
/*
* using LinkedHashMap keeps models ordered as added
*/
- models = new LinkedHashMap<String, ScoreModelI>();
+ models = new LinkedHashMap<>();
BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
- registerScoreModel(new PIDModel());
DNA = loadScoreMatrix("scoreModel/dna.scm");
+ registerScoreModel(new PIDModel());
registerScoreModel(new FeatureDistanceModel());
}
}
/**
+ * Resets to just the built-in score models
+ */
+ public void reset()
+ {
+ instance = new ScoreModels();
+ }
+
+ /**
* Returns the default peptide or nucleotide score model, currently BLOSUM62
* or DNA
*
{
return matchGaps;
}
+
+ /**
+ * IDE-generated hashCode method
+ */
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + (denominateByShortestLength ? 1231 : 1237);
+ result = prime * result + (includeGappedColumns ? 1231 : 1237);
+ result = prime * result + (includeGaps ? 1231 : 1237);
+ result = prime * result + (matchGaps ? 1231 : 1237);
+ return result;
+ }
+
+ /**
+ * IDE-generated equals method
+ */
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ {
+ return true;
+ }
+ if (obj == null)
+ {
+ return false;
+ }
+ if (getClass() != obj.getClass())
+ {
+ return false;
+ }
+ SimilarityParams other = (SimilarityParams) obj;
+ if (denominateByShortestLength != other.denominateByShortestLength)
+ {
+ return false;
+ }
+ if (includeGappedColumns != other.includeGappedColumns)
+ {
+ return false;
+ }
+ if (includeGaps != other.includeGaps)
+ {
+ return false;
+ }
+ if (matchGaps != other.matchGaps)
+ {
+ return false;
+ }
+ return true;
+ }
}
public abstract TreeModel getCurrentTree();
public abstract void setCurrentTree(TreeModel tree);
+
+ /**
+ * @param update
+ * - set the flag for updating structures on next repaint
+ */
+ void setUpdateStructures(boolean update);
+
+ /**
+ *
+ * @return true if structure views will be updated on next refresh
+ */
+ boolean isUpdateStructures();
+
+ /**
+ * check if structure views need to be updated, and clear the flag afterwards.
+ *
+ * @return if an update is needed
+ */
+ boolean needToUpdateStructureViews();
+
+ /**
+ * Adds sequencegroup to the alignment in the view. Also adds a group to the
+ * complement view if one is defined.
+ *
+ * @param sequenceGroup
+ * - a group defined on sequences in the alignment held by the view
+ */
+ void addSequenceGroup(SequenceGroup sequenceGroup);
}
* @return
*/
void setAttributeName(String... name);
+
+ /**
+ * Answers true if colour has a threshold set, and the feature score (or other
+ * attribute selected for colouring) is outwith the threshold.
+ * <p>
+ * Answers false if not a graduated colour, or no threshold is set, or value
+ * is not outwith the threshold, or value is null or non-numeric.
+ *
+ * @param sf
+ * @return
+ */
+ boolean isOutwithThreshold(SequenceFeature sf);
+
+ /*
+ * Answers a human-readable text description of the colour, suitable for
+ * display as a tooltip, possibly internationalised for the user's locale.
+ *
+ * @return
+ */
+ String getDescription();
}
* <p>
* Returns null if
* <ul>
- * <li>feature type is not visible, or</li>
* <li>feature group is not visible, or</li>
* <li>feature values lie outside any colour threshold, or</li>
* <li>feature is excluded by filter conditions</li>
* </ul>
+ * This method does not check feature type visibility.
*
* @param feature
* @return
*/
Color getColour(SequenceFeature feature);
+
+ /**
+ * Answers true if feature would be shown, else false. A feature is shown if
+ * <ul>
+ * <li>its feature type is set to visible</li>
+ * <li>its feature group is either null, or set to visible</li>
+ * <li>it is not excluded by a colour threshold on score or other numeric
+ * attribute</li>
+ * <li>it is not excluded by a filter condition</li>
+ * </ul>
+ *
+ * @param feature
+ * @return
+ */
+ boolean isVisible(SequenceFeature feature);
}
--- /dev/null
+package jalview.api;
+
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
+
+/**
+ * An interface for searching for a pattern in an aligment
+ */
+public interface FinderI
+{
+
+ /**
+ * Performs a find for the given search string (interpreted as a regular
+ * expression). Search may optionally be case-sensitive, and may optionally
+ * including match in sequence description (sequence id is always searched).
+ * If the viewport has an active selection, then the find is restricted to the
+ * selection region. Sequences matched by id or description can be retrieved
+ * by getIdMatches(), and matched residue patterns by getSearchResults().
+ *
+ * @param theSearchString
+ * @param caseSensitive
+ * @param searchDescription
+ * @return
+ */
+ void findAll(String theSearchString, boolean caseSensitive,
+ boolean searchDescription);
+
+ /**
+ * Finds the next match for the given search string (interpreted as a regular
+ * expression), starting from the position after the last match found. Search
+ * may optionally be case-sensitive, and may optionally including match in
+ * sequence description (sequence id is always searched). If the viewport has
+ * an active selection, then the find is restricted to the selection region.
+ * Sequences matched by id or description can be retrieved by getIdMatches(),
+ * and matched residue patterns by getSearchResults().
+ *
+ * @param theSearchString
+ * @param caseSensitive
+ * @param searchDescription
+ * @return
+ */
+ void findNext(String theSearchString, boolean caseSensitive,
+ boolean searchDescription);
+
+ /**
+ * Returns the (possibly empty) list of sequences matched on sequence name or
+ * description
+ *
+ * @return
+ */
+ List<SequenceI> getIdMatches();
+
+ /**
+ * Answers the search results (possibly empty) from the last search
+ *
+ * @return
+ */
+ SearchResultsI getSearchResults();
+
+}
\ No newline at end of file
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.SequencePoint;
-import java.util.Vector;
+import java.util.List;
/**
* interface implemented by RotatatableCanvas GUI elements (such as point clouds
*/
public interface RotatableCanvasI
{
+ void setPoints(List<SequencePoint> points, int rows);
- void setPoints(Vector<SequencePoint> points, int rows);
+ /**
+ * Zoom the view in (or out) by the given factor, which should be >= 0. A
+ * factor greater than 1 zooms in (expands the display), a factor less than 1
+ * zooms out (shrinks the display).
+ *
+ * @param factor
+ */
+ void zoom(float factor);
+ /**
+ * Rotates the view by the specified number of degrees about the x and/or y
+ * axis
+ *
+ * @param x
+ * @param y
+ */
+ void rotate(float x, float y);
}
{
features = formatter.printJalviewFormat(
viewport.getAlignment().getSequencesArray(),
- getDisplayedFeatureCols(), null, getDisplayedFeatureGroups(),
- true);
+ alignPanel.getFeatureRenderer(), true);
}
else
{
features = formatter.printGffFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols(),
- getDisplayedFeatureGroups(), true);
+ .getSequencesArray(), alignPanel.getFeatureRenderer(), true);
}
if (displayTextbox)
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShader;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.UserColourScheme;
if (colour != null)
{
residueShading = new ResidueShader(
- ColourSchemeProperty.getColourScheme(alignment, colour));
+ ColourSchemeProperty.getColourScheme(this, alignment,
+ colour));
if (residueShading != null)
{
residueShading.setConsensus(hconsensus);
}
else
{
- int width = av.getAlignment().getWidth();
+ int width = av.getAlignment().getVisibleWidth();
int height = av.getAlignment().getHeight();
- if (av.hasHiddenColumns())
- {
- width = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(width);
- }
if (x < 0)
{
x = 0;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
-import jalview.gui.IProgressIndicator;
import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
@Override
public int[] resizeInnerPanel(String data)
{
- // TODO Auto-generated method stub
return null;
}
@Override
public Map<String, Object> getJSpecViewProperty(String arg0)
{
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected IProgressIndicator getIProgressIndicator()
- {
- // no progress indicators on the applet
return null;
}
}
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
-import jalview.gui.IProgressIndicator;
import jalview.io.DataSourceType;
import java.awt.Container;
}
@Override
- protected IProgressIndicator getIProgressIndicator()
- {
- // no progress indicators on applet (could access javascript for this)
- return null;
- }
-
- @Override
public void updateColours(Object source)
{
-
- // TODO Auto-generated method stub
-
}
@Override
protected JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow)
{
- // TODO Auto-generated method stub
return null;
}
@Override
public void releaseReferences(Object svl)
{
- // TODO Auto-generated method stub
-
}
@Override
public Map<String, Object> getJSpecViewProperty(String arg0)
{
- // TODO Auto-generated method stub
return null;
}
if (oldcs.isGraduatedColour())
{
threshline.value = oldcs.getThreshold();
- cs = new FeatureColour((FeatureColour) oldcs, min, max);
+ cs = new FeatureColour(oldcs.getColour(), oldcs.getMinColour(),
+ oldcs.getMaxColour(), oldcs.getNoColour(), min, max);
}
else
{
bl = oldcs.getColour();
}
// original colour becomes the maximum colour
- cs = new FeatureColour(Color.white, bl, mm[0], mm[1]);
+ cs = new FeatureColour(bl, Color.white, bl, Color.white, mm[0],
+ mm[1]);
}
minColour.setBackground(cs.getMinColour());
maxColour.setBackground(cs.getMaxColour());
slider.setEnabled(true);
thresholdValue.setEnabled(true);
- FeatureColour acg = new FeatureColour(minColour.getBackground(),
- maxColour.getBackground(), min, max);
+ Color minc = minColour.getBackground();
+ Color maxc = maxColour.getBackground();
+ FeatureColour acg = new FeatureColour(maxc, minc, maxc, minc, min, max);
acg.setColourByLabel(colourFromLabel.getState());
maxColour.setEnabled(!colourFromLabel.getState());
{
if (thresholdOption == AnnotationColourGradient.ABOVE_THRESHOLD)
{
- acg = new FeatureColour(acg, threshline.value, max);
+ acg = new FeatureColour(acg.getColour(), acg.getMinColour(),
+ acg.getMaxColour(), acg.getNoColour(), threshline.value,
+ max);
}
else
{
- acg = new FeatureColour(acg, min, threshline.value);
+ acg = new FeatureColour(acg.getColour(), acg.getMinColour(),
+ acg.getMaxColour(), acg.getNoColour(), min,
+ threshline.value);
}
}
*/
package jalview.appletgui;
+import jalview.api.AlignViewportI;
+import jalview.api.FinderI;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
import java.awt.Button;
import java.awt.Checkbox;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
-import java.util.Vector;
+import java.util.Map;
public class Finder extends Panel implements ActionListener
{
- AlignmentViewport av;
+ private AlignViewportI av;
- AlignmentPanel ap;
+ private AlignmentPanel ap;
- Frame frame;
+ private TextField textfield = new TextField();
- SearchResultsI searchResults;
+ private Button findAll = new Button();
- int seqIndex = 0;
+ private Button findNext = new Button();
- int resIndex = -1;
+ private Button createFeatures = new Button();
+
+ private Checkbox caseSensitive = new Checkbox();
+
+ private Checkbox searchDescription = new Checkbox();
+
+ private SearchResultsI searchResults;
+
+ /*
+ * Finder agent per viewport searched
+ */
+ Map<AlignViewportI, FinderI> finders;
public Finder(final AlignmentPanel ap)
{
+ finders = new HashMap<>();
+
try
{
jbInit();
this.av = ap.av;
this.ap = ap;
- frame = new Frame();
+ Frame frame = new Frame();
frame.add(this);
jalview.bin.JalviewLite.addFrame(frame,
MessageManager.getString("action.find"), 340, 120);
else if (evt.getSource() == findAll)
{
- resIndex = -1;
- seqIndex = 0;
doSearch(true);
}
- else if (evt.getSource() == createNewGroup)
+ else if (evt.getSource() == createFeatures)
{
- createNewGroup_actionPerformed();
+ createFeatures_actionPerformed();
}
}
- public void createNewGroup_actionPerformed()
+ public void createFeatures_actionPerformed()
{
- List<SequenceI> seqs = new ArrayList<SequenceI>();
- List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
String searchString = textfield.getText().trim();
for (SearchResultMatchI match : searchResults.getResults())
}
}
- void doSearch(boolean findAll)
+ void doSearch(boolean doFindAll)
{
if (ap.av.applet.currentAlignFrame != null)
{
ap = ap.av.applet.currentAlignFrame.alignPanel;
av = ap.av;
}
- createNewGroup.setEnabled(false);
- jalview.analysis.Finder finder = new jalview.analysis.Finder(
- av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
- finder.setCaseSensitive(caseSensitive.getState());
- finder.setIncludeDescription(searchDescription.getState());
- finder.setFindAll(findAll);
+ createFeatures.setEnabled(false);
+ FinderI finder = finders.get(av);
+ if (finder == null)
+ {
+ /*
+ * first time we searched this viewport
+ */
+ finder = new jalview.analysis.Finder(av);
+ finders.put(av, finder);
+ }
String searchString = textfield.getText();
-
- finder.find(searchString);
- seqIndex = finder.getSeqIndex();
- resIndex = finder.getResIndex();
- searchResults = finder.getSearchResults();
- Vector<SequenceI> idMatch = finder.getIdMatch();
- boolean haveResults = false;
- // set or reset the GUI
- if ((idMatch.size() > 0))
+ boolean isCaseSensitive = caseSensitive.getState();
+ boolean doSearchDescription = searchDescription.getState();
+ if (doFindAll)
{
- haveResults = true;
- ap.idPanel.highlightSearchResults(idMatch);
+ finder.findAll(searchString, isCaseSensitive, doSearchDescription);
}
else
{
- ap.idPanel.highlightSearchResults(null);
+ finder.findNext(searchString, isCaseSensitive, doSearchDescription);
}
- if (searchResults.getSize() > 0)
- {
- haveResults = true;
- createNewGroup.setEnabled(true);
+ searchResults = finder.getSearchResults();
+
+ List<SequenceI> idMatches = finder.getIdMatches();
+ ap.idPanel.highlightSearchResults(idMatches);
+ if (searchResults.isEmpty())
+ {
+ searchResults = null;
}
else
{
- searchResults = null;
+ createFeatures.setEnabled(true);
}
// if allResults is null, this effectively switches displaySearch flag in
ap.highlightSearchResults(searchResults);
// TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
// 'SelectRegion' selection
- if (!haveResults)
+ if (idMatches.isEmpty() && searchResults == null)
{
ap.alignFrame.statusBar.setText(
MessageManager.getString("label.finished_searching"));
- resIndex = -1;
- seqIndex = 0;
}
else
{
- if (findAll)
+ if (doFindAll)
{
- String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
+ String message = (idMatches.size() > 0) ? "" + idMatches.size() + " IDs"
: "";
- if (idMatch.size() > 0 && searchResults != null
+ if (idMatches.size() > 0 && searchResults != null
&& searchResults.getSize() > 0)
{
message += " and ";
}
}
- Label jLabel1 = new Label();
-
- protected TextField textfield = new TextField();
-
- protected Button findAll = new Button();
-
- protected Button findNext = new Button();
-
- Panel actionsPanel = new Panel();
-
- GridLayout gridLayout1 = new GridLayout();
-
- protected Button createNewGroup = new Button();
-
- Checkbox caseSensitive = new Checkbox();
-
- Checkbox searchDescription = new Checkbox();
-
private void jbInit() throws Exception
{
+ Label jLabel1 = new Label(MessageManager.getString("action.find"));
jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
- jLabel1.setText(MessageManager.getString("action.find"));
jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
this.setLayout(null);
textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
@Override
public void keyTyped(KeyEvent e)
{
- textfield_keyTyped(e);
+ textfield_keyTyped();
}
});
textfield.addActionListener(this);
findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
findNext.setLabel(MessageManager.getString("action.find_next"));
findNext.addActionListener(this);
+
+ Panel actionsPanel = new Panel();
actionsPanel.setBounds(new Rectangle(195, 5, 141, 64));
+ GridLayout gridLayout1 = new GridLayout();
actionsPanel.setLayout(gridLayout1);
gridLayout1.setHgap(0);
gridLayout1.setRows(3);
gridLayout1.setVgap(2);
- createNewGroup.setEnabled(false);
- createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- createNewGroup.setLabel(MessageManager.getString("label.new_feature"));
- createNewGroup.addActionListener(this);
+ createFeatures.setEnabled(false);
+ createFeatures.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+ createFeatures.setLabel(MessageManager.getString("label.new_feature"));
+ createFeatures.addActionListener(this);
caseSensitive.setLabel(MessageManager.getString("label.match_case"));
caseSensitive.setBounds(new Rectangle(30, 39, 126, 23));
searchDescription.setBounds(new Rectangle(30, 59, 170, 23));
actionsPanel.add(findNext, null);
actionsPanel.add(findAll, null);
- actionsPanel.add(createNewGroup, null);
+ actionsPanel.add(createFeatures, null);
this.add(caseSensitive);
this.add(textfield, null);
this.add(jLabel1, null);
this.add(searchDescription);
}
- void textfield_keyTyped(KeyEvent e)
+ void textfield_keyTyped()
{
findNext.setEnabled(true);
}
protected void drawIdsWrapped(int starty, final boolean doHiddenCheck,
boolean hiddenRows)
{
- int maxwidth = av.getAlignment().getWidth();
+ int maxwidth = av.getAlignment().getVisibleWidth();
int alheight = av.getAlignment().getHeight();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth) - 1;
- }
-
int annotationHeight = 0;
AnnotationLabels labels = null;
{
idCanvas.setHighlighted(list);
- if (list == null)
+ if (list == null || list.isEmpty())
{
return;
}
}
}
+ /**
+ * Nulls references to protect against potential memory leaks
+ */
+ void dispose()
+ {
+ od = null;
+ }
+
}
{
if (od.isPositionInBox(evt.getX(), evt.getY()))
{
- // display drag cursor at mouse position
- setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+ this.getParent()
+ .setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
}
else
{
- // reset cursor
- setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+ this.getParent()
+ .setCursor(
+ Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR));
}
}
od.updateViewportFromMouse(evt.getX(), evt.getY(),
av.getAlignment().getHiddenSequences(),
av.getAlignment().getHiddenColumns());
+ getParent()
+ .setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
}
else
{
} finally
{
av = null;
+ if (oviewCanvas != null)
+ {
+ oviewCanvas.dispose();
+ }
oviewCanvas = null;
ap = null;
od = null;
{
nuclSetting.setState(pcaModel.isNucleotide());
protSetting.setState(!pcaModel.isNucleotide());
- pcaModel.run();
+ pcaModel.calculate();
// ////////////////
xCombobox.select(0);
yCombobox.select(1);
int dim2 = top - yCombobox.getSelectedIndex();
int dim3 = top - zCombobox.getSelectedIndex();
pcaModel.updateRcView(dim1, dim2, dim3);
- rc.img = null;
- rc.rotmat.setIdentity();
- rc.initAxes();
+ rc.resetView();
rc.paint(rc.getGraphics());
}
{
}
;
- Object[] alAndColsel = pcaModel.getSeqtrings()
+ Object[] alAndColsel = pcaModel.getInputData()
.getAlignmentAndHiddenColumns(gc);
if (alAndColsel != null && alAndColsel[0] != null)
package jalview.appletgui;
import jalview.api.RotatableCanvasI;
+import jalview.datamodel.Point;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
import jalview.math.RotatableMatrix;
-import jalview.util.Format;
+import jalview.math.RotatableMatrix.Axis;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
-import java.util.Vector;
+import java.util.List;
public class RotatableCanvas extends Panel implements MouseListener,
MouseMotionListener, KeyListener, RotatableCanvasI
{
- RotatableMatrix idmat = new RotatableMatrix(3, 3);
-
- RotatableMatrix objmat = new RotatableMatrix(3, 3);
-
- RotatableMatrix rotmat = new RotatableMatrix(3, 3);
+ private static final int DIMS = 3;
String tooltip;
- int toolx, tooly;
+ int toolx;
+
+ int tooly;
// RubberbandRectangle rubberband;
boolean drawAxes = true;
- int omx = 0;
-
- int mx = 0;
-
- int omy = 0;
+ int mouseX = 0;
- int my = 0;
+ int mouseY = 0;
Image img;
Dimension prefsize;
- float centre[] = new float[3];
+ Point centre;
- float width[] = new float[3];
+ float[] width = new float[DIMS];
- float max[] = new float[3];
+ float[] max = new float[DIMS];
- float min[] = new float[3];
+ float[] min = new float[DIMS];
float maxwidth;
int npoint;
- Vector points;
+ List<SequencePoint> points;
- float[][] orig;
+ Point[] orig;
- float[][] axes;
+ Point[] axisEndPoints;
int startx;
boolean showLabels = false;
- public RotatableCanvas(AlignmentViewport av)
+ public RotatableCanvas(AlignmentViewport viewport)
{
- this.av = av;
+ this.av = viewport;
+ axisEndPoints = new Point[DIMS];
}
public void showLabels(boolean b)
repaint();
}
- public void setPoints(Vector points, int npoint)
+ @Override
+ public void setPoints(List<SequencePoint> points, int npoint)
{
this.points = points;
this.npoint = npoint;
PaintRefresher.Register(this, av.getSequenceSetId());
prefsize = getPreferredSize();
- orig = new float[npoint][3];
+ orig = new Point[npoint];
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- for (int j = 0; j < 3; j++)
- {
- orig[i][j] = sp.coord[j];
- }
- }
- // Initialize the matrices to identity
-
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- if (i != j)
- {
- idmat.addElement(i, j, 0);
- objmat.addElement(i, j, 0);
- rotmat.addElement(i, j, 0);
- }
- else
- {
- idmat.addElement(i, j, 0);
- objmat.addElement(i, j, 0);
- rotmat.addElement(i, j, 0);
- }
- }
+ SequencePoint sp = points.get(i);
+ orig[i] = sp.coord;
}
- axes = new float[3][3];
- initAxes();
+ resetAxes();
findCentre();
findWidth();
* super.removeNotify(); }
*/
- public void initAxes()
+ /**
+ * Resets axes to the initial state: x-axis to the right, y-axis up, z-axis to
+ * back (so obscured in a 2-D display)
+ */
+ public void resetAxes()
{
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- if (i != j)
- {
- axes[i][j] = 0;
- }
- else
- {
- axes[i][j] = 1;
- }
- }
- }
+ axisEndPoints[0] = new Point(1f, 0f, 0f);
+ axisEndPoints[1] = new Point(0f, 1f, 0f);
+ axisEndPoints[2] = new Point(0f, 0f, 1f);
}
+ /**
+ * Computes and saves the maximum and minimum (x, y, z) positions of any
+ * sequence point, and also the min-max range (width) for each dimension, and
+ * the maximum width for all dimensions
+ */
public void findWidth()
{
max = new float[3];
min = new float[3];
- max[0] = (float) -1e30;
- max[1] = (float) -1e30;
- max[2] = (float) -1e30;
+ max[0] = Float.MIN_VALUE;
+ max[1] = Float.MIN_VALUE;
+ max[2] = Float.MIN_VALUE;
- min[0] = (float) 1e30;
- min[1] = (float) 1e30;
- min[2] = (float) 1e30;
+ min[0] = Float.MAX_VALUE;
+ min[1] = Float.MAX_VALUE;
+ min[2] = Float.MAX_VALUE;
- for (int i = 0; i < 3; i++)
+ for (SequencePoint sp : points)
{
- for (int j = 0; j < npoint; j++)
- {
- SequencePoint sp = (SequencePoint) points.elementAt(j);
- if (sp.coord[i] >= max[i])
- {
- max[i] = sp.coord[i];
- }
- if (sp.coord[i] <= min[i])
- {
- min[i] = sp.coord[i];
- }
- }
+ max[0] = Math.max(max[0], sp.coord.x);
+ max[1] = Math.max(max[1], sp.coord.y);
+ max[2] = Math.max(max[2], sp.coord.z);
+ min[0] = Math.min(min[0], sp.coord.x);
+ min[1] = Math.min(min[1], sp.coord.y);
+ min[2] = Math.min(min[2], sp.coord.z);
}
- // System.out.println("xmax " + max[0] + " min " + min[0]);
- // System.out.println("ymax " + max[1] + " min " + min[1]);
- // System.out.println("zmax " + max[2] + " min " + min[2]);
-
width[0] = Math.abs(max[0] - min[0]);
width[1] = Math.abs(max[1] - min[1]);
width[2] = Math.abs(max[2] - min[2]);
- maxwidth = width[0];
-
- if (width[1] > width[0])
- {
- maxwidth = width[1];
- }
- if (width[2] > width[1])
- {
- maxwidth = width[2];
- }
-
- // System.out.println("Maxwidth = " + maxwidth);
+ maxwidth = Math.max(width[0], Math.max(width[1], width[2]));
}
public float findScale()
{
- int dim, width, height;
+ int dim, w, height;
if (getSize().width != 0)
{
- width = getSize().width;
+ w = getSize().width;
height = getSize().height;
}
else
{
- width = prefsize.width;
+ w = prefsize.width;
height = prefsize.height;
}
- if (width < height)
+ if (w < height)
{
- dim = width;
+ dim = w;
}
else
{
dim = height;
}
- return (float) (dim * scalefactor / (2 * maxwidth));
+ return dim * scalefactor / (2 * maxwidth);
}
+ /**
+ * Computes and saves the position of the centre of the view
+ */
public void findCentre()
{
- // Find centre coordinate
findWidth();
- centre[0] = (max[0] + min[0]) / 2;
- centre[1] = (max[1] + min[1]) / 2;
- centre[2] = (max[2] + min[2]) / 2;
+ float x = (max[0] + min[0]) / 2;
+ float y = (max[1] + min[1]) / 2;
+ float z = (max[2] + min[2]) / 2;
- // System.out.println("Centre x " + centre[0]);
- // System.out.println("Centre y " + centre[1]);
- // System.out.println("Centre z " + centre[2]);
+ centre = new Point(x, y, z);
}
+ @Override
public Dimension getPreferredSize()
{
if (prefsize != null)
}
}
+ @Override
public Dimension getMinimumSize()
{
return getPreferredSize();
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
if (points == null)
drawBackground(ig, Color.black);
drawScene(ig);
- if (drawAxes == true)
+ if (drawAxes)
{
drawAxes(ig);
}
for (int i = 0; i < 3; i++)
{
g.drawLine(getSize().width / 2, getSize().height / 2,
- (int) (axes[i][0] * scale * max[0] + getSize().width / 2),
- (int) (axes[i][1] * scale * max[1] + getSize().height / 2));
+ (int) (axisEndPoints[i].x * scale * max[0] + getSize().width / 2),
+ (int) (axisEndPoints[i].y * scale * max[1] + getSize().height / 2));
}
}
public void drawScene(Graphics g)
{
- // boolean darker = false;
-
- int halfwidth = getSize().width / 2;
- int halfheight = getSize().height / 2;
-
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) + halfwidth;
- int y = (int) ((float) (sp.coord[1] - centre[1]) * scale)
- + halfheight;
- float z = sp.coord[1] - centre[2];
-
- if (av.getSequenceColour(sp.sequence) == Color.black)
- {
- g.setColor(Color.white);
- }
- else
- {
- g.setColor(av.getSequenceColour(sp.sequence));
- }
-
+ SequencePoint sp = points.get(i);
+ SequenceI sequence = sp.getSequence();
+ Color sequenceColour = av.getSequenceColour(sequence);
+ g.setColor(
+ sequenceColour == Color.black ? Color.white : sequenceColour);
if (av.getSelectionGroup() != null)
{
if (av.getSelectionGroup().getSequences(null)
- .contains(((SequencePoint) points.elementAt(i)).sequence))
+ .contains(sequence))
{
g.setColor(Color.gray);
}
}
- if (z < 0)
+
+ if (sp.coord.z < centre.z)
{
g.setColor(g.getColor().darker());
}
+ int halfwidth = getSize().width / 2;
+ int halfheight = getSize().height / 2;
+ int x = (int) ((sp.coord.x - centre.x) * scale) + halfwidth;
+ int y = (int) ((sp.coord.y - centre.y) * scale) + halfheight;
g.fillRect(x - 3, y - 3, 6, 6);
+
if (showLabels)
{
g.setColor(Color.red);
- g.drawString(
- ((SequencePoint) points.elementAt(i)).sequence.getName(),
- x - 3, y - 4);
+ g.drawString(sequence.getName(), x - 3, y - 4);
}
}
}
- public Dimension minimumsize()
- {
- return prefsize;
- }
-
- public Dimension preferredsize()
- {
- return prefsize;
- }
-
+ @Override
public void keyTyped(KeyEvent evt)
{
}
+ @Override
public void keyReleased(KeyEvent evt)
{
}
+ @Override
public void keyPressed(KeyEvent evt)
{
- if (evt.getKeyCode() == KeyEvent.VK_UP)
+ boolean shiftDown = evt.isShiftDown();
+ int keyCode = evt.getKeyCode();
+ if (keyCode == KeyEvent.VK_UP)
+ {
+ if (shiftDown)
+ {
+ rotate(0f, -1f);
+ }
+ else
+ {
+ zoom(1.1f);
+ }
+ }
+ else if (keyCode == KeyEvent.VK_DOWN)
{
- scalefactor = (float) (scalefactor * 1.1);
- scale = findScale();
+ if (shiftDown)
+ {
+ rotate(0f, 1f);
+ }
+ else
+ {
+ zoom(0.9f);
+ }
}
- else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+ else if (shiftDown && keyCode == KeyEvent.VK_LEFT)
{
- scalefactor = (float) (scalefactor * 0.9);
- scale = findScale();
+ rotate(1f, 0f);
+ }
+ else if (shiftDown && keyCode == KeyEvent.VK_RIGHT)
+ {
+ rotate(-1f, 0f);
}
else if (evt.getKeyChar() == 's')
{
repaint();
}
- public void printPoints()
- {
- for (int i = 0; i < npoint; i++)
- {
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- Format.print(System.out, "%5d ", i);
- for (int j = 0; j < 3; j++)
- {
- Format.print(System.out, "%13.3f ", sp.coord[j]);
- }
- System.out.println();
- }
- }
-
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
}
+ @Override
public void mousePressed(MouseEvent evt)
{
int x = evt.getX();
int y = evt.getY();
- mx = x;
- my = y;
-
- omx = mx;
- omy = my;
+ mouseX = x;
+ mouseY = y;
startx = x;
starty = y;
rectx2 = -1;
recty2 = -1;
- SequenceI found = findPoint(x, y);
+ SequenceI found = findSequenceAtPoint(x, y);
if (found != null)
{
repaint();
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
- SequenceI found = findPoint(evt.getX(), evt.getY());
+ SequenceI found = findSequenceAtPoint(evt.getX(), evt.getY());
if (found == null)
{
tooltip = null;
repaint();
}
+ @Override
public void mouseDragged(MouseEvent evt)
{
- mx = evt.getX();
- my = evt.getY();
-
- rotmat.setIdentity();
+ int xPos = evt.getX();
+ int yPos = evt.getY();
- rotmat.rotate((float) (my - omy), 'x');
- rotmat.rotate((float) (mx - omx), 'y');
-
- for (int i = 0; i < npoint; i++)
+ if (xPos == mouseX && yPos == mouseY)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- sp.coord[0] -= centre[0];
- sp.coord[1] -= centre[1];
- sp.coord[2] -= centre[2];
-
- // Now apply the rotation matrix
- sp.coord = rotmat.vectorMultiply(sp.coord);
-
- // Now translate back again
- sp.coord[0] += centre[0];
- sp.coord[1] += centre[1];
- sp.coord[2] += centre[2];
+ return;
}
- for (int i = 0; i < 3; i++)
- {
- axes[i] = rotmat.vectorMultiply(axes[i]);
- }
- omx = mx;
- omy = my;
+ int xDelta = xPos - mouseX;
+ int yDelta = yPos - mouseY;
- paint(this.getGraphics());
+ rotate(xDelta, yDelta);
+ repaint();
}
public void rectSelect(int x1, int y1, int x2, int y2)
// boolean changedSel = false;
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int tmp1 = (int) ((sp.coord[0] - centre[0]) * scale
- + (float) getSize().width / 2.0);
- int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale
- + (float) getSize().height / 2.0);
+ SequencePoint sp = points.get(i);
+ int tmp1 = (int) ((sp.coord.x - centre.x) * scale
+ + getSize().width / 2.0);
+ int tmp2 = (int) ((sp.coord.y - centre.y) * scale
+ + getSize().height / 2.0);
+ SequenceI sequence = sp.getSequence();
if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)
{
if (av != null)
{
if (!av.getSelectionGroup().getSequences(null)
- .contains(sp.sequence))
+ .contains(sequence))
{
- av.getSelectionGroup().addSequence(sp.sequence, true);
+ av.getSelectionGroup().addSequence(sequence, true);
}
}
}
}
}
- public SequenceI findPoint(int x, int y)
+ /**
+ * Answers the first sequence found whose point on the display is within 2
+ * pixels of the given coordinates, or null if none is found
+ *
+ * @param x
+ * @param y
+ *
+ * @return
+ */
+ public SequenceI findSequenceAtPoint(int x, int y)
{
-
int halfwidth = getSize().width / 2;
int halfheight = getSize().height / 2;
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int px = (int) ((float) (sp.coord[0] - centre[0]) * scale)
+ SequencePoint sp = points.get(i);
+ int px = (int) ((sp.coord.x - centre.x) * scale)
+ halfwidth;
- int py = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+ int py = (int) ((sp.coord.y - centre.y) * scale)
+ halfheight;
if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3)
{
found = i;
+ break;
}
}
+
if (found != -1)
{
- return ((SequencePoint) points.elementAt(found)).sequence;
+ return points.get(found).getSequence();
}
else
{
}
}
+ /**
+ * Resets the view to initial state (no rotation)
+ */
+ public void resetView()
+ {
+ img = null;
+ resetAxes();
+ }
+
+ @Override
+ public void zoom(float factor)
+ {
+ if (factor > 0f)
+ {
+ scalefactor *= factor;
+ }
+ scale = findScale();
+ }
+
+ @Override
+ public void rotate(float x, float y)
+ {
+ if (x == 0f && y == 0f)
+ {
+ return;
+ }
+
+ /*
+ * get the identity transformation...
+ */
+ RotatableMatrix rotmat = new RotatableMatrix();
+
+ /*
+ * rotate around the X axis for change in Y
+ * (mouse movement up/down); note we are equating a
+ * number of pixels with degrees of rotation here!
+ */
+ if (y != 0)
+ {
+ rotmat.rotate(y, Axis.X);
+ }
+
+ /*
+ * rotate around the Y axis for change in X
+ * (mouse movement left/right)
+ */
+ if (x != 0)
+ {
+ rotmat.rotate(x, Axis.Y);
+ }
+
+ /*
+ * apply the composite transformation to sequence points
+ */
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = points.get(i);
+ sp.translate(-centre.x, -centre.y, -centre.z);
+
+ // Now apply the rotation matrix
+ sp.coord = rotmat.vectorMultiply(sp.coord);
+
+ // Now translate back again
+ sp.translate(centre.x, centre.y, centre.z);
+ }
+
+ /*
+ * rotate the x/y/z axis positions
+ */
+ for (int i = 0; i < DIMS; i++)
+ {
+ axisEndPoints[i] = rotmat.vectorMultiply(axisEndPoints[i]);
+ }
+ }
+
}
.visibleToAbsoluteColumn(endx);
}
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth) - 1;
- }
-
// WEST SCALE
for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
int endx;
int ypos = hgap;
- int maxwidth = av.getAlignment().getWidth();
-
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth);
- }
+ int maxwidth = av.getAlignment().getVisibleWidth();
while ((ypos <= canvasHeight) && (startRes < maxwidth))
{
int blockEnd;
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- VisibleContigsIterator regions = (VisibleContigsIterator) hidden
+ VisibleContigsIterator regions = hidden
.getVisContigsIterator(startRes, endRes + 1, true);
while (regions.hasNext())
Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
- Vector<SequenceI> sequences = new Vector<SequenceI>();
+ Vector<SequenceI> sequences = new Vector<>();
for (int j = 0; j < l.size(); j++)
{
SequenceI s1 = (SequenceI) l.elementAt(j).element();
}
else
{
- cs = ColourSchemeProperty.getColourScheme(sg, ColourSchemeProperty
+ cs = ColourSchemeProperty.getColourScheme(av, sg,
+ ColourSchemeProperty
.getColourName(av.getGlobalColourScheme()));
}
// cs is null if shading is an annotationColourGradient
* service</li>
* <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
* collecting usage statistics</li>
- * <li>DAS_LOCAL_SOURCE list of local das sources</li>
* <li>SHOW_OVERVIEW boolean for overview window display</li>
* <li>ANTI_ALIAS boolean for smooth fonts</li>
* <li>RIGHT_ALIGN_IDS boolean</li>
* sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
* <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
* jalview.utils.GroupURLLink for more info</li>
- * <li>DAS_REGISTRY_URL the registry to query</li>
* <li>DEFAULT_BROWSER for unix</li>
- * <li>DAS_ACTIVE_SOURCE list of active sources</li>
* <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
* (false)</li>
* <li>VERSION_CHECK (true) check for the latest release version from
*/
public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
- public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
-
- public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
-
- public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
-
/**
* Sifts settings
*/
return def;
}
+ public static int getDefault(String property, int def)
+ {
+ String string = getProperty(property);
+ if (string != null)
+ {
+ try
+ {
+ def = Integer.parseInt(string);
+ } catch (NumberFormatException e)
+ {
+ System.out.println("Error parsing int property '" + property
+ + "' with value '" + string + "'");
+ }
+ }
+
+ return def;
+ }
+
/**
* These methods are used when checking if the saved preference is different
* to the default setting
FileFormatI format = null;
DataSourceType protocol = null;
FileLoader fileLoader = new FileLoader(!headless);
- Vector<String> getFeatures = null; // vector of das source nicknames to
- // fetch
- // features from
- // loading is done.
+
String groovyscript = null; // script to execute after all loading is
// completed one way or another
// extract groovy argument and execute if necessary
data.replaceAll("%20", " ");
ColourSchemeI cs = ColourSchemeProperty
- .getColourScheme(af.getViewport().getAlignment(), data);
+ .getColourScheme(af.getViewport(),
+ af.getViewport().getAlignment(), data);
if (cs != null)
{
// TODO - load PDB structure(s) to alignment JAL-629
// (associate with identical sequence in alignment, or a specified
// sequence)
-
- getFeatures = checkDasArguments(aparser);
- if (af != null && getFeatures != null)
- {
- FeatureFetcher ff = startFeatureFetching(getFeatures);
- if (ff != null)
- {
- while (!ff.allFinished() || af.operationInProgress())
- {
- // wait around until fetching is finished.
- try
- {
- Thread.sleep(100);
- } catch (Exception e)
- {
-
- }
- }
- }
- getFeatures = null; // have retrieved features - forget them now.
- }
if (groovyscript != null)
{
// Execute the groovy script after we've done all the rendering stuff
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
- getFeatures = checkDasArguments(aparser);
// extract groovy arguments before anything else.
}
- // If the user has specified features to be retrieved,
- // or a groovy script to be executed, do them if they
- // haven't been done already
- // fetch features for the default alignment
- if (getFeatures != null)
- {
- if (startUpAlframe != null)
- {
- startFeatureFetching(getFeatures);
- }
- }
+
// Once all other stuff is done, execute any groovy scripts (in order)
if (groovyscript != null)
{
// (quote the 'PROPERTY=VALUE' pair to ensure spaces are
// passed in correctly)"
+ "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
- + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
- + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
- + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
+ "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
// +
// "-vdoc vamsas-document\tImport vamsas document into new
}
}
- /**
- * Check commandline for any das server definitions or any fetchfrom switches
- *
- * @return vector of DAS source nicknames to retrieve from
- */
- private static Vector<String> checkDasArguments(ArgsParser aparser)
- {
- Vector<String> source = null;
- String data;
- String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
- while ((data = aparser.getValue("dasserver", true)) != null)
- {
- String nickname = null;
- String url = null;
- int pos = data.indexOf('=');
- // determine capabilities
- if (pos > 0)
- {
- nickname = data.substring(0, pos);
- }
- url = data.substring(pos + 1);
- if (url != null && (url.startsWith("http:")
- || url.startsWith("sequence:http:")))
- {
- if (nickname == null)
- {
- nickname = url;
- }
- if (locsources == null)
- {
- locsources = "";
- }
- else
- {
- locsources += "\t";
- }
- locsources = locsources + nickname + "|" + url;
- System.err.println(
- "NOTE! dasserver parameter not yet really supported (got args of "
- + nickname + "|" + url);
- if (source == null)
- {
- source = new Vector<>();
- }
- source.addElement(nickname);
- }
- System.out.println(
- "CMD [-dasserver " + data + "] executed successfully!");
- } // loop until no more server entries are found.
- if (locsources != null && locsources.indexOf('|') > -1)
- {
- Cache.log.debug("Setting local source list in properties file to:\n"
- + locsources);
- Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
- }
- while ((data = aparser.getValue("fetchfrom", true)) != null)
- {
- System.out.println("adding source '" + data + "'");
- if (source == null)
- {
- source = new Vector<>();
- }
- source.addElement(data);
- }
- return source;
- }
-
- /**
- * start a feature fetcher for every alignment frame
- *
- * @param dasSources
- */
- private FeatureFetcher startFeatureFetching(
- final Vector<String> dasSources)
- {
- FeatureFetcher ff = new FeatureFetcher();
- AlignFrame afs[] = Desktop.getAlignFrames();
- if (afs == null || afs.length == 0)
- {
- return null;
- }
- for (int i = 0; i < afs.length; i++)
- {
- ff.addFetcher(afs[i], dasSources);
- }
- return ff;
- }
-
public static boolean isHeadlessMode()
{
String isheadless = System.getProperty("java.awt.headless");
*/
package jalview.commands;
+import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.ContiguousI;
+import jalview.datamodel.Range;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.Comparison;
import jalview.util.ReverseListIterator;
import jalview.util.StringUtils;
public abstract Action getUndoAction();
};
- private List<Edit> edits = new ArrayList<Edit>();
+ private List<Edit> edits = new ArrayList<>();
String description;
int position, int number, AlignmentI al, boolean performEdit,
AlignmentI[] views)
{
- Edit edit = new Edit(command, seqs, position, number,
- al.getGapCharacter());
- if (al.getHeight() == seqs.length)
- {
- edit.al = al;
- edit.fullAlignmentHeight = true;
- }
-
- addEdit(edit);
-
- if (performEdit)
- {
- performEdit(edit, views);
- }
+ Edit edit = new Edit(command, seqs, position, number, al);
+ appendEdit(edit, al, performEdit, views);
}
/**
command.string[i] = sequence.getSequence(command.position,
command.position + command.number);
SequenceI oldds = sequence.getDatasetSequence();
+ ContiguousI cutPositions = sequence.findPositions(
+ command.position + 1, command.position + command.number);
+ boolean cutIsInternal = cutPositions != null
+ && sequence.getStart() != cutPositions
+ .getBegin() && sequence.getEnd() != cutPositions.getEnd();
+
+ /*
+ * perform the cut; if this results in a new dataset sequence, add
+ * that to the alignment dataset
+ */
+ SequenceI ds = sequence.getDatasetSequence();
+ sequence.deleteChars(command.position, command.position
+ + command.number);
+
if (command.oldds != null && command.oldds[i] != null)
{
- // we are redoing an undone cut.
- sequence.setDatasetSequence(null);
- }
- sequence.deleteChars(command.position,
- command.position + command.number);
- if (command.oldds != null && command.oldds[i] != null)
- {
- // oldds entry contains the cut dataset sequence.
+ /*
+ * we are Redoing a Cut, or Undoing a Paste - so
+ * oldds entry contains the cut dataset sequence,
+ * with sequence features in expected place
+ */
sequence.setDatasetSequence(command.oldds[i]);
command.oldds[i] = oldds;
}
else
{
- // modify the oldds if necessary
+ /*
+ * new cut operation: save the dataset sequence
+ * so it can be restored in an Undo
+ */
+ if (command.oldds == null)
+ {
+ command.oldds = new SequenceI[command.seqs.length];
+ }
+ command.oldds[i] = oldds;// todo not if !cutIsInternal?
+
+ // do we need to edit sequence features for new sequence ?
if (oldds != sequence.getDatasetSequence()
- || sequence.getFeatures().hasFeatures())
+ || (cutIsInternal
+ && sequence.getFeatures().hasFeatures()))
+ // todo or just test cutIsInternal && cutPositions != null ?
{
- if (command.oldds == null)
+ if (cutPositions != null)
{
- command.oldds = new SequenceI[command.seqs.length];
+ cutFeatures(command, sequence, cutPositions.getBegin(),
+ cutPositions.getEnd(), cutIsInternal);
}
- command.oldds[i] = oldds;
- // FIXME JAL-2541 JAL-2526 get correct positions if on a gap
- adjustFeatures(
- command,
- i,
- sequence.findPosition(command.position),
- sequence.findPosition(command.position + command.number),
- false);
}
}
+ SequenceI newDs = sequence.getDatasetSequence();
+ if (newDs != ds && command.al != null
+ && command.al.getDataset() != null
+ && !command.al.getDataset().getSequences().contains(newDs))
+ {
+ command.al.getDataset().addSequence(newDs);
+ }
}
if (sequence.getLength() < 1)
*/
static void paste(Edit command, AlignmentI[] views)
{
- StringBuffer tmp;
- boolean newDSNeeded;
- boolean newDSWasNeeded;
- int newstart, newend;
boolean seqWasDeleted = false;
- int start = 0, end = 0;
for (int i = 0; i < command.seqs.length; i++)
{
- newDSNeeded = false;
- newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
- if (command.seqs[i].getLength() < 1)
+ boolean newDSNeeded = false;
+ boolean newDSWasNeeded = command.oldds != null
+ && command.oldds[i] != null;
+ SequenceI sequence = command.seqs[i];
+ if (sequence.getLength() < 1)
{
- // ie this sequence was deleted, we need to
- // readd it to the alignment
+ /*
+ * sequence was deleted; re-add it to the alignment
+ */
if (command.alIndex[i] < command.al.getHeight())
{
List<SequenceI> sequences;
{
if (!(command.alIndex[i] < 0))
{
- sequences.add(command.alIndex[i], command.seqs[i]);
+ sequences.add(command.alIndex[i], sequence);
}
}
}
else
{
- command.al.addSequence(command.seqs[i]);
+ command.al.addSequence(sequence);
}
seqWasDeleted = true;
}
- newstart = command.seqs[i].getStart();
- newend = command.seqs[i].getEnd();
+ int newStart = sequence.getStart();
+ int newEnd = sequence.getEnd();
- tmp = new StringBuffer();
- tmp.append(command.seqs[i].getSequence());
+ StringBuilder tmp = new StringBuilder();
+ tmp.append(sequence.getSequence());
// Undo of a delete does not replace original dataset sequence on to
// alignment sequence.
+ int start = 0;
+ int length = 0;
+
if (command.string != null && command.string[i] != null)
{
if (command.position >= tmp.length())
{
// This occurs if padding is on, and residues
// are removed from end of alignment
- int length = command.position - tmp.length();
- while (length > 0)
+ int len = command.position - tmp.length();
+ while (len > 0)
{
tmp.append(command.gapChar);
- length--;
+ len--;
}
}
tmp.insert(command.position, command.string[i]);
for (int s = 0; s < command.string[i].length; s++)
{
- if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)
+ if (!Comparison.isGap(command.string[i][s]))
{
+ length++;
if (!newDSNeeded)
{
newDSNeeded = true;
- start = command.seqs[i].findPosition(command.position);
- end = command.seqs[i]
- .findPosition(command.position + command.number);
+ start = sequence.findPosition(command.position);
+ // end = sequence
+ // .findPosition(command.position + command.number);
}
- if (command.seqs[i].getStart() == start)
+ if (sequence.getStart() == start)
{
- newstart--;
+ newStart--;
}
else
{
- newend++;
+ newEnd++;
}
}
}
command.string[i] = null;
}
- command.seqs[i].setSequence(tmp.toString());
- command.seqs[i].setStart(newstart);
- command.seqs[i].setEnd(newend);
+ sequence.setSequence(tmp.toString());
+ sequence.setStart(newStart);
+ sequence.setEnd(newEnd);
+
+ /*
+ * command and Undo share the same dataset sequence if cut was
+ * at start or end of sequence
+ */
+ boolean sameDatasetSequence = false;
if (newDSNeeded)
{
- if (command.seqs[i].getDatasetSequence() != null)
+ if (sequence.getDatasetSequence() != null)
{
SequenceI ds;
if (newDSWasNeeded)
{
// make a new DS sequence
// use new ds mechanism here
- ds = new Sequence(command.seqs[i].getName(),
- jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- command.seqs[i].getSequenceAsString()),
- command.seqs[i].getStart(), command.seqs[i].getEnd());
- ds.setDescription(command.seqs[i].getDescription());
+ String ungapped = AlignSeq.extractGaps(Comparison.GapChars,
+ sequence.getSequenceAsString());
+ ds = new Sequence(sequence.getName(), ungapped,
+ sequence.getStart(), sequence.getEnd());
+ ds.setDescription(sequence.getDescription());
}
if (command.oldds == null)
{
command.oldds = new SequenceI[command.seqs.length];
}
- command.oldds[i] = command.seqs[i].getDatasetSequence();
- command.seqs[i].setDatasetSequence(ds);
+ command.oldds[i] = sequence.getDatasetSequence();
+ sameDatasetSequence = ds == sequence.getDatasetSequence();
+ ds.setSequenceFeatures(sequence.getSequenceFeatures());
+ if (!sameDatasetSequence && command.al.getDataset() != null)
+ {
+ // delete 'undone' sequence from alignment dataset
+ command.al.getDataset()
+ .deleteSequence(sequence.getDatasetSequence());
+ }
+ sequence.setDatasetSequence(ds);
}
- adjustFeatures(command, i, start, end, true);
+ undoCutFeatures(command, command.seqs[i], start, length,
+ sameDatasetSequence);
}
}
adjustAnnotations(command, true, seqWasDeleted, views);
static void replace(Edit command)
{
- StringBuffer tmp;
+ StringBuilder tmp;
String oldstring;
int start = command.position;
int end = command.number;
{
boolean newDSWasNeeded = command.oldds != null
&& command.oldds[i] != null;
+ boolean newStartEndWasNeeded = command.oldStartEnd!=null && command.oldStartEnd[i]!=null;
/**
* cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
* EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
*
*/
+ ContiguousI beforeEditedPositions = command.seqs[i].findPositions(1,
+ start);
+ ContiguousI afterEditedPositions = command.seqs[i]
+ .findPositions(end + 1, command.seqs[i].getLength());
+
oldstring = command.seqs[i].getSequenceAsString();
- tmp = new StringBuffer(oldstring.substring(0, start));
+ tmp = new StringBuilder(oldstring.substring(0, start));
tmp.append(command.string[i]);
- String nogaprep = jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
+ String nogaprep = AlignSeq.extractGaps(Comparison.GapChars,
new String(command.string[i]));
- int ipos = command.seqs[i].findPosition(start)
- - command.seqs[i].getStart();
- tmp.append(oldstring.substring(end));
+ if (end < oldstring.length())
+ {
+ tmp.append(oldstring.substring(end));
+ }
+ // stash end prior to updating the sequence object so we can save it if
+ // need be.
+ Range oldstartend = new Range(command.seqs[i].getStart(),
+ command.seqs[i].getEnd());
command.seqs[i].setSequence(tmp.toString());
- command.string[i] = oldstring.substring(start, end).toCharArray();
- String nogapold = jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
+ command.string[i] = oldstring
+ .substring(start, Math.min(end, oldstring.length()))
+ .toCharArray();
+ String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
new String(command.string[i]));
+
if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
{
- if (newDSWasNeeded)
+ // we may already have dataset and limits stashed...
+ if (newDSWasNeeded || newStartEndWasNeeded)
{
+ if (newDSWasNeeded)
+ {
+ // then just switch the dataset sequence
SequenceI oldds = command.seqs[i].getDatasetSequence();
command.seqs[i].setDatasetSequence(command.oldds[i]);
command.oldds[i] = oldds;
+ }
+ if (newStartEndWasNeeded)
+ {
+ Range newStart = command.oldStartEnd[i];
+ command.oldStartEnd[i] = oldstartend;
+ command.seqs[i].setStart(newStart.getBegin());
+ command.seqs[i].setEnd(newStart.getEnd());
+ }
}
- else
+ else
{
- if (command.oldds == null)
+ // decide if we need a new dataset sequence or modify start/end
+ // first edit the original dataset sequence string
+ SequenceI oldds = command.seqs[i].getDatasetSequence();
+ String osp = oldds.getSequenceAsString();
+ int beforeStartOfEdit = -oldds.getStart() + 1
+ + (beforeEditedPositions == null
+ ? ((afterEditedPositions != null)
+ ? afterEditedPositions.getBegin() - 1
+ : oldstartend.getBegin()
+ + nogapold.length())
+ : beforeEditedPositions.getEnd()
+ );
+ int afterEndOfEdit = -oldds.getStart() + 1
+ + ((afterEditedPositions == null)
+ ? oldstartend.getEnd()
+ : afterEditedPositions.getBegin() - 1);
+ String fullseq = osp.substring(0,
+ beforeStartOfEdit)
+ + nogaprep
+ + osp.substring(afterEndOfEdit);
+
+ // and check if new sequence data is different..
+ if (!fullseq.equalsIgnoreCase(osp))
{
- command.oldds = new SequenceI[command.seqs.length];
- }
- command.oldds[i] = command.seqs[i].getDatasetSequence();
- SequenceI newds = new Sequence(
- command.seqs[i].getDatasetSequence());
- String fullseq, osp = newds.getSequenceAsString();
- fullseq = osp.substring(0, ipos) + nogaprep
- + osp.substring(ipos + nogaprep.length());
- newds.setSequence(fullseq.toUpperCase());
- // TODO: JAL-1131 ensure newly created dataset sequence is added to
- // the set of
- // dataset sequences associated with the alignment.
- // TODO: JAL-1131 fix up any annotation associated with new dataset
- // sequence to ensure that original sequence/annotation relationships
- // are preserved.
- command.seqs[i].setDatasetSequence(newds);
+ // old ds and edited ds are different, so
+ // create the new dataset sequence
+ SequenceI newds = new Sequence(oldds);
+ newds.setSequence(fullseq);
+
+ if (command.oldds == null)
+ {
+ command.oldds = new SequenceI[command.seqs.length];
+ }
+ command.oldds[i] = command.seqs[i].getDatasetSequence();
+ // And preserve start/end for good-measure
+
+ if (command.oldStartEnd == null)
+ {
+ command.oldStartEnd = new Range[command.seqs.length];
+ }
+ command.oldStartEnd[i] = oldstartend;
+ // TODO: JAL-1131 ensure newly created dataset sequence is added to
+ // the set of
+ // dataset sequences associated with the alignment.
+ // TODO: JAL-1131 fix up any annotation associated with new dataset
+ // sequence to ensure that original sequence/annotation
+ // relationships
+ // are preserved.
+ command.seqs[i].setDatasetSequence(newds);
+ }
+ else
+ {
+ if (command.oldStartEnd == null)
+ {
+ command.oldStartEnd = new Range[command.seqs.length];
+ }
+ command.oldStartEnd[i] = new Range(command.seqs[i].getStart(),
+ command.seqs[i].getEnd());
+ if (beforeEditedPositions != null
+ && afterEditedPositions == null)
+ {
+ // modification at end
+ command.seqs[i].setEnd(
+ beforeEditedPositions.getEnd() + nogaprep.length()
+ - nogapold.length());
+ }
+ else if (afterEditedPositions != null
+ && beforeEditedPositions == null)
+ {
+ // modification at start
+ command.seqs[i].setStart(
+ afterEditedPositions.getBegin() - nogaprep.length());
+ }
+ else
+ {
+ // edit covered both start and end. Here we can only guess the
+ // new
+ // start/end
+ String nogapalseq = AlignSeq.extractGaps(Comparison.GapChars,
+ command.seqs[i].getSequenceAsString().toUpperCase());
+ int newStart = command.seqs[i].getDatasetSequence()
+ .getSequenceAsString().indexOf(nogapalseq);
+ if (newStart == -1)
+ {
+ throw new Error(
+ "Implementation Error: could not locate start/end "
+ + "in dataset sequence after an edit of the sequence string");
+ }
+ int newEnd = newStart + nogapalseq.length() - 1;
+ command.seqs[i].setStart(newStart);
+ command.seqs[i].setEnd(newEnd);
+ }
+ }
}
}
tmp = null;
if (modifyVisibility && !insert)
{
// only occurs if a sequence was added or deleted.
- command.deletedAnnotationRows = new Hashtable<SequenceI, AlignmentAnnotation[]>();
+ command.deletedAnnotationRows = new Hashtable<>();
}
if (command.fullAlignmentHeight)
{
}
// and then duplicate added annotation on every other alignment
// view
- for (int vnum = 0; views != null
- && vnum < views.length; vnum++)
+ for (int vnum = 0; views != null && vnum < views.length; vnum++)
{
if (views[vnum] != command.al)
{
if (!insert)
{
- command.deletedAnnotations = new Hashtable<String, Annotation[]>();
+ command.deletedAnnotations = new Hashtable<>();
}
int aSize;
}
}
- final static void adjustFeatures(Edit command, int index, final int i,
- final int j, boolean insert)
+ /**
+ * Restores features to the state before a Cut.
+ * <ul>
+ * <li>re-add any features deleted by the cut</li>
+ * <li>remove any truncated features created by the cut</li>
+ * <li>shift right any features to the right of the cut</li>
+ * </ul>
+ *
+ * @param command
+ * the Cut command
+ * @param seq
+ * the sequence the Cut applied to
+ * @param start
+ * the start residue position of the cut
+ * @param length
+ * the number of residues cut
+ * @param sameDatasetSequence
+ * true if dataset sequence and frame of reference were left
+ * unchanged by the Cut
+ */
+ final static void undoCutFeatures(Edit command, SequenceI seq,
+ final int start, final int length, boolean sameDatasetSequence)
{
- SequenceI seq = command.seqs[index];
SequenceI sequence = seq.getDatasetSequence();
if (sequence == null)
{
sequence = seq;
}
- if (insert)
+ /*
+ * shift right features that lie to the right of the restored cut (but not
+ * if dataset sequence unchanged - so coordinates were changed by Cut)
+ */
+ if (!sameDatasetSequence)
{
- if (command.editedFeatures != null
- && command.editedFeatures.containsKey(seq))
+ /*
+ * shift right all features right of and not
+ * contiguous with the cut position
+ */
+ seq.getFeatures().shiftFeatures(start + 1, length);
+
+ /*
+ * shift right any features that start at the cut position,
+ * unless they were truncated
+ */
+ List<SequenceFeature> sfs = seq.getFeatures().findFeatures(start,
+ start);
+ for (SequenceFeature sf : sfs)
{
- sequence.setSequenceFeatures(command.editedFeatures.get(seq));
+ if (sf.getBegin() == start)
+ {
+ if (!command.truncatedFeatures.containsKey(seq)
+ || !command.truncatedFeatures.get(seq).contains(sf))
+ {
+ /*
+ * feature was shifted left to cut position (not truncated),
+ * so shift it back right
+ */
+ SequenceFeature shifted = new SequenceFeature(sf, sf.getBegin()
+ + length, sf.getEnd() + length, sf.getFeatureGroup(),
+ sf.getScore());
+ seq.addSequenceFeature(shifted);
+ seq.deleteFeature(sf);
+ }
+ }
}
-
- return;
}
- List<SequenceFeature> sf = sequence.getFeatures()
- .getPositionalFeatures();
-
- if (sf.isEmpty())
- {
- return;
- }
-
- List<SequenceFeature> oldsf = new ArrayList<SequenceFeature>();
-
- int cSize = j - i;
-
- for (SequenceFeature feature : sf)
+ /*
+ * restore any features that were deleted or truncated
+ */
+ if (command.deletedFeatures != null
+ && command.deletedFeatures.containsKey(seq))
{
- SequenceFeature copy = new SequenceFeature(feature);
-
- oldsf.add(copy);
-
- if (feature.getEnd() < i)
- {
- continue;
- }
-
- if (feature.getBegin() > j)
- {
- int newBegin = copy.getBegin() - cSize;
- int newEnd = copy.getEnd() - cSize;
- SequenceFeature newSf = new SequenceFeature(feature, newBegin,
- newEnd, feature.getFeatureGroup(), feature.getScore());
- sequence.deleteFeature(feature);
- sequence.addSequenceFeature(newSf);
- // feature.setBegin(newBegin);
- // feature.setEnd(newEnd);
- continue;
- }
-
- int newBegin = feature.getBegin();
- int newEnd = feature.getEnd();
- if (newBegin >= i)
- {
- newBegin = i;
- // feature.setBegin(i);
- }
-
- if (newEnd < j)
+ for (SequenceFeature deleted : command.deletedFeatures.get(seq))
{
- newEnd = j - 1;
- // feature.setEnd(j - 1);
+ sequence.addSequenceFeature(deleted);
}
- newEnd = newEnd - cSize;
- // feature.setEnd(feature.getEnd() - (cSize));
-
- sequence.deleteFeature(feature);
- if (newEnd >= newBegin)
- {
- sequence.addSequenceFeature(new SequenceFeature(feature, newBegin,
- newEnd, feature.getFeatureGroup(), feature.getScore()));
- }
- // if (feature.getBegin() > feature.getEnd())
- // {
- // sequence.deleteFeature(feature);
- // }
}
- if (command.editedFeatures == null)
+ /*
+ * delete any truncated features
+ */
+ if (command.truncatedFeatures != null
+ && command.truncatedFeatures.containsKey(seq))
{
- command.editedFeatures = new Hashtable<SequenceI, List<SequenceFeature>>();
+ for (SequenceFeature amended : command.truncatedFeatures.get(seq))
+ {
+ sequence.deleteFeature(amended);
+ }
}
-
- command.editedFeatures.put(seq, oldsf);
-
}
/**
*/
public Map<SequenceI, SequenceI> priorState(boolean forUndo)
{
- Map<SequenceI, SequenceI> result = new HashMap<SequenceI, SequenceI>();
+ Map<SequenceI, SequenceI> result = new HashMap<>();
if (getEdits() == null)
{
return result;
* Work backwards through the edit list, deriving the sequences before each
* was applied. The final result is the sequence set before any edits.
*/
- Iterator<Edit> editList = new ReverseListIterator<Edit>(getEdits());
+ Iterator<Edit> editList = new ReverseListIterator<>(getEdits());
while (editList.hasNext())
{
Edit oldEdit = editList.next();
public class Edit
{
- public SequenceI[] oldds;
+ private SequenceI[] oldds;
- boolean fullAlignmentHeight = false;
+ /**
+ * start and end of sequence prior to edit
+ */
+ private Range[] oldStartEnd;
- Hashtable<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
+ private boolean fullAlignmentHeight = false;
- Hashtable<String, Annotation[]> deletedAnnotations;
+ private Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
- Hashtable<SequenceI, List<SequenceFeature>> editedFeatures;
+ private Map<String, Annotation[]> deletedAnnotations;
- AlignmentI al;
+ /*
+ * features deleted by the cut (re-add on Undo)
+ * (including the original of any shortened features)
+ */
+ private Map<SequenceI, List<SequenceFeature>> deletedFeatures;
+
+ /*
+ * shortened features added by the cut (delete on Undo)
+ */
+ private Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
+
+ private AlignmentI al;
- Action command;
+ final private Action command;
char[][] string;
SequenceI[] seqs;
- int[] alIndex;
+ private int[] alIndex;
+
+ private int position;
- int position, number;
+ private int number;
- char gapChar;
+ private char gapChar;
+
+ /*
+ * flag that identifies edits inserted to balance
+ * user edits in a 'locked editing' region
+ */
+ private boolean systemGenerated;
public Edit(Action cmd, SequenceI[] sqs, int pos, int count,
char gap)
Edit(Action cmd, SequenceI[] sqs, int pos, int count,
AlignmentI align)
{
- this.gapChar = align.getGapCharacter();
- this.command = cmd;
- this.seqs = sqs;
- this.position = pos;
- this.number = count;
+ this(cmd, sqs, pos, count, align.getGapCharacter());
+
this.al = align;
alIndex = new int[sqs.length];
fullAlignmentHeight = (align.getHeight() == sqs.length);
}
+ /**
+ * Constructor given a REPLACE command and the replacement string
+ *
+ * @param cmd
+ * @param sqs
+ * @param pos
+ * @param count
+ * @param align
+ * @param replace
+ */
Edit(Action cmd, SequenceI[] sqs, int pos, int count,
AlignmentI align, String replace)
{
- this.command = cmd;
- this.seqs = sqs;
- this.position = pos;
- this.number = count;
- this.al = align;
- this.gapChar = align.getGapCharacter();
+ this(cmd, sqs, pos, count, align);
+
string = new char[sqs.length][];
for (int i = 0; i < sqs.length; i++)
{
string[i] = replace.toCharArray();
}
-
- fullAlignmentHeight = (align.getHeight() == sqs.length);
}
public SequenceI[] getSequences()
{
return gapChar;
}
+
+ public void setSystemGenerated(boolean b)
+ {
+ systemGenerated = b;
+ }
+
+ public boolean isSystemGenerated()
+ {
+ return systemGenerated;
+ }
}
/**
}
else
{
- return new ReverseListIterator<Edit>(getEdits());
+ return new ReverseListIterator<>(getEdits());
+ }
+ }
+
+ /**
+ * Adjusts features for Cut, and saves details of changes made to allow Undo
+ * <ul>
+ * <li>features left of the cut are unchanged</li>
+ * <li>features right of the cut are shifted left</li>
+ * <li>features internal to the cut region are deleted</li>
+ * <li>features that overlap or span the cut are shortened</li>
+ * <li>the originals of any deleted or shortened features are saved, to re-add
+ * on Undo</li>
+ * <li>any added (shortened) features are saved, to delete on Undo</li>
+ * </ul>
+ *
+ * @param command
+ * @param seq
+ * @param fromPosition
+ * @param toPosition
+ * @param cutIsInternal
+ */
+ protected static void cutFeatures(Edit command, SequenceI seq,
+ int fromPosition, int toPosition, boolean cutIsInternal)
+ {
+ /*
+ * if the cut is at start or end of sequence
+ * then we don't modify the sequence feature store
+ */
+ if (!cutIsInternal)
+ {
+ return;
+ }
+ List<SequenceFeature> added = new ArrayList<>();
+ List<SequenceFeature> removed = new ArrayList<>();
+
+ SequenceFeaturesI featureStore = seq.getFeatures();
+ if (toPosition < fromPosition || featureStore == null)
+ {
+ return;
+ }
+
+ int cutStartPos = fromPosition;
+ int cutEndPos = toPosition;
+ int cutWidth = cutEndPos - cutStartPos + 1;
+
+ synchronized (featureStore)
+ {
+ /*
+ * get features that overlap the cut region
+ */
+ List<SequenceFeature> toAmend = featureStore.findFeatures(
+ cutStartPos, cutEndPos);
+
+ /*
+ * add any contact features that span the cut region
+ * (not returned by findFeatures)
+ */
+ for (SequenceFeature contact : featureStore.getContactFeatures())
+ {
+ if (contact.getBegin() < cutStartPos
+ && contact.getEnd() > cutEndPos)
+ {
+ toAmend.add(contact);
+ }
+ }
+
+ /*
+ * adjust start-end of overlapping features;
+ * delete features enclosed by the cut;
+ * delete partially overlapping contact features
+ */
+ for (SequenceFeature sf : toAmend)
+ {
+ int sfBegin = sf.getBegin();
+ int sfEnd = sf.getEnd();
+ int newBegin = sfBegin;
+ int newEnd = sfEnd;
+ boolean toDelete = false;
+ boolean follows = false;
+
+ if (sfBegin >= cutStartPos && sfEnd <= cutEndPos)
+ {
+ /*
+ * feature lies within cut region - delete it
+ */
+ toDelete = true;
+ }
+ else if (sfBegin < cutStartPos && sfEnd > cutEndPos)
+ {
+ /*
+ * feature spans cut region - left-shift the end
+ */
+ newEnd -= cutWidth;
+ }
+ else if (sfEnd <= cutEndPos)
+ {
+ /*
+ * feature overlaps left of cut region - truncate right
+ */
+ newEnd = cutStartPos - 1;
+ if (sf.isContactFeature())
+ {
+ toDelete = true;
+ }
+ }
+ else if (sfBegin >= cutStartPos)
+ {
+ /*
+ * remaining case - feature overlaps right
+ * truncate left, adjust end of feature
+ */
+ newBegin = cutIsInternal ? cutStartPos : cutEndPos + 1;
+ newEnd = newBegin + sfEnd - cutEndPos - 1;
+ if (sf.isContactFeature())
+ {
+ toDelete = true;
+ }
+ }
+
+ seq.deleteFeature(sf);
+ if (!follows)
+ {
+ removed.add(sf);
+ }
+ if (!toDelete)
+ {
+ SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
+ sf.getFeatureGroup(), sf.getScore());
+ seq.addSequenceFeature(copy);
+ if (!follows)
+ {
+ added.add(copy);
+ }
+ }
+ }
+
+ /*
+ * and left shift any features lying to the right of the cut region
+ */
+
+ featureStore.shiftFeatures(cutEndPos + 1, -cutWidth);
+ }
+
+ /*
+ * save deleted and amended features, so that Undo can
+ * re-add or delete them respectively
+ */
+ if (command.deletedFeatures == null)
+ {
+ command.deletedFeatures = new HashMap<>();
+ }
+ if (command.truncatedFeatures == null)
+ {
+ command.truncatedFeatures = new HashMap<>();
}
+ command.deletedFeatures.put(seq, removed);
+ command.truncatedFeatures.put(seq, added);
}
}
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
+import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
import java.awt.Color;
viewport.getAlignment().deleteAllGroups();
viewport.clearSequenceColours();
viewport.setSelectionGroup(null);
+ ColourSchemeI colours = viewport.getGlobalColourScheme();
// set view properties for each group
for (int g = 0; g < gps.length; g++)
{
// gps[g].setShowunconserved(viewport.getShowUnconserved());
gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
viewport.getAlignment().addGroup(gps[g]);
- Color col = new Color((int) (Math.random() * 255),
- (int) (Math.random() * 255), (int) (Math.random() * 255));
- col = col.brighter();
- for (SequenceI sq : gps[g].getSequences(null))
+ if (colours != null)
{
- viewport.setSequenceColour(sq, col);
+ gps[g].setColourScheme(colours.getInstance(viewport, gps[g]));
}
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
+ gps[g].idColour = col;
+ viewport.setUpdateStructures(true);
+ viewport.addSequenceGroup(gps[g]);
}
return true;
}
for (int i = 0; i < sequences.size(); i++)
{
- if (getSequenceAt(i).getLength() > maxLength)
- {
- maxLength = getSequenceAt(i).getLength();
- }
+ maxLength = Math.max(maxLength, getSequenceAt(i).getLength());
}
-
return maxLength;
}
- /*
+
@Override
- public int getWidth()
+ public int getVisibleWidth()
{
- final Wrapper temp = new Wrapper();
-
- forEachSequence(new Consumer<SequenceI>()
+ int w = getWidth();
+ if (hiddenCols != null)
{
- @Override
- public void accept(SequenceI s)
- {
- if (s.getLength() > temp.inner)
- {
- temp.inner = s.getLength();
- }
- }
- }, 0, sequences.size() - 1);
-
- return temp.inner;
+ w -= hiddenCols.getSize();
+ }
+ return w;
}
-
- public static class Wrapper
- {
- public int inner;
- }*/
/**
* DOCUMENT ME!
}
@Override
- public void setHiddenColumns(HiddenColumns cols)
+ public boolean setHiddenColumns(HiddenColumns cols)
{
+ boolean changed = cols == null ? hiddenCols != null
+ : !cols.equals(hiddenCols);
hiddenCols = cols;
+ return changed;
}
@Override
/**
*
- * Calculates the maximum width of the alignment, including gaps.
+ * Answers the width of the alignment, including gaps, that is, the length of
+ * the longest sequence, or -1 if there are no sequences. Avoid calling this
+ * method repeatedly where possible, as it has to perform a calculation. Note
+ * that this width includes any hidden columns.
*
- * @return Greatest sequence length within alignment, or -1 if no sequences
- * present
+ * @return
+ * @see AlignmentI#getVisibleWidth()
*/
@Override
int getWidth();
/**
+ *
+ * Answers the visible width of the alignment, including gaps, that is, the
+ * length of the longest sequence, excluding any hidden columns. Answers -1 if
+ * there are no sequences. Avoid calling this method repeatedly where
+ * possible, as it has to perform a calculation.
+ *
+ * @return
+ */
+ int getVisibleWidth();
+
+ /**
* Calculates if this set of sequences (visible and invisible) are all the
* same length
*
AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
/**
- * Set the hidden columns collection on the alignment
+ * Set the hidden columns collection on the alignment. Answers true if the
+ * hidden column selection changed, else false.
*
* @param cols
+ * @return
*/
- public void setHiddenColumns(HiddenColumns cols);
+ public boolean setHiddenColumns(HiddenColumns cols);
/**
* Set the first sequence as representative and hide its insertions. Typically
ScGroup()
{
- seqs = new ArrayList<SeqCigar>();
+ seqs = new ArrayList<>();
}
/**
SequenceI[] selseqs;
if (selection != null && selection.getSize() > 0)
{
- List<SequenceI> sel = selection.getSequences(null);
this.selected = new ScGroup();
selseqs = selection.getSequencesInOrder(alignment,
selectedRegionOnly);
selseqs = alignment.getSequencesArray();
}
- List<List<SequenceI>> seqsets = new ArrayList<List<SequenceI>>();
+ List<List<SequenceI>> seqsets = new ArrayList<>();
// get the alignment's group list and make a copy
- List<SequenceGroup> grps = new ArrayList<SequenceGroup>();
+ List<SequenceGroup> grps = new ArrayList<>();
List<SequenceGroup> gg = alignment.getGroups();
grps.addAll(gg);
ScGroup[] sgrps = null;
// strip out any groups that do not actually intersect with the
// visible and selected region
int ssel = selection.getStartRes(), esel = selection.getEndRes();
- List<SequenceGroup> isg = new ArrayList<SequenceGroup>();
+ List<SequenceGroup> isg = new ArrayList<>();
for (SequenceGroup sg : grps)
{
if (!(sg.getStartRes() > esel || sg.getEndRes() < ssel))
{
if (scGroups == null)
{
- scGroups = new ArrayList<ScGroup>();
+ scGroups = new ArrayList<>();
}
addedgps[sg] = true;
scGroups.add(sgrps[sg]);
import java.util.BitSet;
import java.util.Collections;
import java.util.List;
+import java.util.regex.PatternSyntaxException;
/**
* Data class holding the selected columns and hidden column ranges for a view.
*/
IntList()
{
- order = new ArrayList<Integer>();
+ order = new ArrayList<>();
_uorder = Collections.unmodifiableList(order);
selected = new BitSet();
}
*/
List<int[]> getRanges()
{
- List<int[]> rlist = new ArrayList<int[]>();
+ List<int[]> rlist = new ArrayList<>();
if (selected.isEmpty())
{
return rlist;
}
}
- IntList selection = new IntList();
+ private IntList selection = new IntList();
/**
* Add a column to the selection
return (selection != null && selection.size() > 0);
}
- public boolean filterAnnotations(Annotation[] annotations,
+ /**
+ * Selects columns where the given annotation matches the provided filter
+ * condition(s). Any existing column selections are first cleared. Answers the
+ * number of columns added.
+ *
+ * @param annotations
+ * @param filterParams
+ * @return
+ */
+ public int filterAnnotations(Annotation[] annotations,
AnnotationFilterParameter filterParams)
{
// JBPNote - this method needs to be refactored to become independent of
// viewmodel package
this.clear();
- int count = 0;
+ int addedCount = 0;
+ int column = 0;
do
{
- if (annotations[count] != null)
+ Annotation ann = annotations[column];
+ if (ann != null)
{
+ boolean matched = false;
- boolean itemMatched = false;
-
+ /*
+ * filter may have multiple conditions -
+ * these are or'd until a match is found
+ */
if (filterParams
.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
- && annotations[count].value >= filterParams
- .getThresholdValue())
+ && ann.value > filterParams.getThresholdValue())
{
- itemMatched = true;
+ matched = true;
}
- if (filterParams
+
+ if (!matched && filterParams
.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
- && annotations[count].value <= filterParams
- .getThresholdValue())
+ && ann.value < filterParams.getThresholdValue())
{
- itemMatched = true;
+ matched = true;
}
- if (filterParams.isFilterAlphaHelix()
- && annotations[count].secondaryStructure == 'H')
+ if (!matched && filterParams.isFilterAlphaHelix()
+ && ann.secondaryStructure == 'H')
{
- itemMatched = true;
+ matched = true;
}
- if (filterParams.isFilterBetaSheet()
- && annotations[count].secondaryStructure == 'E')
+ if (!matched && filterParams.isFilterBetaSheet()
+ && ann.secondaryStructure == 'E')
{
- itemMatched = true;
+ matched = true;
}
- if (filterParams.isFilterTurn()
- && annotations[count].secondaryStructure == 'S')
+ if (!matched && filterParams.isFilterTurn()
+ && ann.secondaryStructure == 'S')
{
- itemMatched = true;
+ matched = true;
}
String regexSearchString = filterParams.getRegexString();
- if (regexSearchString != null
- && !filterParams.getRegexSearchFields().isEmpty())
+ if (!matched && regexSearchString != null)
{
List<SearchableAnnotationField> fields = filterParams
.getRegexSearchFields();
- try
+ for (SearchableAnnotationField field : fields)
{
- if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
- && annotations[count].displayCharacter
- .matches(regexSearchString))
+ String compareTo = field == SearchableAnnotationField.DISPLAY_STRING
+ ? ann.displayCharacter // match 'Label'
+ : ann.description; // and/or 'Description'
+ if (compareTo != null)
{
- itemMatched = true;
- }
- } catch (java.util.regex.PatternSyntaxException pse)
- {
- if (annotations[count].displayCharacter
- .equals(regexSearchString))
- {
- itemMatched = true;
+ try
+ {
+ if (compareTo.matches(regexSearchString))
+ {
+ matched = true;
+ }
+ } catch (PatternSyntaxException pse)
+ {
+ if (compareTo.equals(regexSearchString))
+ {
+ matched = true;
+ }
+ }
+ if (matched)
+ {
+ break;
+ }
}
}
- if (fields.contains(SearchableAnnotationField.DESCRIPTION)
- && annotations[count].description != null
- && annotations[count].description
- .matches(regexSearchString))
- {
- itemMatched = true;
- }
}
- if (itemMatched)
+ if (matched)
{
- this.addElement(count);
+ this.addElement(column);
+ addedCount++;
}
}
- count++;
- } while (count < annotations.length);
- return false;
+ column++;
+ } while (column < annotations.length);
+
+ return addedCount;
}
/**
}
}
+ /**
+ * Answers true if obj is an instance of HiddenColumns, and holds the same
+ * array of start-end column ranges as this, else answers false
+ */
@Override
public boolean equals(Object obj)
{
--- /dev/null
+package jalview.datamodel;
+
+/**
+ * A bean that models an (x, y, z) position in 3-D space
+ */
+public final class Point
+{
+ public final float x;
+
+ public final float y;
+
+ public final float z;
+
+ public Point(float xVal, float yVal, float zVal)
+ {
+ x = xVal;
+ y = yVal;
+ z = zVal;
+ }
+
+ /**
+ * toString for convenience of inspection in debugging or logging
+ */
+ @Override
+ public String toString()
+ {
+ return String.format("[%f, %f, %f]", x, y, z);
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + Float.floatToIntBits(x);
+ result = prime * result + Float.floatToIntBits(y);
+ result = prime * result + Float.floatToIntBits(z);
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ {
+ return true;
+ }
+ if (obj == null)
+ {
+ return false;
+ }
+ if (getClass() != obj.getClass())
+ {
+ return false;
+ }
+ Point other = (Point) obj;
+ if (Float.floatToIntBits(x) != Float.floatToIntBits(other.x))
+ {
+ return false;
+ }
+ if (Float.floatToIntBits(y) != Float.floatToIntBits(other.y))
+ {
+ return false;
+ }
+ if (Float.floatToIntBits(z) != Float.floatToIntBits(other.z))
+ {
+ return false;
+ }
+ return true;
+ }
+}
*/
int getEnd();
+ /**
+ * Answers true if this match is for the given sequence and includes (matches
+ * or encloses) the given start-end range
+ *
+ * @param seq
+ * @param start
+ * @param end
+ * @return
+ */
+ boolean contains(SequenceI seq, int start, int end);
}
\ No newline at end of file
}
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultMatchI#getSequence()
- */
@Override
public SequenceI getSequence()
{
return sequence;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultMatchI#getStart()
- */
@Override
public int getStart()
{
return start;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultMatchI#getEnd()
- */
@Override
public int getEnd()
{
return (sequence == m.getSequence() && start == m.getStart()
&& end == m.getEnd());
}
+
+ @Override
+ public boolean contains(SequenceI seq, int from, int to)
+ {
+ return (sequence == seq && start <= from && end >= to);
+ }
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#addResult(jalview.datamodel.SequenceI, int, int)
- */
@Override
public SearchResultMatchI addResult(SequenceI seq, int start, int end)
{
Match m = new Match(seq, start, end);
- matches.add(m);
+ if (!matches.contains(m))
+ {
+ matches.add(m);
+ }
return m;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#involvesSequence(jalview.datamodel.SequenceI)
- */
@Override
public boolean involvesSequence(SequenceI sequence)
{
return false;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResults(jalview.datamodel.SequenceI, int, int)
- */
@Override
public int[] getResults(SequenceI sequence, int start, int end)
{
return count;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getSize()
- */
@Override
public int getSize()
{
return matches.size();
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#isEmpty()
- */
@Override
public boolean isEmpty()
{
return matches.isEmpty();
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResults()
- */
@Override
public List<SearchResultMatchI> getResults()
{
{
/**
- * Adds one region to the results
+ * Adds one region to the results (unless already added, to avoid duplicates)
*
* @param seq
- * Sequence
* @param start
- * int
* @param end
- * int
* @return
*/
SearchResultMatchI addResult(SequenceI seq, int start, int end);
/**
*
- * Implements the SequenceI interface for a char[] based sequence object.
- *
- * @author $author$
- * @version $Revision$
+ * Implements the SequenceI interface for a char[] based sequence object
*/
public class Sequence extends ASequence implements SequenceI
{
* preserve end residue column provided cursor was valid
*/
int endColumn = isValidCursor(cursor) ? cursor.lastColumnPosition : 0;
+
if (residuePos == this.end)
{
endColumn = column;
/*
* move left or right to find pos from hint.position
*/
- int col = curs.columnPosition - 1; // convert from base 1 to 0-based array
- // index
+ int col = curs.columnPosition - 1; // convert from base 1 to base 0
int newPos = curs.residuePosition;
int delta = newPos > pos ? -1 : 1;
* {@inheritDoc}
*/
@Override
- public Range findPositions(int fromColumn, int toColumn)
+ public ContiguousI findPositions(int fromColumn, int toColumn)
{
if (toColumn < fromColumn || fromColumn < 1)
{
boolean createNewDs = false;
// TODO: take a (second look) at the dataset creation validation method for
// the very large sequence case
+
int startIndex = findIndex(start) - 1;
int endIndex = findIndex(end) - 1;
int startDeleteColumn = -1; // for dataset sequence deletions
int deleteCount = 0;
- for (int s = i; s < j; s++)
+ for (int s = i; s < j && s < sequence.length; s++)
{
if (Comparison.isGap(sequence[s]))
{
List<SequenceFeature> result = getFeatures().findFeatures(startPos,
endPos, types);
+ if (datasetSequence != null)
+ {
+ result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
+ types);
+ }
+ else
+ {
+ result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
+ }
/*
* if end column is gapped, endPos may be to the right,
public interface SequenceCollectionI
{
+ /**
+ *
+ * @return (visible) sequences in this collection. This may be a direct
+ * reference to the collection so not thread safe
+ */
List<SequenceI> getSequences();
+ /**
+ * FIXME: AlignmentI.getSequences(hiddenReps) doesn't actually obey this
+ * contract!
+ *
+ * @param hiddenReps
+ * @return the full set of sequences in this collection, including any
+ * sequences represented by sequences in the collection.
+ */
List<SequenceI> getSequences(
Map<SequenceI, SequenceCollectionI> hiddenReps);
/**
* group members
*/
- private List<SequenceI> sequences = new ArrayList<>();
+ private List<SequenceI> sequences;
/**
* representative sequence for this group (if any)
*/
public ResidueShaderI cs;
- // start column (base 0)
- int startRes = 0;
+ /**
+ * start column (base 0)
+ */
+ private int startRes = 0;
- // end column (base 0)
- int endRes = 0;
+ /**
+ * end column (base 0)
+ */
+ private int endRes = 0;
public Color outlineColour = Color.black;
{
groupName = "JGroup:" + this.hashCode();
cs = new ResidueShader();
+ sequences = new ArrayList<>();
}
/**
displayBoxes = seqsel.displayBoxes;
displayText = seqsel.displayText;
colourText = seqsel.colourText;
+
startRes = seqsel.startRes;
endRes = seqsel.endRes;
cs = new ResidueShader((ResidueShader) seqsel.cs);
}
}
+ /**
+ * Constructor that copies the given list of sequences
+ *
+ * @param seqs
+ */
+ public SequenceGroup(List<SequenceI> seqs)
+ {
+ this();
+ this.sequences.addAll(seqs);
+ }
+
public boolean isShowSequenceLogo()
{
return showSequenceLogo;
/**
* Set the first column selected by this group. Runs from 0<=i<N_cols
*
- * @param i
+ * @param newStart
*/
- public void setStartRes(int i)
+ public void setStartRes(int newStart)
{
int before = startRes;
- startRes = i;
- changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+ startRes= Math.max(0,newStart); // sanity check for negative start column positions
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+
+
+
}
/**
* get a range on the sequence as a string
*
* @param start
- * position relative to start of sequence including gaps (from 0)
+ * (inclusive) position relative to start of sequence including gaps
+ * (from 0)
* @param end
- * position relative to start of sequence including gaps (from 0)
+ * (exclusive) position relative to start of sequence including gaps
+ * (from 0)
*
* @return String containing all gap and symbols in specified range
*/
public int findPosition(int i);
/**
- * Returns the from-to sequence positions (start..) for the given column
- * positions (1..), or null if no residues are included in the range
+ * Returns the sequence positions for first and last residues lying within the
+ * given column positions [fromColum,toColumn] (where columns are numbered
+ * from 1), or null if no residues are included in the range
*
* @param fromColum
+ * - first column base 1
* @param toColumn
+ * - last column, base 1
* @return
*/
- public Range findPositions(int fromColum, int toColumn);
+ public ContiguousI findPositions(int fromColum, int toColumn);
/**
* Returns an int array where indices correspond to each residue in the
package jalview.datamodel;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * A bean that models a set of (x, y, z) values and a reference to a sequence.
+ * As used in Principal Component Analysis, the (x, y, z) values are the
+ * sequence's score for the currently selected first, second and third
+ * dimensions of the PCA.
*/
public class SequencePoint
{
- // SMJS PUBLIC
+ /*
+ * Associated alignment sequence, or dummy sequence object
+ */
+ private final SequenceI sequence;
+
+ /*
+ * x, y, z values
+ */
+ public Point coord;
+
/**
- * for points with no real physical association with an alignment sequence
+ * Constructor
+ *
+ * @param sequence
+ * @param coord
*/
- public boolean isPlaceholder = false;
+ public SequencePoint(SequenceI sequence, Point pt)
+ {
+ this.sequence = sequence;
+ this.coord = pt;
+ }
/**
- * Associated alignment sequence, or dummy sequence object.
+ * Constructor given a sequence and an array of x, y, z coordinate positions
+ *
+ * @param sequence
+ * @param coords
+ * @throws ArrayIndexOutOfBoundsException
+ * if array length is less than 3
*/
- public SequenceI sequence;
+ public SequencePoint(SequenceI sequence, float[] coords)
+ {
+ this(sequence, new Point(coords[0], coords[1], coords[2]));
+ }
+
+ public SequenceI getSequence()
+ {
+ return sequence;
+ }
/**
- * array of coordinates in embedded sequence space.
+ * Applies a translation to the (x, y, z) coordinates
+ *
+ * @param centre
*/
- public float[] coord;
+ public void translate(float x, float y, float z)
+ {
+ coord = new Point(coord.x + x, coord.y + y, coord.z + z);
+ }
- // SMJS ENDPUBLIC
- public SequencePoint(SequenceI sequence, float[] coord)
+ /**
+ * string representation for ease of inspection in debugging or logging only
+ */
+ @Override
+ public String toString()
{
- this.sequence = sequence;
- this.coord = coord;
+ return sequence.getName() + " " + coord.toString();
}
}
*/
package jalview.datamodel.features;
-import jalview.datamodel.ContiguousI;
+import intervalstore.api.IntervalI;
/**
- * An extension of ContiguousI that allows start/end values to be interpreted
+ * An extension of IntervalI that allows start/end values to be interpreted
* instead as two contact positions
*/
-public interface FeatureLocationI extends ContiguousI
+public interface FeatureLocationI extends IntervalI
{
boolean isContactFeature();
}
*/
package jalview.datamodel.features;
-import jalview.datamodel.ContiguousI;
import jalview.datamodel.SequenceFeature;
import java.util.ArrayList;
import java.util.Collections;
-import java.util.Comparator;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
+import intervalstore.api.IntervalStoreI;
+import intervalstore.impl.BinarySearcher;
+import intervalstore.impl.IntervalStore;
+
/**
* A data store for a set of sequence features that supports efficient lookup of
* features overlapping a given range. Intended for (but not limited to) storage
*/
public class FeatureStore
{
- /**
- * a class providing criteria for performing a binary search of a list
- */
- abstract static class SearchCriterion
- {
- /**
- * Answers true if the entry passes the search criterion test
- *
- * @param entry
- * @return
- */
- abstract boolean compare(SequenceFeature entry);
-
- /**
- * serves a search condition for finding the first feature whose start
- * position follows a given target location
- *
- * @param target
- * @return
- */
- static SearchCriterion byStart(final long target)
- {
- return new SearchCriterion() {
-
- @Override
- boolean compare(SequenceFeature entry)
- {
- return entry.getBegin() >= target;
- }
- };
- }
-
- /**
- * serves a search condition for finding the first feature whose end
- * position is at or follows a given target location
- *
- * @param target
- * @return
- */
- static SearchCriterion byEnd(final long target)
- {
- return new SearchCriterion()
- {
-
- @Override
- boolean compare(SequenceFeature entry)
- {
- return entry.getEnd() >= target;
- }
- };
- }
-
- /**
- * serves a search condition for finding the first feature which follows the
- * given range as determined by a supplied comparator
- *
- * @param target
- * @return
- */
- static SearchCriterion byFeature(final ContiguousI to,
- final Comparator<ContiguousI> rc)
- {
- return new SearchCriterion()
- {
-
- @Override
- boolean compare(SequenceFeature entry)
- {
- return rc.compare(entry, to) >= 0;
- }
- };
- }
- }
-
/*
* Non-positional features have no (zero) start/end position.
* Kept as a separate list in case this criterion changes in future.
List<SequenceFeature> nonPositionalFeatures;
/*
- * An ordered list of features, with the promise that no feature in the list
- * properly contains any other. This constraint allows bounded linear search
- * of the list for features overlapping a region.
- * Contact features are not included in this list.
- */
- List<SequenceFeature> nonNestedFeatures;
-
- /*
* contact features ordered by first contact position
*/
List<SequenceFeature> contactFeatureStarts;
List<SequenceFeature> contactFeatureEnds;
/*
- * Nested Containment List is used to hold any features that are nested
- * within (properly contained by) any other feature. This is a recursive tree
- * which supports depth-first scan for features overlapping a range.
- * It is used here as a 'catch-all' fallback for features that cannot be put
- * into a simple ordered list without invalidating the search methods.
+ * IntervalStore holds remaining features and provides efficient
+ * query for features overlapping any given interval
*/
- NCList<SequenceFeature> nestedFeatures;
+ IntervalStoreI<SequenceFeature> features;
/*
* Feature groups represented in stored positional features
*/
public FeatureStore()
{
- nonNestedFeatures = new ArrayList<SequenceFeature>();
- positionalFeatureGroups = new HashSet<String>();
- nonPositionalFeatureGroups = new HashSet<String>();
+ features = new IntervalStore<>();
+ positionalFeatureGroups = new HashSet<>();
+ nonPositionalFeatureGroups = new HashSet<>();
positionalMinScore = Float.NaN;
positionalMaxScore = Float.NaN;
nonPositionalMinScore = Float.NaN;
nonPositionalMaxScore = Float.NaN;
- // we only construct nonPositionalFeatures, contactFeatures
- // or the NCList if we need to
+ // we only construct nonPositionalFeatures, contactFeatures if we need to
}
/**
positionalFeatureGroups.add(feature.getFeatureGroup());
}
- boolean added = false;
-
if (feature.isContactFeature())
{
- added = addContactFeature(feature);
+ addContactFeature(feature);
}
else if (feature.isNonPositional())
{
- added = addNonPositionalFeature(feature);
+ addNonPositionalFeature(feature);
}
else
{
- added = addNonNestedFeature(feature);
- if (!added)
- {
- /*
- * detected a nested feature - put it in the NCList structure
- */
- added = addNestedFeature(feature);
- }
+ addNestedFeature(feature);
}
- if (added)
- {
- /*
- * record the total extent of positional features, to make
- * getTotalFeatureLength possible; we count the length of a
- * contact feature as 1
- */
- totalExtent += getFeatureLength(feature);
+ /*
+ * record the total extent of positional features, to make
+ * getTotalFeatureLength possible; we count the length of a
+ * contact feature as 1
+ */
+ totalExtent += getFeatureLength(feature);
- /*
- * record the minimum and maximum score for positional
- * and non-positional features
- */
- float score = feature.getScore();
- if (!Float.isNaN(score))
+ /*
+ * record the minimum and maximum score for positional
+ * and non-positional features
+ */
+ float score = feature.getScore();
+ if (!Float.isNaN(score))
+ {
+ if (feature.isNonPositional())
{
- if (feature.isNonPositional())
- {
- nonPositionalMinScore = min(nonPositionalMinScore, score);
- nonPositionalMaxScore = max(nonPositionalMaxScore, score);
- }
- else
- {
- positionalMinScore = min(positionalMinScore, score);
- positionalMaxScore = max(positionalMaxScore, score);
- }
+ nonPositionalMinScore = min(nonPositionalMinScore, score);
+ nonPositionalMaxScore = max(nonPositionalMaxScore, score);
+ }
+ else
+ {
+ positionalMinScore = min(positionalMinScore, score);
+ positionalMaxScore = max(positionalMaxScore, score);
}
}
- return added;
+ return true;
}
/**
contactFeatureStarts, feature);
}
- if (listContains(nonNestedFeatures, feature))
- {
- return true;
- }
-
- return nestedFeatures == null ? false : nestedFeatures
+ return features == null ? false : features
.contains(feature);
}
{
if (nonPositionalFeatures == null)
{
- nonPositionalFeatures = new ArrayList<SequenceFeature>();
+ nonPositionalFeatures = new ArrayList<>();
}
nonPositionalFeatures.add(feature);
}
/**
- * Adds one feature to the NCList that can manage nested features (creating
- * the NCList if necessary), and returns true. If the feature is already
- * stored in the NCList (by equality test), then it is not added, and this
- * method returns false.
- */
- protected synchronized boolean addNestedFeature(SequenceFeature feature)
- {
- if (nestedFeatures == null)
- {
- nestedFeatures = new NCList<>(feature);
- return true;
- }
- return nestedFeatures.add(feature, false);
- }
-
- /**
- * Add a feature to the list of non-nested features, maintaining the ordering
- * of the list. A check is made for whether the feature is nested in (properly
- * contained by) an existing feature. If there is no nesting, the feature is
- * added to the list and the method returns true. If nesting is found, the
- * feature is not added and the method returns false.
- *
- * @param feature
- * @return
- */
- protected boolean addNonNestedFeature(SequenceFeature feature)
- {
- synchronized (nonNestedFeatures)
- {
- /*
- * find the first stored feature which doesn't precede the new one
- */
- int insertPosition = binarySearch(nonNestedFeatures,
- SearchCriterion.byFeature(feature, RangeComparator.BY_START_POSITION));
-
- /*
- * fail if we detect feature enclosure - of the new feature by
- * the one preceding it, or of the next feature by the new one
- */
- if (insertPosition > 0)
- {
- if (encloses(nonNestedFeatures.get(insertPosition - 1), feature))
- {
- return false;
- }
- }
- if (insertPosition < nonNestedFeatures.size())
- {
- if (encloses(feature, nonNestedFeatures.get(insertPosition)))
- {
- return false;
- }
- }
-
- /*
- * checks passed - add the feature
- */
- nonNestedFeatures.add(insertPosition, feature);
-
- return true;
- }
- }
-
- /**
- * Answers true if range1 properly encloses range2, else false
- *
- * @param range1
- * @param range2
- * @return
+ * Adds one feature to the IntervalStore that can manage nested features
+ * (creating the IntervalStore if necessary)
*/
- protected boolean encloses(ContiguousI range1, ContiguousI range2)
+ protected synchronized void addNestedFeature(SequenceFeature feature)
{
- int begin1 = range1.getBegin();
- int begin2 = range2.getBegin();
- int end1 = range1.getEnd();
- int end2 = range2.getEnd();
- if (begin1 == begin2 && end1 > end2)
+ if (features == null)
{
- return true;
+ features = new IntervalStore<>();
}
- if (begin1 < begin2 && end1 >= end2)
- {
- return true;
- }
- return false;
+ features.add(feature);
}
/**
{
if (contactFeatureStarts == null)
{
- contactFeatureStarts = new ArrayList<SequenceFeature>();
+ contactFeatureStarts = new ArrayList<>();
}
if (contactFeatureEnds == null)
{
- contactFeatureEnds = new ArrayList<SequenceFeature>();
+ contactFeatureEnds = new ArrayList<>();
}
/*
+ * insert into list sorted by start (first contact position):
* binary search the sorted list to find the insertion point
*/
- int insertPosition = binarySearch(contactFeatureStarts,
- SearchCriterion.byFeature(feature,
- RangeComparator.BY_START_POSITION));
+ int insertPosition = BinarySearcher.findFirst(contactFeatureStarts,
+ f -> f.getBegin() >= feature.getBegin());
contactFeatureStarts.add(insertPosition, feature);
- // and resort to mak siccar...just in case insertion point not quite right
- Collections.sort(contactFeatureStarts, RangeComparator.BY_START_POSITION);
- insertPosition = binarySearch(contactFeatureStarts,
- SearchCriterion.byFeature(feature,
- RangeComparator.BY_END_POSITION));
- contactFeatureEnds.add(feature);
- Collections.sort(contactFeatureEnds, RangeComparator.BY_END_POSITION);
+
+ /*
+ * insert into list sorted by end (second contact position):
+ * binary search the sorted list to find the insertion point
+ */
+ insertPosition = BinarySearcher.findFirst(contactFeatureEnds,
+ f -> f.getEnd() >= feature.getEnd());
+ contactFeatureEnds.add(insertPosition, feature);
return true;
}
/*
* locate the first entry in the list which does not precede the feature
*/
- int pos = binarySearch(features,
- SearchCriterion.byFeature(feature, RangeComparator.BY_START_POSITION));
+ // int pos = binarySearch(features,
+ // SearchCriterion.byFeature(feature, RangeComparator.BY_START_POSITION));
+ int pos = BinarySearcher.findFirst(features,
+ val -> val.getBegin() >= feature.getBegin());
int len = features.size();
while (pos < len)
{
{
List<SequenceFeature> result = new ArrayList<>();
- findNonNestedFeatures(start, end, result);
-
findContactFeatures(start, end, result);
- if (nestedFeatures != null)
+ if (features != null)
{
- result.addAll(nestedFeatures.findOverlaps(start, end));
+ result.addAll(features.findOverlaps(start, end));
}
return result;
{
if (contactFeatureStarts != null)
{
- findContactStartFeatures(from, to, result);
+ findContactStartOverlaps(from, to, result);
}
if (contactFeatureEnds != null)
{
- findContactEndFeatures(from, to, result);
+ findContactEndOverlaps(from, to, result);
}
}
* @param to
* @param result
*/
- protected void findContactEndFeatures(long from, long to,
+ protected void findContactEndOverlaps(long from, long to,
List<SequenceFeature> result)
{
/*
- * find the first contact feature (if any) that does not lie
- * entirely before the target range
+ * find the first contact feature (if any)
+ * whose end point is not before the target range
*/
- int startPosition = binarySearch(contactFeatureEnds,
- SearchCriterion.byEnd(from));
- for (; startPosition < contactFeatureEnds.size(); startPosition++)
+ int index = BinarySearcher.findFirst(contactFeatureEnds,
+ f -> f.getEnd() >= from);
+
+ while (index < contactFeatureEnds.size())
{
- SequenceFeature sf = contactFeatureEnds.get(startPosition);
+ SequenceFeature sf = contactFeatureEnds.get(index);
if (!sf.isContactFeature())
{
System.err.println("Error! non-contact feature type "
+ sf.getType() + " in contact features list");
+ index++;
continue;
}
* this feature's first contact position lies in the search range
* so we don't include it in results a second time
*/
+ index++;
continue;
}
- int end = sf.getEnd();
- if (end >= from && end <= to)
- {
- result.add(sf);
- }
- if (end > to)
+ if (sf.getEnd() > to)
{
+ /*
+ * this feature (and all following) has end point after the target range
+ */
break;
}
- }
- }
- /**
- * Adds non-nested features to the result list that lie within the target
- * range. Non-positional features (start=end=0), contact features and nested
- * features are excluded.
- *
- * @param from
- * @param to
- * @param result
- */
- protected void findNonNestedFeatures(long from, long to,
- List<SequenceFeature> result)
- {
- /*
- * find the first feature whose end position is
- * after the target range start
- */
- int startIndex = binarySearch(nonNestedFeatures,
- SearchCriterion.byEnd(from));
-
- final int startIndex1 = startIndex;
- int i = startIndex1;
- while (i < nonNestedFeatures.size())
- {
- SequenceFeature sf = nonNestedFeatures.get(i);
- if (sf.getBegin() > to)
- {
- break;
- }
- if (sf.getBegin() <= to && sf.getEnd() >= from)
- {
- result.add(sf);
- }
- i++;
+ /*
+ * feature has end >= from and end <= to
+ * i.e. contact end point lies within overlap search range
+ */
+ result.add(sf);
+ index++;
}
}
* @param to
* @param result
*/
- protected void findContactStartFeatures(long from, long to,
+ protected void findContactStartOverlaps(long from, long to,
List<SequenceFeature> result)
{
- int startPosition = binarySearch(contactFeatureStarts,
- SearchCriterion.byStart(from));
+ int index = BinarySearcher.findFirst(contactFeatureStarts,
+ f -> f.getBegin() >= from);
- for (; startPosition < contactFeatureStarts.size(); startPosition++)
+ while (index < contactFeatureStarts.size())
{
- SequenceFeature sf = contactFeatureStarts.get(startPosition);
+ SequenceFeature sf = contactFeatureStarts.get(index);
if (!sf.isContactFeature())
{
- System.err.println("Error! non-contact feature type "
- + sf.getType() + " in contact features list");
+ System.err.println("Error! non-contact feature " + sf.toString()
+ + " in contact features list");
+ index++;
continue;
}
- int begin = sf.getBegin();
- if (begin >= from && begin <= to)
+ if (sf.getBegin() > to)
{
- result.add(sf);
+ /*
+ * this feature's start (and all following) follows the target range
+ */
+ break;
}
+
+ /*
+ * feature has begin >= from and begin <= to
+ * i.e. contact start point lies within overlap search range
+ */
+ result.add(sf);
+ index++;
}
}
*/
public List<SequenceFeature> getPositionalFeatures()
{
- /*
- * add non-nested features (may be all features for many cases)
- */
List<SequenceFeature> result = new ArrayList<>();
- result.addAll(nonNestedFeatures);
/*
* add any contact features - from the list by start position
/*
* add any nested features
*/
- if (nestedFeatures != null)
+ if (features != null)
{
- result.addAll(nestedFeatures.getEntries());
+ result.addAll(features);
}
return result;
*/
public synchronized boolean delete(SequenceFeature sf)
{
- /*
- * try the non-nested positional features first
- */
- boolean removed = nonNestedFeatures.remove(sf);
+ boolean removed = false;
/*
- * if not found, try contact positions (and if found, delete
+ * try contact positions (and if found, delete
* from both lists of contact positions)
*/
if (!removed && contactFeatureStarts != null)
/*
* if not found, try nested features
*/
- if (!removed && nestedFeatures != null)
+ if (!removed && features != null)
{
- removed = nestedFeatures.delete(sf);
+ removed = features.remove(sf);
}
if (removed)
*/
public boolean isEmpty()
{
- boolean hasFeatures = !nonNestedFeatures.isEmpty()
- || (contactFeatureStarts != null && !contactFeatureStarts
+ boolean hasFeatures = (contactFeatureStarts != null
+ && !contactFeatureStarts
.isEmpty())
|| (nonPositionalFeatures != null && !nonPositionalFeatures
.isEmpty())
- || (nestedFeatures != null && nestedFeatures.size() > 0);
+ || (features != null && features.size() > 0);
return !hasFeatures;
}
}
/**
- * Performs a binary search of the (sorted) list to find the index of the
- * first entry which returns true for the given comparator function. Returns
- * the length of the list if there is no such entry.
- *
- * @param features
- * @param sc
- * @return
- */
- protected static int binarySearch(List<SequenceFeature> features,
- SearchCriterion sc)
- {
- int start = 0;
- int end = features.size() - 1;
- int matched = features.size();
-
- while (start <= end)
- {
- int mid = (start + end) / 2;
- SequenceFeature entry = features.get(mid);
- boolean compare = sc.compare(entry);
- if (compare)
- {
- matched = mid;
- end = mid - 1;
- }
- else
- {
- start = mid + 1;
- }
- }
-
- return matched;
- }
-
- /**
* Answers the number of positional (or non-positional) features stored.
* Contact features count as 1.
*
.size();
}
- int size = nonNestedFeatures.size();
+ int size = 0;
if (contactFeatureStarts != null)
{
size += contactFeatureStarts.size();
}
- if (nestedFeatures != null)
+ if (features != null)
{
- size += nestedFeatures.size();
+ size += features.size();
}
return size;
}
/**
- * Adds the shift value to the start and end of all positional features.
- * Returns true if at least one feature was updated, else false.
+ * Adds the shift amount to the start and end of all positional features whose
+ * start position is at or after fromPosition. Returns true if at least one
+ * feature was shifted, else false.
*
- * @param shift
+ * @param fromPosition
+ * @param shiftBy
* @return
*/
- public synchronized boolean shiftFeatures(int shift)
+ public synchronized boolean shiftFeatures(int fromPosition, int shiftBy)
{
/*
* Because begin and end are final fields (to ensure the data store's
boolean modified = false;
for (SequenceFeature sf : getPositionalFeatures())
{
- modified = true;
- int newBegin = sf.getBegin() + shift;
- int newEnd = sf.getEnd() + shift;
-
- /*
- * sanity check: don't shift left of the first residue
- */
- if (newEnd > 0)
+ if (sf.getBegin() >= fromPosition)
{
- newBegin = Math.max(1, newBegin);
- SequenceFeature sf2 = new SequenceFeature(sf, newBegin, newEnd,
- sf.getFeatureGroup(), sf.getScore());
- addFeature(sf2);
+ modified = true;
+ int newBegin = sf.getBegin() + shiftBy;
+ int newEnd = sf.getEnd() + shiftBy;
+
+ /*
+ * sanity check: don't shift left of the first residue
+ */
+ if (newEnd > 0)
+ {
+ newBegin = Math.max(1, newBegin);
+ SequenceFeature sf2 = new SequenceFeature(sf, newBegin, newEnd,
+ sf.getFeatureGroup(), sf.getScore());
+ addFeature(sf2);
+ }
+ delete(sf);
}
- delete(sf);
}
return modified;
}
+++ /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.datamodel.features;
-
-import jalview.datamodel.ContiguousI;
-import jalview.datamodel.Range;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-/**
- * An adapted implementation of NCList as described in the paper
- *
- * <pre>
- * Nested Containment List (NCList): a new algorithm for accelerating
- * interval query of genome alignment and interval databases
- * - Alexander V. Alekseyenko, Christopher J. Lee
- * https://doi.org/10.1093/bioinformatics/btl647
- * </pre>
- */
-public class NCList<T extends ContiguousI>
-{
- /*
- * the number of ranges represented
- */
- private int size;
-
- /*
- * a list, in start position order, of sublists of ranges ordered so
- * that each contains (or is the same as) the one that follows it
- */
- private List<NCNode<T>> subranges;
-
- /**
- * Constructor given a list of things that are each located on a contiguous
- * interval. Note that the constructor may reorder the list.
- * <p>
- * We assume here that for each range, start <= end. Behaviour for reverse
- * ordered ranges is undefined.
- *
- * @param ranges
- */
- public NCList(List<T> ranges)
- {
- this();
- build(ranges);
- }
-
- /**
- * Sort and group ranges into sublists where each sublist represents a region
- * and its contained subregions
- *
- * @param ranges
- */
- protected void build(List<T> ranges)
- {
- /*
- * sort by start ascending so that contained intervals
- * follow their containing interval
- */
- Collections.sort(ranges, RangeComparator.BY_START_POSITION);
-
- List<Range> sublists = buildSubranges(ranges);
-
- /*
- * convert each subrange to an NCNode consisting of a range and
- * (possibly) its contained NCList
- */
- for (Range sublist : sublists)
- {
- subranges.add(new NCNode<T>(ranges.subList(sublist.start,
- sublist.end + 1)));
- }
-
- size = ranges.size();
- }
-
- public NCList(T entry)
- {
- this();
- subranges.add(new NCNode<>(entry));
- size = 1;
- }
-
- public NCList()
- {
- subranges = new ArrayList<NCNode<T>>();
- }
-
- /**
- * Traverses the sorted ranges to identify sublists, within which each
- * interval contains the one that follows it
- *
- * @param ranges
- * @return
- */
- protected List<Range> buildSubranges(List<T> ranges)
- {
- List<Range> sublists = new ArrayList<>();
-
- if (ranges.isEmpty())
- {
- return sublists;
- }
-
- int listStartIndex = 0;
- long lastEndPos = Long.MAX_VALUE;
-
- for (int i = 0; i < ranges.size(); i++)
- {
- ContiguousI nextInterval = ranges.get(i);
- long nextStart = nextInterval.getBegin();
- long nextEnd = nextInterval.getEnd();
- if (nextStart > lastEndPos || nextEnd > lastEndPos)
- {
- /*
- * this interval is not contained in the preceding one
- * close off the last sublist
- */
- sublists.add(new Range(listStartIndex, i - 1));
- listStartIndex = i;
- }
- lastEndPos = nextEnd;
- }
-
- sublists.add(new Range(listStartIndex, ranges.size() - 1));
- return sublists;
- }
-
- /**
- * Adds one entry to the stored set (with duplicates allowed)
- *
- * @param entry
- */
- public void add(T entry)
- {
- add(entry, true);
- }
-
- /**
- * Adds one entry to the stored set, and returns true, unless allowDuplicates
- * is set to false and it is already contained (by object equality test), in
- * which case it is not added and this method returns false.
- *
- * @param entry
- * @param allowDuplicates
- * @return
- */
- public synchronized boolean add(T entry, boolean allowDuplicates)
- {
- if (!allowDuplicates && contains(entry))
- {
- return false;
- }
-
- size++;
- long start = entry.getBegin();
- long end = entry.getEnd();
-
- /*
- * cases:
- * - precedes all subranges: add as NCNode on front of list
- * - follows all subranges: add as NCNode on end of list
- * - enclosed by a subrange - add recursively to subrange
- * - encloses one or more subranges - push them inside it
- * - none of the above - add as a new node and resort nodes list (?)
- */
-
- /*
- * find the first subrange whose end does not precede entry's start
- */
- int candidateIndex = findFirstOverlap(start);
- if (candidateIndex == -1)
- {
- /*
- * all subranges precede this one - add it on the end
- */
- subranges.add(new NCNode<>(entry));
- return true;
- }
-
- /*
- * search for maximal span of subranges i-k that the new entry
- * encloses; or a subrange that encloses the new entry
- */
- boolean enclosing = false;
- int firstEnclosed = 0;
- int lastEnclosed = 0;
- boolean overlapping = false;
-
- for (int j = candidateIndex; j < subranges.size(); j++)
- {
- NCNode<T> subrange = subranges.get(j);
-
- if (end < subrange.getBegin() && !overlapping && !enclosing)
- {
- /*
- * new entry lies between subranges j-1 j
- */
- subranges.add(j, new NCNode<>(entry));
- return true;
- }
-
- if (subrange.getBegin() <= start && subrange.getEnd() >= end)
- {
- /*
- * push new entry inside this subrange as it encloses it
- */
- subrange.add(entry);
- return true;
- }
-
- if (start <= subrange.getBegin())
- {
- if (end >= subrange.getEnd())
- {
- /*
- * new entry encloses this subrange (and possibly preceding ones);
- * continue to find the maximal list it encloses
- */
- if (!enclosing)
- {
- firstEnclosed = j;
- }
- lastEnclosed = j;
- enclosing = true;
- continue;
- }
- else
- {
- /*
- * entry spans from before this subrange to inside it
- */
- if (enclosing)
- {
- /*
- * entry encloses one or more preceding subranges
- */
- addEnclosingRange(entry, firstEnclosed, lastEnclosed);
- return true;
- }
- else
- {
- /*
- * entry spans two subranges but doesn't enclose any
- * so just add it
- */
- subranges.add(j, new NCNode<>(entry));
- return true;
- }
- }
- }
- else
- {
- overlapping = true;
- }
- }
-
- /*
- * drops through to here if new range encloses all others
- * or overlaps the last one
- */
- if (enclosing)
- {
- addEnclosingRange(entry, firstEnclosed, lastEnclosed);
- }
- else
- {
- subranges.add(new NCNode<>(entry));
- }
-
- return true;
- }
-
- /**
- * Answers true if this NCList contains the given entry (by object equality
- * test), else false
- *
- * @param entry
- * @return
- */
- public boolean contains(T entry)
- {
- /*
- * find the first sublist that might overlap, i.e.
- * the first whose end position is >= from
- */
- int candidateIndex = findFirstOverlap(entry.getBegin());
-
- if (candidateIndex == -1)
- {
- return false;
- }
-
- int to = entry.getEnd();
-
- for (int i = candidateIndex; i < subranges.size(); i++)
- {
- NCNode<T> candidate = subranges.get(i);
- if (candidate.getBegin() > to)
- {
- /*
- * we are past the end of our target range
- */
- break;
- }
- if (candidate.contains(entry))
- {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Update the tree so that the range of the new entry encloses subranges i to
- * j (inclusive). That is, replace subranges i-j (inclusive) with a new
- * subrange that contains them.
- *
- * @param entry
- * @param i
- * @param j
- */
- protected synchronized void addEnclosingRange(T entry, final int i,
- final int j)
- {
- NCList<T> newNCList = new NCList<>();
- newNCList.addNodes(subranges.subList(i, j + 1));
- NCNode<T> newNode = new NCNode<>(entry, newNCList);
- for (int k = j; k >= i; k--)
- {
- subranges.remove(k);
- }
- subranges.add(i, newNode);
- }
-
- protected void addNodes(List<NCNode<T>> nodes)
- {
- for (NCNode<T> node : nodes)
- {
- subranges.add(node);
- size += node.size();
- }
- }
-
- /**
- * Returns a (possibly empty) list of items whose extent overlaps the given
- * range
- *
- * @param from
- * start of overlap range (inclusive)
- * @param to
- * end of overlap range (inclusive)
- * @return
- */
- public List<T> findOverlaps(long from, long to)
- {
- List<T> result = new ArrayList<>();
-
- findOverlaps(from, to, result);
-
- return result;
- }
-
- /**
- * Recursively searches the NCList adding any items that overlap the from-to
- * range to the result list
- *
- * @param from
- * @param to
- * @param result
- */
- protected void findOverlaps(long from, long to, List<T> result)
- {
- /*
- * find the first sublist that might overlap, i.e.
- * the first whose end position is >= from
- */
- int candidateIndex = findFirstOverlap(from);
-
- if (candidateIndex == -1)
- {
- return;
- }
-
- for (int i = candidateIndex; i < subranges.size(); i++)
- {
- NCNode<T> candidate = subranges.get(i);
- if (candidate.getBegin() > to)
- {
- /*
- * we are past the end of our target range
- */
- break;
- }
- candidate.findOverlaps(from, to, result);
- }
-
- }
-
- /**
- * Search subranges for the first one whose end position is not before the
- * target range's start position, i.e. the first one that may overlap the
- * target range. Returns the index in the list of the first such range found,
- * or -1 if none found.
- *
- * @param from
- * @return
- */
- protected int findFirstOverlap(long from)
- {
- /*
- * The NCList paper describes binary search for this step,
- * but this not implemented here as (a) I haven't understood it yet
- * and (b) it seems to imply complications for adding to an NCList
- */
-
- int i = 0;
- if (subranges != null)
- {
- for (NCNode<T> subrange : subranges)
- {
- if (subrange.getEnd() >= from)
- {
- return i;
- }
- i++;
- }
- }
- return -1;
- }
-
- /**
- * Formats the tree as a bracketed list e.g.
- *
- * <pre>
- * [1-100 [10-30 [10-20]], 15-30 [20-20]]
- * </pre>
- */
- @Override
- public String toString()
- {
- return subranges.toString();
- }
-
- /**
- * Returns a string representation of the data where containment is shown by
- * indentation on new lines
- *
- * @return
- */
- public String prettyPrint()
- {
- StringBuilder sb = new StringBuilder(512);
- int offset = 0;
- int indent = 2;
- prettyPrint(sb, offset, indent);
- sb.append(System.lineSeparator());
- return sb.toString();
- }
-
- /**
- * @param sb
- * @param offset
- * @param indent
- */
- void prettyPrint(StringBuilder sb, int offset, int indent)
- {
- boolean first = true;
- for (NCNode<T> subrange : subranges)
- {
- if (!first)
- {
- sb.append(System.lineSeparator());
- }
- first = false;
- subrange.prettyPrint(sb, offset, indent);
- }
- }
-
- /**
- * Answers true if the data held satisfy the rules of construction of an
- * NCList, else false.
- *
- * @return
- */
- public boolean isValid()
- {
- return isValid(Integer.MIN_VALUE, Integer.MAX_VALUE);
- }
-
- /**
- * Answers true if the data held satisfy the rules of construction of an
- * NCList bounded within the given start-end range, else false.
- * <p>
- * Each subrange must lie within start-end (inclusive). Subranges must be
- * ordered by start position ascending.
- * <p>
- *
- * @param start
- * @param end
- * @return
- */
- boolean isValid(final int start, final int end)
- {
- int lastStart = start;
- for (NCNode<T> subrange : subranges)
- {
- if (subrange.getBegin() < lastStart)
- {
- System.err.println("error in NCList: range " + subrange.toString()
- + " starts before " + lastStart);
- return false;
- }
- if (subrange.getEnd() > end)
- {
- System.err.println("error in NCList: range " + subrange.toString()
- + " ends after " + end);
- return false;
- }
- lastStart = subrange.getBegin();
-
- if (!subrange.isValid())
- {
- return false;
- }
- }
- return true;
- }
-
- /**
- * Answers the lowest start position enclosed by the ranges
- *
- * @return
- */
- public int getStart()
- {
- return subranges.isEmpty() ? 0 : subranges.get(0).getBegin();
- }
-
- /**
- * Returns the number of ranges held (deep count)
- *
- * @return
- */
- public int size()
- {
- return size;
- }
-
- /**
- * Returns a list of all entries stored
- *
- * @return
- */
- public List<T> getEntries()
- {
- List<T> result = new ArrayList<>();
- getEntries(result);
- return result;
- }
-
- /**
- * Adds all contained entries to the given list
- *
- * @param result
- */
- void getEntries(List<T> result)
- {
- for (NCNode<T> subrange : subranges)
- {
- subrange.getEntries(result);
- }
- }
-
- /**
- * Deletes the given entry from the store, returning true if it was found (and
- * deleted), else false. This method makes no assumption that the entry is in
- * the 'expected' place in the store, in case it has been modified since it
- * was added. Only the first 'same object' match is deleted, not 'equal' or
- * multiple objects.
- *
- * @param entry
- */
- public synchronized boolean delete(T entry)
- {
- if (entry == null)
- {
- return false;
- }
- for (int i = 0; i < subranges.size(); i++)
- {
- NCNode<T> subrange = subranges.get(i);
- NCList<T> subRegions = subrange.getSubRegions();
-
- if (subrange.getRegion() == entry)
- {
- /*
- * if the subrange is rooted on this entry, promote its
- * subregions (if any) to replace the subrange here;
- * NB have to resort subranges after doing this since e.g.
- * [10-30 [12-20 [16-18], 13-19]]
- * after deleting 12-20, 16-18 is promoted to sibling of 13-19
- * but should follow it in the list of subranges of 10-30
- */
- subranges.remove(i);
- if (subRegions != null)
- {
- subranges.addAll(subRegions.subranges);
- Collections.sort(subranges, RangeComparator.BY_START_POSITION);
- }
- size--;
- return true;
- }
- else
- {
- if (subRegions != null && subRegions.delete(entry))
- {
- size--;
- subrange.deleteSubRegionsIfEmpty();
- return true;
- }
- }
- }
- return false;
- }
-}
+++ /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.datamodel.features;
-
-import jalview.datamodel.ContiguousI;
-
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * Each node of the NCList tree consists of a range, and (optionally) the NCList
- * of ranges it encloses
- *
- * @param <V>
- */
-class NCNode<V extends ContiguousI> implements ContiguousI
-{
- /*
- * deep size (number of ranges included)
- */
- private int size;
-
- private V region;
-
- /*
- * null, or an object holding contained subregions of this nodes region
- */
- private NCList<V> subregions;
-
- /**
- * Constructor given a list of ranges
- *
- * @param ranges
- */
- NCNode(List<V> ranges)
- {
- build(ranges);
- }
-
- /**
- * Constructor given a single range
- *
- * @param range
- */
- NCNode(V range)
- {
- List<V> ranges = new ArrayList<>();
- ranges.add(range);
- build(ranges);
- }
-
- NCNode(V entry, NCList<V> newNCList)
- {
- region = entry;
- subregions = newNCList;
- size = 1 + newNCList.size();
- }
-
- /**
- * @param ranges
- */
- protected void build(List<V> ranges)
- {
- size = ranges.size();
-
- if (!ranges.isEmpty())
- {
- region = ranges.get(0);
- }
- if (ranges.size() > 1)
- {
- subregions = new NCList<V>(ranges.subList(1, ranges.size()));
- }
- }
-
- @Override
- public int getBegin()
- {
- return region.getBegin();
- }
-
- @Override
- public int getEnd()
- {
- return region.getEnd();
- }
-
- /**
- * Formats the node as a bracketed list e.g.
- *
- * <pre>
- * [1-100 [10-30 [10-20]], 15-30 [20-20]]
- * </pre>
- */
- @Override
- public String toString() {
- StringBuilder sb = new StringBuilder(10 * size);
- sb.append(region.getBegin()).append("-").append(region.getEnd());
- if (subregions != null)
- {
- sb.append(" ").append(subregions.toString());
- }
- return sb.toString();
- }
-
- void prettyPrint(StringBuilder sb, int offset, int indent) {
- for (int i = 0 ; i < offset ; i++) {
- sb.append(" ");
- }
- sb.append(region.getBegin()).append("-").append(region.getEnd());
- if (subregions != null)
- {
- sb.append(System.lineSeparator());
- subregions.prettyPrint(sb, offset + 2, indent);
- }
- }
- /**
- * Add any ranges that overlap the from-to range to the result list
- *
- * @param from
- * @param to
- * @param result
- */
- void findOverlaps(long from, long to, List<V> result)
- {
- if (region.getBegin() <= to && region.getEnd() >= from)
- {
- result.add(region);
- }
- if (subregions != null)
- {
- subregions.findOverlaps(from, to, result);
- }
- }
-
- /**
- * Add one range to this subrange
- *
- * @param entry
- */
- synchronized void add(V entry)
- {
- if (entry.getBegin() < region.getBegin() || entry.getEnd() > region.getEnd()) {
- throw new IllegalArgumentException(String.format(
- "adding improper subrange %d-%d to range %d-%d",
- entry.getBegin(), entry.getEnd(), region.getBegin(),
- region.getEnd()));
- }
- if (subregions == null)
- {
- subregions = new NCList<V>(entry);
- }
- else
- {
- subregions.add(entry);
- }
- size++;
- }
-
- /**
- * Answers true if the data held satisfy the rules of construction of an
- * NCList, else false.
- *
- * @return
- */
- boolean isValid()
- {
- /*
- * we don't handle reverse ranges
- */
- if (region != null && region.getBegin() > region.getEnd())
- {
- return false;
- }
- if (subregions == null)
- {
- return true;
- }
- return subregions.isValid(getBegin(), getEnd());
- }
-
- /**
- * Adds all contained entries to the given list
- *
- * @param entries
- */
- void getEntries(List<V> entries)
- {
- entries.add(region);
- if (subregions != null)
- {
- subregions.getEntries(entries);
- }
- }
-
- /**
- * Answers true if this object contains the given entry (by object equals
- * test), else false
- *
- * @param entry
- * @return
- */
- boolean contains(V entry)
- {
- if (entry == null)
- {
- return false;
- }
- if (entry.equals(region))
- {
- return true;
- }
- return subregions == null ? false : subregions.contains(entry);
- }
-
- /**
- * Answers the 'root' region modelled by this object
- *
- * @return
- */
- V getRegion()
- {
- return region;
- }
-
- /**
- * Answers the (possibly null) contained regions within this object
- *
- * @return
- */
- NCList<V> getSubRegions()
- {
- return subregions;
- }
-
- /**
- * Nulls the subregion reference if it is empty (after a delete entry
- * operation)
- */
- void deleteSubRegionsIfEmpty()
- {
- if (subregions != null && subregions.size() == 0)
- {
- subregions = null;
- }
- }
-
- /**
- * Answers the (deep) size of this node i.e. the number of ranges it models
- *
- * @return
- */
- int size()
- {
- return size;
- }
-}
+++ /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.datamodel.features;
-
-import jalview.datamodel.ContiguousI;
-
-import java.util.Comparator;
-
-/**
- * A comparator that orders ranges by either start position or end position
- * ascending. If the position matches, ordering is resolved by end position (or
- * start position).
- *
- * @author gmcarstairs
- *
- */
-public class RangeComparator implements Comparator<ContiguousI>
-{
- public static final Comparator<ContiguousI> BY_START_POSITION = new RangeComparator(
- true);
-
- public static final Comparator<ContiguousI> BY_END_POSITION = new RangeComparator(
- false);
-
- boolean byStart;
-
- /**
- * Constructor
- *
- * @param byStartPosition
- * if true, order based on start position, if false by end position
- */
- RangeComparator(boolean byStartPosition)
- {
- byStart = byStartPosition;
- }
-
- @Override
- public int compare(ContiguousI o1, ContiguousI o2)
- {
- int len1 = o1.getEnd() - o1.getBegin();
- int len2 = o2.getEnd() - o2.getBegin();
-
- if (byStart)
- {
- return compare(o1.getBegin(), o2.getBegin(), len1, len2);
- }
- else
- {
- return compare(o1.getEnd(), o2.getEnd(), len1, len2);
- }
- }
-
- /**
- * Compares two ranges for ordering
- *
- * @param pos1
- * first range positional ordering criterion
- * @param pos2
- * second range positional ordering criterion
- * @param len1
- * first range length ordering criterion
- * @param len2
- * second range length ordering criterion
- * @return
- */
- public int compare(long pos1, long pos2, int len1, int len2)
- {
- int order = Long.compare(pos1, pos2);
- if (order == 0)
- {
- /*
- * if tied on position order, longer length sorts to left
- * i.e. the negation of normal ordering by length
- */
- order = -Integer.compare(len1, len2);
- }
- return order;
- }
-}
*/
package jalview.datamodel.features;
-import jalview.datamodel.ContiguousI;
import jalview.datamodel.SequenceFeature;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
+import intervalstore.api.IntervalI;
+
/**
* A class that stores sequence features in a way that supports efficient
* querying by type and location (overlap). Intended for (but not limited to)
*/
public class SequenceFeatures implements SequenceFeaturesI
{
- /**
- * a comparator for sorting features by start position ascending
- */
- private static Comparator<ContiguousI> FORWARD_STRAND = new Comparator<ContiguousI>()
- {
- @Override
- public int compare(ContiguousI o1, ContiguousI o2)
- {
- return Integer.compare(o1.getBegin(), o2.getBegin());
- }
- };
-
- /**
- * a comparator for sorting features by end position descending
- */
- private static Comparator<ContiguousI> REVERSE_STRAND = new Comparator<ContiguousI>()
- {
- @Override
- public int compare(ContiguousI o1, ContiguousI o2)
- {
- return Integer.compare(o2.getEnd(), o1.getEnd());
- }
- };
/*
* map from feature type to structured store of features for that type
* @param features
* @param forwardStrand
*/
- public static void sortFeatures(List<SequenceFeature> features,
+ public static void sortFeatures(List<? extends IntervalI> features,
final boolean forwardStrand)
{
- Collections.sort(features, forwardStrand ? FORWARD_STRAND
- : REVERSE_STRAND);
+ IntervalI.sortIntervals(features, forwardStrand);
}
/**
* {@inheritDoc}
*/
@Override
- public boolean shiftFeatures(int shift)
+ public boolean shiftFeatures(int fromPosition, int shiftBy)
{
boolean modified = false;
for (FeatureStore fs : featureStore.values())
{
- modified |= fs.shiftFeatures(shift);
+ modified |= fs.shiftFeatures(fromPosition, shiftBy);
}
return modified;
}
-}
\ No newline at end of file
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void deleteAll()
+ {
+ featureStore.clear();
+ }
+}
float getMaximumScore(String type, boolean positional);
/**
- * Adds the shift amount to the start and end of all positional features,
- * returning true if at least one feature was shifted, else false
+ * Adds the shift amount to the start and end of all positional features whose
+ * start position is at or after fromPosition. Returns true if at least one
+ * feature was shifted, else false.
*
- * @param shift
+ * @param fromPosition
+ * @param shiftBy
*/
- abstract boolean shiftFeatures(int shift);
-}
\ No newline at end of file
+ boolean shiftFeatures(int fromPosition, int shiftBy);
+
+ /**
+ * Deletes all positional and non-positional features
+ */
+ void deleteAll();
+}
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
import java.util.ArrayList;
for (SequenceFeature sf : sfs)
{
String parentFeature = (String) sf.getValue(PARENT);
- if (("transcript:" + accId).equals(parentFeature))
+ if (accId.equals(parentFeature))
{
result.add(sf);
}
for (SequenceFeature sf : sfs)
{
String parentFeature = (String) sf.getValue(PARENT);
- if (("transcript:" + accId).equals(parentFeature))
+ if ( accId.equals(parentFeature))
{
result.add(sf);
}
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.io.DataSourceType;
-import jalview.io.FeaturesFile;
-import jalview.io.FileParse;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.JSONUtils;
import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
+import java.util.Iterator;
import java.util.List;
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
/**
* A client for fetching and processing Ensembl feature data in GFF format by
* calling the overlap REST service
{
return null;
}
- FeaturesFile fr = new FeaturesFile(
- new FileParse(fp, null, DataSourceType.URL));
- return new Alignment(fr.getSeqsAsArray());
+
+ SequenceI seq = parseFeaturesJson(fp);
+ return new Alignment(new SequenceI[] { seq });
+ }
+
+ /**
+ * Parses the JSON response into Jalview sequence features and attaches them
+ * to a dummy sequence
+ *
+ * @param br
+ * @return
+ */
+ private SequenceI parseFeaturesJson(BufferedReader br)
+ {
+ SequenceI seq = new Sequence("Dummy", "");
+
+ JSONParser jp = new JSONParser();
+ try
+ {
+ JSONArray responses = (JSONArray) jp.parse(br);
+ Iterator rvals = responses.iterator();
+ while (rvals.hasNext())
+ {
+ try
+ {
+ JSONObject obj = (JSONObject) rvals.next();
+ String type = obj.get("feature_type").toString();
+ int start = Integer.parseInt(obj.get("start").toString());
+ int end = Integer.parseInt(obj.get("end").toString());
+ String source = obj.get("source").toString();
+ String strand = obj.get("strand").toString();
+ String alleles = JSONUtils
+ .arrayToList((JSONArray) obj.get("alleles"));
+ String clinSig = JSONUtils
+ .arrayToList(
+ (JSONArray) obj.get("clinical_significance"));
+
+ /*
+ * convert 'variation' to 'sequence_variant', and 'cds' to 'CDS'
+ * so as to have a valid SO term for the feature type
+ * ('gene', 'exon', 'transcript' don't need any conversion)
+ */
+ if ("variation".equals(type))
+ {
+ type = SequenceOntologyI.SEQUENCE_VARIANT;
+ }
+ else if (SequenceOntologyI.CDS.equalsIgnoreCase((type)))
+ {
+ type = SequenceOntologyI.CDS;
+ }
+
+ String desc = getFirstNotNull(obj, "alleles", "external_name",
+ JSON_ID);
+ SequenceFeature sf = new SequenceFeature(type, desc, start, end,
+ source);
+ sf.setStrand("1".equals(strand) ? "+" : "-");
+ setFeatureAttribute(sf, obj, "id");
+ setFeatureAttribute(sf, obj, "Parent");
+ setFeatureAttribute(sf, obj, "consequence_type");
+ sf.setValue("alleles", alleles);
+ sf.setValue("clinical_significance", clinSig);
+
+ seq.addSequenceFeature(sf);
+ } catch (Throwable t)
+ {
+ // ignore - keep trying other features
+ }
+ }
+ } catch (ParseException | IOException e)
+ {
+ // ignore
+ }
+
+ return seq;
+ }
+
+ /**
+ * Returns the first non-null attribute found (if any) as a string, formatted
+ * suitably for display as feature description or tooltip. Answers null if
+ * none of the attribute keys is present.
+ *
+ * @param obj
+ * @param keys
+ * @return
+ */
+ protected String getFirstNotNull(JSONObject obj, String... keys)
+ {
+ String desc = null;
+
+ for (String key : keys)
+ {
+ Object val = obj.get(key);
+ if (val != null)
+ {
+ String s = val instanceof JSONArray
+ ? JSONUtils.arrayToList((JSONArray) val)
+ : val.toString();
+ if (!s.isEmpty())
+ {
+ return s;
+ }
+ }
+ }
+ return desc;
+ }
+
+ /**
+ * A helper method that reads the 'key' entry in the JSON object, and if not
+ * null, sets its string value as an attribute on the sequence feature
+ *
+ * @param sf
+ * @param obj
+ * @param key
+ */
+ protected void setFeatureAttribute(SequenceFeature sf, JSONObject obj,
+ String key)
+ {
+ Object object = obj.get(key);
+ if (object != null)
+ {
+ sf.setValue(key, object.toString());
+ }
}
/**
urlstring.append(getDomain()).append("/overlap/id/").append(ids.get(0));
// @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
- urlstring.append("?content-type=text/x-gff3");
+ urlstring.append("?content-type=" + getResponseMimeType());
/*
* specify object_type=gene in case is shared by transcript and/or protein;
@Override
protected String getRequestMimeType()
{
- return "text/x-gff3";
+ return "application/json";
}
/**
- * Returns the MIME type for GFF3
+ * Returns the MIME type wanted for the response
*/
@Override
protected String getResponseMimeType()
{
- return "text/x-gff3";
+ return "application/json";
}
/**
*/
public class EnsemblGene extends EnsemblSeqProxy
{
- private static final String GENE_PREFIX = "gene:";
-
/*
* accepts anything as we will attempt lookup of gene or
* transcript id or gene name
* look for exon features of the transcript, failing that for CDS
* (for example ENSG00000124610 has 1 CDS but no exon features)
*/
- String parentId = "transcript:" + accId;
+ String parentId = accId;
List<SequenceFeature> splices = findFeatures(gene,
SequenceOntologyI.EXON, parentId);
if (splices.isEmpty())
* Ensembl has gene name as transcript Name
* EnsemblGenomes doesn't, but has a url-encoded description field
*/
- String description = (String) transcriptFeature.getValue(NAME);
+ String description = transcriptFeature.getDescription();
if (description == null)
{
description = (String) transcriptFeature.getValue(DESCRIPTION);
*/
protected String getTranscriptId(SequenceFeature feature)
{
- return (String) feature.getValue("transcript_id");
+ return (String) feature.getValue(JSON_ID);
}
/**
{
List<SequenceFeature> transcriptFeatures = new ArrayList<>();
- String parentIdentifier = GENE_PREFIX + accId;
+ String parentIdentifier = accId;
List<SequenceFeature> sfs = geneSequence.getFeatures()
.getFeaturesByOntology(SequenceOntologyI.TRANSCRIPT);
.getFeaturesByOntology(SequenceOntologyI.GENE);
for (SequenceFeature sf : sfs)
{
- // NB features as gff use 'ID'; rest services return as 'id'
- String id = (String) sf.getValue("ID");
- if ((GENE_PREFIX + accId).equalsIgnoreCase(id))
+ String id = (String) sf.getValue(JSON_ID);
+ if (accId.equalsIgnoreCase(id))
{
result.add(sf);
}
if (isTranscript(type))
{
String parent = (String) sf.getValue(PARENT);
- if (!(GENE_PREFIX + accessionId).equalsIgnoreCase(parent))
+ if (!accessionId.equalsIgnoreCase(parent))
{
return false;
}
SequenceOntologyI.NMD_TRANSCRIPT_VARIANT);
for (SequenceFeature sf : sfs)
{
- // NB features as gff use 'ID'; rest services return as 'id'
- String id = (String) sf.getValue("ID");
- if (("transcript:" + accId).equals(id))
+ String id = (String) sf.getValue(JSON_ID);
+ if (accId.equals(id))
{
result.add(sf);
}
/*
* update these constants when Jalview has been checked / updated for
- * changes to Ensembl REST API (ref JAL-2105)
+ * changes to Ensembl REST API, and updated JAL-3018
* @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
* @see http://rest.ensembl.org/info/rest?content-type=application/json
*/
- private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "7.0";
+ private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "9.0";
- private static final String LATEST_ENSEMBL_REST_VERSION = "7.0";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "9.0";
private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
*/
public abstract class EnsemblSeqProxy extends EnsemblRestClient
{
- protected static final String NAME = "Name";
-
protected static final String DESCRIPTION = "description";
/*
protected boolean featureMayBelong(SequenceFeature sf, String identifier)
{
String parent = (String) sf.getValue(PARENT);
- // using contains to allow for prefix "gene:", "transcript:" etc
if (parent != null
- && !parent.toUpperCase().contains(identifier.toUpperCase()))
+ && !parent.equalsIgnoreCase(identifier))
{
// this genomic feature belongs to a different transcript
return false;
return true;
}
+ /**
+ * Answers a short description of the sequence fetcher
+ */
@Override
public String getDescription()
{
/**
* Answers true if the feature type is either 'NMD_transcript_variant' or
- * 'transcript' or one of its sub-types in the Sequence Ontology. This is
- * needed because NMD_transcript_variant behaves like 'transcript' in Ensembl
+ * 'transcript' (or one of its sub-types in the Sequence Ontology). This is
+ * because NMD_transcript_variant behaves like 'transcript' in Ensembl
* although strictly speaking it is not (it is a sub-type of
* sequence_variant).
+ * <p>
+ * (This test was needed when fetching transcript features as GFF. As we are
+ * now fetching as JSON, all features have type 'transcript' so the check for
+ * NMD_transcript_variant is redundant. Left in for any future case arising.)
*
* @param featureType
* @return
*/
package jalview.ext.ensembl;
+import jalview.analysis.AlignmentUtils;
import jalview.bin.Cache;
import jalview.datamodel.DBRefSource;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
protected static final String PARENT = "Parent";
- protected static final String JSON_ID = "id";
+ protected static final String JSON_ID = AlignmentUtils.VARIANT_ID; // "id";
protected static final String OBJECT_TYPE = "object_type";
* this allows an easy change from http to https in future if needed
*/
ensemblDomain = Cache.getDefault(ENSEMBL_BASEURL,
- DEFAULT_ENSEMBL_BASEURL);
+ DEFAULT_ENSEMBL_BASEURL).trim();
ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
- DEFAULT_ENSEMBL_GENOMES_BASEURL);
+ DEFAULT_ENSEMBL_GENOMES_BASEURL).trim();
domain = ensemblDomain;
}
protected void setDomain(String d)
{
- domain = d;
+ domain = d == null ? null : d.trim();
}
}
return chainNames;
}
- protected abstract IProgressIndicator getIProgressIndicator();
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return null;
+ }
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
{
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.Dimension;
+import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
@SuppressWarnings("serial")
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
{
+ private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
+
protected JInternalFrame mainFrame = new JInternalFrame(
getFTSFrameTitle());
Integer height = getTempUserPrefs().get("FTSPanel.height") == null ? 400
: getTempUserPrefs().get("FTSPanel.height");
lbl_warning.setVisible(false);
- lbl_warning.setFont(new java.awt.Font("Verdana", 0, 12));
+ lbl_warning.setFont(VERDANA_12);
lbl_loading.setVisible(false);
- lbl_loading.setFont(new java.awt.Font("Verdana", 0, 12));
+ lbl_loading.setFont(VERDANA_12);
lbl_blank.setVisible(true);
- lbl_blank.setFont(new java.awt.Font("Verdana", 0, 12));
+ lbl_blank.setFont(VERDANA_12);
tbl_summary.setAutoCreateRowSorter(true);
tbl_summary.getTableHeader().setReorderingAllowed(false);
}
});
+ JButton txt_help = new JButton("?");
+ txt_help.setFont(VERDANA_12);
+ txt_help.setPreferredSize(new Dimension(15, 15));
+ txt_help.setToolTipText(MessageManager.getString("action.help"));
+ txt_help.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showHelp();
+ }
+ });
+
btn_autosearch.setText(MessageManager.getString("option.autosearch"));
btn_autosearch.setToolTipText(
MessageManager.getString("option.enable_disable_autosearch"));
Boolean.toString(btn_autosearch.isSelected()));
}
});
- btn_back.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_back.setFont(VERDANA_12);
btn_back.setText(MessageManager.getString("action.back"));
btn_back.addActionListener(new java.awt.event.ActionListener()
{
});
btn_ok.setEnabled(false);
- btn_ok.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_ok.setFont(VERDANA_12);
btn_ok.setText(MessageManager.getString("action.ok"));
btn_ok.addActionListener(new java.awt.event.ActionListener()
{
btn_next_page.setEnabled(false);
btn_next_page.setToolTipText(
MessageManager.getString("label.next_page_tooltip"));
- btn_next_page.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_next_page.setFont(VERDANA_12);
btn_next_page.setText(MessageManager.getString("action.next_page"));
btn_next_page.addActionListener(new java.awt.event.ActionListener()
{
btn_prev_page.setEnabled(false);
btn_prev_page.setToolTipText(
MessageManager.getString("label.prev_page_tooltip"));
- btn_prev_page.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_prev_page.setFont(VERDANA_12);
btn_prev_page.setText(MessageManager.getString("action.prev_page"));
btn_prev_page.addActionListener(new java.awt.event.ActionListener()
{
btn_next_page.setVisible(false);
}
- btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_cancel.setFont(VERDANA_12);
btn_cancel.setText(MessageManager.getString("action.cancel"));
btn_cancel.addActionListener(new java.awt.event.ActionListener()
{
});
scrl_searchResult.setPreferredSize(new Dimension(width, height));
- cmb_searchTarget.setFont(new java.awt.Font("Verdana", 0, 12));
+ cmb_searchTarget.setFont(VERDANA_12);
cmb_searchTarget.addItemListener(new ItemListener()
{
@Override
}
});
- txt_search.setFont(new java.awt.Font("Verdana", 0, 12));
+ txt_search.setFont(VERDANA_12);
txt_search.getEditor().getEditorComponent()
.addKeyListener(new KeyAdapter()
pnl_results.add(tabbedPane);
pnl_inputs.add(cmb_searchTarget);
pnl_inputs.add(txt_search);
+ pnl_inputs.add(txt_help);
pnl_inputs.add(btn_autosearch);
pnl_inputs.add(lbl_loading);
pnl_inputs.add(lbl_warning);
Desktop.addInternalFrame(mainFrame, getFTSFrameTitle(), width, height);
}
+ abstract protected void showHelp();
+
protected void closeAction()
{
getTempUserPrefs().put("FTSPanel.width", this.getWidth());
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.core.GFTSPanel;
+import jalview.gui.Help;
+import jalview.gui.Help.HelpId;
import jalview.gui.SequenceFetcher;
import jalview.util.MessageManager;
import java.util.HashSet;
import java.util.Map;
+import javax.help.HelpSetException;
+
@SuppressWarnings("serial")
public class PDBFTSPanel extends GFTSPanel
{
private static String defaultFTSFrameTitle = MessageManager
.getString("label.pdb_sequence_fetcher");
- private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
+ private static Map<String, Integer> tempUserPrefs = new HashMap<>();
private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
// mainFrame.dispose();
disableActionButtons();
StringBuilder selectedIds = new StringBuilder();
- HashSet<String> selectedIdsSet = new HashSet<String>();
+ HashSet<String> selectedIdsSet = new HashSet<>();
int primaryKeyColIndex = 0;
try
{
{
return PDB_AUTOSEARCH;
}
+
+ @Override
+ protected void showHelp()
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.PdbFts);
+ } catch (HelpSetException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
}
\ No newline at end of file
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.core.GFTSPanel;
+import jalview.gui.Help;
+import jalview.gui.Help.HelpId;
import jalview.gui.SequenceFetcher;
import jalview.util.MessageManager;
import java.util.HashSet;
import java.util.Map;
+import javax.help.HelpSetException;
+
@SuppressWarnings("serial")
public class UniprotFTSPanel extends GFTSPanel
{
{
return UNIPROT_AUTOSEARCH;
}
+
+ @Override
+ protected void showHelp()
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.UniprotFts);
+ } catch (HelpSetException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
}
import jalview.analysis.AlignmentUtils;
import jalview.analysis.CrossRef;
import jalview.analysis.Dna;
+import jalview.analysis.GeneticCodeI;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignExportSettingI;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
+import jalview.io.BackupFiles;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import java.util.List;
import java.util.Vector;
+import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JEditorPane;
import javax.swing.JInternalFrame;
return progressBar.operationInProgress();
}
+ /**
+ * Sets the text of the status bar. Note that setting a null or empty value
+ * will cause the status bar to be hidden, with possibly undesirable flicker
+ * of the screen layout.
+ */
@Override
public void setStatus(String text)
{
}
else
{
+ // create backupfiles object and get new temp filename destination
+ BackupFiles backupfiles = new BackupFiles(file);
+
try
{
- // PrintWriter out = new PrintWriter(new FileWriter(file));
- PrintWriter out = new PrintWriter(new FileWriter(file), true);
+ PrintWriter out = new PrintWriter(
+ new FileWriter(backupfiles.getTempFilePath()));
// TESTING code here
boolean TESTING = true;
success = false;
ex.printStackTrace();
}
+
+ backupfiles.setWriteSuccess(success);
+ // do the backup file roll and rename the temp file to actual file
+ success = backupfiles.rollBackupsAndRenameTempFile();
+
}
}
@Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
- SequenceGroup sg = new SequenceGroup();
-
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
- }
+ SequenceGroup sg = new SequenceGroup(
+ viewport.getAlignment().getSequences());
sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
+ viewport.isSelectionGroupChanged(true);
viewport.sendSelection();
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
if (viewport.getViewName() == null)
{
- viewport.setViewName(
- MessageManager.getString("label.view_name_original"));
+ viewport.setViewName(MessageManager
+ .getString("label.view_name_original"));
}
/*
newap.av.setRedoList(viewport.getRedoList());
/*
+ * copy any visualisation settings that are not saved in the project
+ */
+ newap.av.setColourAppliesToAllGroups(
+ viewport.getColourAppliesToAllGroups());
+
+ /*
* Views share the same mappings; need to deregister any new mappings
* created by copyAlignPanel, and register the new reference to the shared
* mappings
viewport.setFollowHighlight(state);
if (state)
{
- alignPanel.scrollToPosition(viewport.getSearchResults(), false);
+ alignPanel.scrollToPosition(viewport.getSearchResults());
}
}
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
* otherwise set the chosen colour scheme (or null for 'None')
*/
ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
+ viewport,
viewport.getAlignment(), viewport.getHiddenRepSequences());
changeColour(cs);
}
* frame's DNA sequences to their aligned protein (amino acid) equivalents.
*/
@Override
- public void showTranslation_actionPerformed(ActionEvent e)
+ public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
AlignmentI al = null;
try
{
Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
- al = dna.translateCdna();
+ al = dna.translateCdna(codeTable);
} catch (Exception ex)
{
jalview.bin.Cache.log.error(
af.setFileFormat(this.currentFileFormat);
final String newTitle = MessageManager
.formatMessage("label.translation_of_params", new Object[]
- { this.getTitle() });
+ { this.getTitle(), codeTable.getId() });
af.setTitle(newTitle);
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true, true);
+ alignPanel.paintAlignment(true,
+ viewport.needToUpdateStructureViews());
}
}
colourMenu.add(textColour);
colourMenu.addSeparator();
- ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
- false);
+ ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
+ viewport.getAlignment(), false);
+ colourMenu.add(annotationColour);
+ bg.add(annotationColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(modifyConservation);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
- colourMenu.add(annotationColour);
ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
ResidueColourScheme.NONE);
}
ColourSchemeI colourScheme = ColourSchemeProperty
- .getColourScheme(alignment, schemeName);
+ .getColourScheme(this, alignment, schemeName);
residueShading = new ResidueShader(colourScheme);
if (colourScheme instanceof UserColourScheme)
{
residueShading.setConsensus(hconsensus);
}
+ setColourAppliesToAllGroups(true);
}
boolean validCharWidth;
AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
newAlignFrame.setTitle(title);
- newAlignFrame.statusBar.setText(MessageManager
+ newAlignFrame.setStatus(MessageManager
.formatMessage("label.successfully_loaded_file", new Object[]
{ title }));
}
/**
- * Highlight the given results on the alignment.
+ * Highlight the given results on the alignment
*
*/
public void highlightSearchResults(SearchResultsI results)
{
- boolean scrolled = scrollToPosition(results, 0, true, false);
+ boolean scrolled = scrollToPosition(results, 0, false);
boolean noFastPaint = scrolled && av.getWrapAlignment();
* (if any)
*
* @param searchResults
- * @param redrawOverview
* @return
*/
- public boolean scrollToPosition(SearchResultsI searchResults,
- boolean redrawOverview)
+ public boolean scrollToPosition(SearchResultsI searchResults)
{
- return scrollToPosition(searchResults, 0, redrawOverview, false);
+ return scrollToPosition(searchResults, 0, false);
}
/**
* @param verticalOffset
* if greater than zero, allows scrolling to a position below the
* first displayed sequence
- * @param redrawOverview
- * - when set, the overview will be recalculated (takes longer)
* @param centre
* if true, try to centre the search results horizontally in the view
* @return
*/
protected boolean scrollToPosition(SearchResultsI results,
- int verticalOffset, boolean redrawOverview, boolean centre)
+ int verticalOffset, boolean centre)
{
int startv, endv, starts, ends;
ViewportRanges ranges = av.getRanges();
scrollNeeded = ranges.scrollToWrappedVisible(start);
}
- paintAlignment(redrawOverview, false);
+ paintAlignment(false, false);
return scrollNeeded;
}
addNotify();
// TODO: many places call this method and also paintAlignment with various
// different settings. this means multiple redraws are triggered...
- paintAlignment(true, false);
+ paintAlignment(true, av.needToUpdateStructureViews());
}
/**
}
else
{
- int width = av.getAlignment().getWidth();
+ int width = av.getAlignment().getVisibleWidth();
int height = av.getAlignment().getHeight();
- if (av.hasHiddenColumns())
- {
- // reset the width to exclude hidden columns
- width = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(width);
- }
-
hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
- final int alignmentWidth = av.getAlignment().getWidth();
- final int pagesWide = (alignmentWidth / totalRes) + 1;
+ final int alignmentWidth = av.getAlignment().getVisibleWidth();
+ int pagesWide = (alignmentWidth / totalRes) + 1;
final int startRes = (pageIndex % pagesWide) * totalRes;
final int endRes = Math.min(startRes + totalRes - 1,
int idWidth = getVisibleIdWidth(false);
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth) - 1;
- }
+ int maxwidth = av.getAlignment().getVisibleWidth();
int resWidth = getSeqPanel().seqCanvas
.getWrappedCanvasWidth(pageWidth - idWidth);
public AlignmentDimension getAlignmentDimension()
{
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth);
- }
+ int maxwidth = av.getAlignment().getVisibleWidth();
int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
+ getScalePanel().getHeight();
*/
protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
{
- scrollToPosition(sr, verticalOffset, true, true);
+ scrollToPosition(sr, verticalOffset, true);
}
/**
{
setAnnotationVisibility(true);
- // copied from AnnotationLabel.actionPerformed (after show/hide row)...
- // TODO should drive this functionality into AlignmentPanel
ap.updateAnnotation();
- // this.ap.annotationPanel.adjustPanelHeight();
- // this.ap.alabels.setSize(this.ap.alabels.getSize().width,
- // this.ap.annotationPanel.getSize().height);
- // this.ap.validate();
- this.ap.paintAlignment(true, false);
}
/**
}
}
ap.updateAnnotation();
- // // this.ap.annotationPanel.adjustPanelHeight();
- // this.ap.alabels.setSize(this.ap.alabels.getSize().width,
- // this.ap.annotationPanel.getSize().height);
- // this.ap.validate();
- this.ap.paintAlignment(true, false);
}
/**
{
setAnnotationVisibility(false);
- this.ap.updateAnnotation();
- // this.ap.annotationPanel.adjustPanelHeight();
- this.ap.paintAlignment(true, false);
+ ap.updateAnnotation();
}
/**
@Override
public void reset()
{
- av.setGlobalColourScheme(oldcs);
+ this.ap.alignFrame.changeColour(oldcs);
if (av.getAlignment().getGroups() != null)
{
acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
- av.setGlobalColourScheme(acg);
+ this.ap.alignFrame.changeColour(acg);
if (av.getAlignment().getGroups() != null)
{
continue;
}
sg.setColourScheme(
- acg.getInstance(sg, ap.av.getHiddenRepSequences()));
+ acg.getInstance(av, sg));
}
}
}
super.sliderDragReleased();
ap.paintAlignment(true, true);
}
-
}
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.KeyEvent;
}
}
});
+ searchBox.getEditor().getEditorComponent()
+ .addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ searchStringAction();
+ }
+ });
JvSwingUtils.jvInitComponent(displayName, "label.label");
displayName.addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- discriptionCheckboxAction();
+ descriptionCheckboxAction();
}
});
aColChooser.updateView();
}
- public void discriptionCheckboxAction()
+ public void descriptionCheckboxAction()
{
aColChooser.setCurrentSearchPanel(this);
aColChooser.updateView();
*/
package jalview.gui;
-import jalview.api.FeatureColourI;
+import jalview.api.FeatureRenderer;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.io.AnnotationFile;
import jalview.io.FeaturesFile;
import jalview.io.JalviewFileChooser;
import java.awt.event.ActionListener;
import java.io.FileWriter;
import java.io.PrintWriter;
-import java.util.List;
-import java.util.Map;
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
{
String text;
SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
- Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
- .getDisplayedFeatureCols();
- Map<String, FeatureMatcherSetI> featureFilters = ap.getFeatureRenderer()
- .getFeatureFilters();
- List<String> featureGroups = ap.getFeatureRenderer()
- .getDisplayedFeatureGroups();
boolean includeNonPositional = ap.av.isShowNPFeats();
FeaturesFile formatter = new FeaturesFile();
+ final FeatureRenderer fr = ap.getFeatureRenderer();
if (GFFFormat.isSelected())
{
- text = formatter.printGffFormat(sequences, featureColours,
- featureGroups, includeNonPositional);
+ text = formatter.printGffFormat(sequences, fr, includeNonPositional);
}
else
{
- text = formatter.printJalviewFormat(sequences, featureColours,
- featureFilters, featureGroups, includeNonPositional);
+ text = formatter.printJalviewFormat(sequences, fr,
+ includeNonPositional);
}
return text;
}
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.awt.geom.AffineTransform;
-import java.awt.image.BufferedImage;
-import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator;
-import java.util.regex.Pattern;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JMenuItem;
public class AnnotationLabels extends JPanel
implements MouseListener, MouseMotionListener, ActionListener
{
+ private static final String HTML_END_TAG = "</html>";
+
+ private static final String HTML_START_TAG = "<html>";
+
/**
* width in pixels within which height adjuster arrows are shown and active
*/
*/
private static int HEIGHT_ADJUSTER_HEIGHT = 10;
- private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
- .compile("<");
-
private static final Font font = new Font("Arial", Font.PLAIN, 11);
private static final String TOGGLE_LABELSCALE = MessageManager
AlignmentUtils.showOrHideSequenceAnnotations(
ap.av.getAlignment(), Collections.singleton(label),
null, false, false);
- // for (AlignmentAnnotation ann : ap.av.getAlignment()
- // .getAlignmentAnnotation())
- // {
- // if (ann.sequenceRef != null && ann.label != null
- // && ann.label.equals(label))
- // {
- // ann.visible = false;
- // }
- // }
ap.refresh(true);
}
});
}
else if (label.indexOf("Consensus") > -1)
{
- pop.addSeparator();
- // av and sequencegroup need to implement same interface for
- final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- MessageManager.getString("label.ignore_gaps_consensus"),
- (aa[selectedRow].groupRef != null)
- ? aa[selectedRow].groupRef.getIgnoreGapsConsensus()
- : ap.av.isIgnoreGapsConsensus());
- final AlignmentAnnotation aaa = aa[selectedRow];
- cbmi.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (aaa.groupRef != null)
- {
- // TODO: pass on reference to ap so the view can be updated.
- aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
- ap.getAnnotationPanel()
- .paint(ap.getAnnotationPanel().getGraphics());
- }
- else
- {
- ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
- }
- ap.alignmentChanged();
- }
- });
- pop.add(cbmi);
- // av and sequencegroup need to implement same interface for
+ addConsensusMenuOptions(ap, aa[selectedRow], pop);
+
+ final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+ consclipbrd.addActionListener(this);
+ pop.add(consclipbrd);
+ }
+ }
+ pop.show(this, evt.getX(), evt.getY());
+ }
+
+ /**
+ * A helper method that adds menu options for calculation and visualisation of
+ * group and/or alignment consensus annotation to a popup menu. This is
+ * designed to be reusable for either unwrapped mode (popup menu is shown on
+ * component AnnotationLabels), or wrapped mode (popup menu is shown on
+ * IdPanel when the mouse is over an annotation label).
+ *
+ * @param ap
+ * @param ann
+ * @param pop
+ */
+ static void addConsensusMenuOptions(AlignmentPanel ap,
+ AlignmentAnnotation ann,
+ JPopupMenu pop)
+ {
+ pop.addSeparator();
+
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ MessageManager.getString("label.ignore_gaps_consensus"),
+ (ann.groupRef != null) ? ann.groupRef.getIgnoreGapsConsensus()
+ : ap.av.isIgnoreGapsConsensus());
+ final AlignmentAnnotation aaa = ann;
+ cbmi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
if (aaa.groupRef != null)
{
- final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_histogram"),
- aa[selectedRow].groupRef.isShowConsensusHistogram());
- chist.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- aaa.groupRef.setShowConsensusHistogram(chist.getState());
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(chist);
- final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_logo"),
- aa[selectedRow].groupRef.isShowSequenceLogo());
- cprofl.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- aaa.groupRef.setshowSequenceLogo(cprofl.getState());
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(cprofl);
- final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_group_logo"),
- aa[selectedRow].groupRef.isNormaliseSequenceLogo());
- cproflnorm.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
-
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
- // automatically enable logo display if we're clicked
- aaa.groupRef.setshowSequenceLogo(true);
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(cproflnorm);
+ aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+ ap.getAnnotationPanel()
+ .paint(ap.getAnnotationPanel().getGraphics());
}
else
{
- final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_histogram"),
- av.isShowConsensusHistogram());
- chist.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- av.setShowConsensusHistogram(chist.getState());
- ap.alignFrame.setMenusForViewport();
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(chist);
- final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_logo"),
- av.isShowSequenceLogo());
- cprof.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- av.setShowSequenceLogo(cprof.getState());
- ap.alignFrame.setMenusForViewport();
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(cprof);
- final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_logo"),
- av.isNormaliseSequenceLogo());
- cprofnorm.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- av.setShowSequenceLogo(true);
- av.setNormaliseSequenceLogo(cprofnorm.getState());
- ap.alignFrame.setMenusForViewport();
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(cprofnorm);
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
}
- final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
- consclipbrd.addActionListener(this);
- pop.add(consclipbrd);
+ ap.alignmentChanged();
}
+ });
+ pop.add(cbmi);
+
+ if (aaa.groupRef != null)
+ {
+ /*
+ * group consensus options
+ */
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_histogram"),
+ ann.groupRef.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ aaa.groupRef.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_logo"),
+ ann.groupRef.isShowSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ aaa.groupRef.setshowSequenceLogo(cprofl.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprofl);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ ann.groupRef.isNormaliseSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ aaa.groupRef.setshowSequenceLogo(true);
+ ap.repaint();
+ }
+ });
+ pop.add(cproflnorm);
+ }
+ else
+ {
+ /*
+ * alignment consensus options
+ */
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_histogram"),
+ ap.av.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.setShowConsensusHistogram(chist.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_logo"),
+ ap.av.isShowSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.setShowSequenceLogo(cprof.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ }
+ });
+ pop.add(cprof);
+ final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_logo"),
+ ap.av.isNormaliseSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.setShowSequenceLogo(true);
+ ap.av.setNormaliseSequenceLogo(cprofnorm.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ }
+ });
+ pop.add(cprofnorm);
}
- pop.show(this, evt.getX(), evt.getY());
}
/**
if (selectedRow > -1 && ap.av.getAlignment()
.getAlignmentAnnotation().length > selectedRow)
{
- AlignmentAnnotation aa = ap.av.getAlignment()
- .getAlignmentAnnotation()[selectedRow];
+ AlignmentAnnotation[] anns = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ AlignmentAnnotation aa = anns[selectedRow];
+
+ String desc = getTooltip(aa);
+ this.setToolTipText(desc);
+ String msg = getStatusMessage(aa, anns);
+ ap.alignFrame.setStatus(msg);
+ }
+ }
+
+ /**
+ * Constructs suitable text to show in the status bar when over an annotation
+ * label, containing the associated sequence name (if any), and the annotation
+ * labels (or all labels for a graph group annotation)
+ *
+ * @param aa
+ * @param anns
+ * @return
+ */
+ static String getStatusMessage(AlignmentAnnotation aa,
+ AlignmentAnnotation[] anns)
+ {
+ if (aa == null)
+ {
+ return null;
+ }
- StringBuffer desc = new StringBuffer();
- if (aa.description != null
- && !aa.description.equals("New description"))
+ StringBuilder msg = new StringBuilder(32);
+ if (aa.sequenceRef != null)
+ {
+ msg.append(aa.sequenceRef.getName()).append(" : ");
+ }
+
+ if (aa.graphGroup == -1)
+ {
+ msg.append(aa.label);
+ }
+ else if (anns != null)
+ {
+ boolean first = true;
+ for (int i = anns.length - 1; i >= 0; i--)
{
- // TODO: we could refactor and merge this code with the code in
- // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
- // tooltips
- desc.append(aa.getDescription(true).trim());
- // check to see if the description is an html fragment.
- if (desc.length() < 6 || (desc.substring(0, 6).toLowerCase()
- .indexOf("<html>") < 0))
+ if (anns[i].graphGroup == aa.graphGroup)
{
- // clean the description ready for embedding in html
- desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
- .replaceAll("<"));
- desc.insert(0, "<html>");
- }
- else
- {
- // remove terminating html if any
- int i = desc.substring(desc.length() - 7).toLowerCase()
- .lastIndexOf("</html>");
- if (i > -1)
+ if (!first)
{
- desc.setLength(desc.length() - 7 + i);
+ msg.append(", ");
}
+ msg.append(anns[i].label);
+ first = false;
}
- if (aa.hasScore())
- {
- desc.append("<br/>");
- }
- // if (aa.hasProperties())
- // {
- // desc.append("<table>");
- // for (String prop : aa.getProperties())
- // {
- // desc.append("<tr><td>" + prop + "</td><td>"
- // + aa.getProperty(prop) + "</td><tr>");
- // }
- // desc.append("</table>");
- // }
}
- else
+ }
+
+ return msg.toString();
+ }
+
+ /**
+ * Answers a tooltip, formatted as html, containing the annotation description
+ * (prefixed by associated sequence id if applicable), and the annotation
+ * (non-positional) score if it has one. Answers null if neither description
+ * nor score is found.
+ *
+ * @param aa
+ * @return
+ */
+ static String getTooltip(AlignmentAnnotation aa)
+ {
+ if (aa == null)
+ {
+ return null;
+ }
+ StringBuilder tooltip = new StringBuilder();
+ if (aa.description != null && !aa.description.equals("New description"))
+ {
+ // TODO: we could refactor and merge this code with the code in
+ // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
+ // tooltips
+ String desc = aa.getDescription(true).trim();
+ if (!desc.toLowerCase().startsWith(HTML_START_TAG))
{
- // begin the tooltip's html fragment
- desc.append("<html>");
- if (aa.hasScore())
- {
- // TODO: limit precision of score to avoid noise from imprecise
- // doubles
- // (64.7 becomes 64.7+/some tiny value).
- desc.append(" Score: " + aa.score);
- }
+ tooltip.append(HTML_START_TAG);
+ desc = desc.replace("<", "<");
}
- if (desc.length() > 6)
+ else if (desc.toLowerCase().endsWith(HTML_END_TAG))
{
- desc.append("</html>");
- this.setToolTipText(desc.toString());
+ desc = desc.substring(0, desc.length() - HTML_END_TAG.length());
}
- else
+ tooltip.append(desc);
+ }
+ else
+ {
+ // begin the tooltip's html fragment
+ tooltip.append(HTML_START_TAG);
+ }
+ if (aa.hasScore())
+ {
+ if (tooltip.length() > HTML_START_TAG.length())
{
- this.setToolTipText(null);
+ tooltip.append("<br/>");
}
+ // TODO: limit precision of score to avoid noise from imprecise
+ // doubles
+ // (64.7 becomes 64.7+/some tiny value).
+ tooltip.append(" Score: ").append(String.valueOf(aa.score));
+ }
+
+ if (tooltip.length() > HTML_START_TAG.length())
+ {
+ return tooltip.append(HTML_END_TAG).toString();
}
+
+ /*
+ * nothing in the tooltip (except "<html>")
+ */
+ return null;
}
/**
package jalview.gui;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
MouseListener, MouseWheelListener, MouseMotionListener,
ActionListener, AdjustmentListener, Scrollable, ViewportListenerI
{
+ enum DragMode
+ {
+ Select, Resize, Undefined
+ };
+
String HELIX = MessageManager.getString("label.helix");
String SHEET = MessageManager.getString("label.sheet");
// Used For mouse Dragging and resizing graphs
int graphStretch = -1;
- int graphStretchY = -1;
+ int mouseDragLastX = -1;
- int min; // used by mouseDragged to see if user
+ int mouseDragLastY = -1;
- int max; // used by mouseDragged to see if user
+ DragMode dragMode = DragMode.Undefined;
boolean mouseDragging = false;
}
/**
- * DOCUMENT ME!
+ * Action on right mouse pressed on Mac is to show a pop-up menu for the
+ * annotation. Action on left mouse pressed is to find which annotation is
+ * pressed and mark the start of a column selection or graph resize operation.
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void mousePressed(MouseEvent evt)
{
return;
}
+ mouseDragLastX = evt.getX();
+ mouseDragLastY = evt.getY();
+ /*
+ * add visible annotation heights until we reach the y
+ * position, to find which annotation it is in
+ */
int height = 0;
activeRow = -1;
}
else if (aa[i].graph > 0)
{
- // Stretch Graph
+ /*
+ * we have clicked on a resizable graph annotation
+ */
graphStretch = i;
- graphStretchY = y;
}
-
break;
}
}
}
/**
- * DOCUMENT ME!
+ * Action on mouse up is to clear mouse drag data and call mouseReleased on
+ * ScalePanel, to deal with defining the selection group (if any) defined by
+ * the mouse drag
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void mouseReleased(MouseEvent evt)
{
graphStretch = -1;
- graphStretchY = -1;
+ mouseDragLastX = -1;
+ mouseDragLastY = -1;
mouseDragging = false;
+ dragMode = DragMode.Undefined;
ap.getScalePanel().mouseReleased(evt);
/*
@Override
public void mouseDragged(MouseEvent evt)
{
- if (graphStretch > -1)
+ /*
+ * todo: if dragMode is Undefined:
+ * - set to Select if dx > dy
+ * - set to Resize if dy > dx
+ * - do nothing if dx == dy
+ */
+ final int x = evt.getX();
+ final int y = evt.getY();
+ if (dragMode == DragMode.Undefined)
{
- av.getAlignment()
- .getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
- - evt.getY();
- if (av.getAlignment()
- .getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+ int dx = Math.abs(x - mouseDragLastX);
+ int dy = Math.abs(y - mouseDragLastY);
+ if (graphStretch == -1 || dx > dy)
{
- av.getAlignment()
- .getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+ /*
+ * mostly horizontal drag, or not a graph annotation
+ */
+ dragMode = DragMode.Select;
+ }
+ else if (dy > dx)
+ {
+ /*
+ * mostly vertical drag
+ */
+ dragMode = DragMode.Resize;
}
- graphStretchY = evt.getY();
- adjustPanelHeight();
- ap.paintAlignment(false, false);
}
- else
+
+ if (dragMode == DragMode.Undefined)
{
- ap.getScalePanel().mouseDragged(evt);
+ /*
+ * drag is diagonal - defer deciding whether to
+ * treat as up/down or left/right
+ */
+ return;
+ }
+
+ try
+ {
+ if (dragMode == DragMode.Resize)
+ {
+ /*
+ * resize graph annotation if mouse was dragged up or down
+ */
+ int deltaY = mouseDragLastY - evt.getY();
+ if (deltaY != 0)
+ {
+ AlignmentAnnotation graphAnnotation = av.getAlignment()
+ .getAlignmentAnnotation()[graphStretch];
+ int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY);
+ graphAnnotation.graphHeight = newHeight;
+ adjustPanelHeight();
+ ap.paintAlignment(false, false);
+ }
+ }
+ else
+ {
+ /*
+ * for mouse drag left or right, delegate to
+ * ScalePanel to adjust the column selection
+ */
+ ap.getScalePanel().mouseDragged(evt);
+ }
+ } finally
+ {
+ mouseDragLastX = x;
+ mouseDragLastY = y;
}
}
@Override
public void mouseMoved(MouseEvent evt)
{
+ int yPos = evt.getY();
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
- if (aa == null)
- {
- this.setToolTipText(null);
- return;
- }
-
- int row = -1;
- int height = 0;
-
- for (int i = 0; i < aa.length; i++)
- {
- if (aa[i].visible)
- {
- height += aa[i].height;
- }
-
- if (evt.getY() < height)
- {
- row = i;
- break;
- }
- }
+ int row = getRowIndex(yPos, aa);
if (row == -1)
{
int column = (evt.getX() / av.getCharWidth())
+ av.getRanges().getStartRes();
+ column = Math.min(column, av.getRanges().getEndRes());
if (av.hasHiddenColumns())
{
if (row > -1 && ann.annotations != null
&& column < ann.annotations.length)
{
- buildToolTip(ann, column, aa);
- setStatusMessage(column, ann);
+ setToolTipText(buildToolTip(ann, column, aa));
+ String msg = getStatusMessage(av.getAlignment(), column, ann);
+ ap.alignFrame.setStatus(msg);
}
else
{
this.setToolTipText(null);
- ap.alignFrame.statusBar.setText(" ");
+ ap.alignFrame.setStatus(" ");
+ }
+ }
+
+ /**
+ * Answers the index in the annotations array of the visible annotation at the
+ * given y position. This is done by adding the heights of visible annotations
+ * until the y position has been exceeded. Answers -1 if no annotations are
+ * visible, or the y position is below all annotations.
+ *
+ * @param yPos
+ * @param aa
+ * @return
+ */
+ static int getRowIndex(int yPos, AlignmentAnnotation[] aa)
+ {
+ if (aa == null)
+ {
+ return -1;
}
+ int row = -1;
+ int height = 0;
+
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].visible)
+ {
+ height += aa[i].height;
+ }
+
+ if (height > yPos)
+ {
+ row = i;
+ break;
+ }
+ }
+ return row;
}
/**
- * Builds a tooltip for the annotation at the current mouse position.
+ * Answers a tooltip for the annotation at the current mouse position
*
* @param ann
* @param column
* @param anns
*/
- void buildToolTip(AlignmentAnnotation ann, int column,
+ static String buildToolTip(AlignmentAnnotation ann, int column,
AlignmentAnnotation[] anns)
{
+ String tooltip = null;
if (ann.graphGroup > -1)
{
StringBuilder tip = new StringBuilder(32);
if (tip.length() != 6)
{
tip.setLength(tip.length() - 4);
- this.setToolTipText(tip.toString() + "</html>");
+ tooltip = tip.toString() + "</html>";
}
}
- else if (ann.annotations[column] != null)
+ else if (column < ann.annotations.length
+ && ann.annotations[column] != null)
{
String description = ann.annotations[column].description;
if (description != null && description.length() > 0)
{
- this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
+ tooltip = JvSwingUtils.wrapTooltip(true, description);
}
else
{
- this.setToolTipText(null); // no tooltip if null or empty description
+ tooltip = null; // no tooltip if null or empty description
}
}
else
{
// clear the tooltip.
- this.setToolTipText(null);
+ tooltip = null;
}
+ return tooltip;
}
/**
- * Constructs and displays the status bar message
+ * Constructs and returns the status bar message
*
+ * @param al
* @param column
* @param ann
*/
- void setStatusMessage(int column, AlignmentAnnotation ann)
+ static String getStatusMessage(AlignmentI al, int column,
+ AlignmentAnnotation ann)
{
/*
* show alignment column and annotation description if any
text.append(MessageManager.getString("label.column")).append(" ")
.append(column + 1);
- if (ann.annotations[column] != null)
+ if (column < ann.annotations.length && ann.annotations[column] != null)
{
String description = ann.annotations[column].description;
if (description != null && description.trim().length() > 0)
SequenceI seqref = ann.sequenceRef;
if (seqref != null)
{
- int seqIndex = av.getAlignment().findIndex(seqref);
+ int seqIndex = al.findIndex(seqref);
if (seqIndex != -1)
{
text.append(", ").append(MessageManager.getString("label.sequence"))
{
text.append(" ");
String name;
- if (av.getAlignment().isNucleotide())
+ if (al.isNucleotide())
{
name = ResidueProperties.nucleotideName
.get(String.valueOf(residue));
}
}
- ap.alignFrame.statusBar.setText(text.toString());
+ return text.toString();
}
/**
import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
import jalview.datamodel.SequenceGroup;
import jalview.util.MessageManager;
final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
- List<String> tips = new ArrayList<String>();
+ List<String> tips = new ArrayList<>();
/*
* the most recently opened PCA results panel
*/
protected JComboBox<String> buildModelOptionsList()
{
- final JComboBox<String> scoreModelsCombo = new JComboBox<String>();
+ final JComboBox<String> scoreModelsCombo = new JComboBox<>();
scoreModelsCombo.setRenderer(renderer);
/*
{
Object curSel = comboBox.getSelectedItem();
toolTips.clear();
- DefaultComboBoxModel<String> model = new DefaultComboBoxModel<String>();
+ DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>();
+
+ /*
+ * select the score models applicable to the alignment type
+ */
+ boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+ List<ScoreModelI> models = getApplicableScoreModels(nucleotide,
+ pca.isSelected());
/*
* now we can actually add entries to the combobox,
* remembering their descriptions for tooltips
*/
- ScoreModels scoreModels = ScoreModels.getInstance();
boolean selectedIsPresent = false;
- for (ScoreModelI sm : scoreModels.getModels())
+ for (ScoreModelI sm : models)
{
- boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
- if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
+ if (curSel != null && sm.getName().equals(curSel))
+ {
+ selectedIsPresent = true;
+ curSel = sm.getName();
+ }
+ model.addElement(sm.getName());
+
+ /*
+ * tooltip is description if provided, else text lookup with
+ * fallback on the model name
+ */
+ String tooltip = sm.getDescription();
+ if (tooltip == null)
{
- if (curSel != null && sm.getName().equals(curSel))
- {
- selectedIsPresent = true;
- curSel = sm.getName();
- }
- model.addElement(sm.getName());
-
- /*
- * tooltip is description if provided, else text lookup with
- * fallback on the model name
- */
- String tooltip = sm.getDescription();
- if (tooltip == null)
- {
- tooltip = MessageManager.getStringOrReturn("label.score_model_",
- sm.getName());
- }
- toolTips.add(tooltip);
+ tooltip = MessageManager.getStringOrReturn("label.score_model_",
+ sm.getName());
}
+ toolTips.add(tooltip);
}
+
if (selectedIsPresent)
{
model.setSelectedItem(curSel);
}
/**
+ * Builds a list of score models which are applicable for the alignment and
+ * calculation type (peptide or generic models for protein, nucleotide or
+ * generic models for nucleotide).
+ * <p>
+ * As a special case, includes BLOSUM62 as an extra option for nucleotide PCA.
+ * This is for backwards compatibility with Jalview prior to 2.8 when BLOSUM62
+ * was the only score matrix supported. This is included if property
+ * BLOSUM62_PCA_FOR_NUCLEOTIDE is set to true in the Jalview properties file.
+ *
+ * @param nucleotide
+ * @param forPca
+ * @return
+ */
+ protected static List<ScoreModelI> getApplicableScoreModels(
+ boolean nucleotide, boolean forPca)
+ {
+ List<ScoreModelI> filtered = new ArrayList<>();
+
+ ScoreModels scoreModels = ScoreModels.getInstance();
+ for (ScoreModelI sm : scoreModels.getModels())
+ {
+ if (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA())
+ {
+ filtered.add(sm);
+ }
+ }
+
+ /*
+ * special case: add BLOSUM62 as last option for nucleotide PCA,
+ * for backwards compatibility with Jalview < 2.8 (JAL-2962)
+ */
+ if (nucleotide && forPca
+ && Cache.getDefault("BLOSUM62_PCA_FOR_NUCLEOTIDE", false))
+ {
+ filtered.add(scoreModels.getBlosum62());
+ }
+
+ return filtered;
+ }
+
+ /**
* Open and calculate the selected tree or PCA on 'OK'
*/
protected void calculate_actionPerformed()
JvOptionPane.WARNING_MESSAGE);
return;
}
+
+ /*
+ * construct the panel and kick off its calculation thread
+ */
pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
+ new Thread(pcaPanel).start();
+
}
/**
*/
final String name = scheme.getSchemeName();
String label = MessageManager.getStringOrReturn(
- "label.colourScheme_" + name.toLowerCase().replace(" ", "_"),
- name);
+ "label.colourScheme_", name.toLowerCase().replace(" ", "_"));
final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
label);
radioItem.setName(name);
af.currentFileFormat = format;
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- af.statusBar.setText(MessageManager
+ af.setStatus(MessageManager
.getString("label.successfully_pasted_alignment_file"));
try
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.bin.Jalview;
+import jalview.io.BackupFiles;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatException;
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
JalviewFileChooser chooser = JalviewFileChooser
- .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+ .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, true);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
@Override
public void saveState_actionPerformed()
{
- JalviewFileChooser chooser = new JalviewFileChooser("jvp",
- "Jalview Project");
+ saveState_actionPerformed(false);
+ }
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_state"));
+ public void saveState_actionPerformed(boolean saveAs)
+ {
+ java.io.File projectFile = getProjectFile();
+ // autoSave indicates we already have a file and don't need to ask
+ boolean autoSave = projectFile != null && !saveAs
+ && BackupFiles.getEnabled();
- int value = chooser.showSaveDialog(this);
+ // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
+ // saveAs="+saveAs+", Backups
+ // "+(BackupFiles.getEnabled()?"enabled":"disabled"));
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ boolean approveSave = false;
+ if (!autoSave)
{
- final Desktop me = this;
- final java.io.File choice = chooser.getSelectedFile();
- setProjectFile(choice);
+ JalviewFileChooser chooser = new JalviewFileChooser("jvp",
+ "Jalview Project");
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager.getString("label.save_state"));
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ projectFile = chooser.getSelectedFile();
+ setProjectFile(projectFile);
+ approveSave = true;
+ }
+ }
+
+ if (approveSave || autoSave)
+ {
+ final Desktop me = this;
+ final java.io.File chosenFile = projectFile;
new Thread(new Runnable()
{
@Override
// TODO: refactor to Jalview desktop session controller action.
setProgressBar(MessageManager.formatMessage(
"label.saving_jalview_project", new Object[]
- { choice.getName() }), choice.hashCode());
+ { chosenFile.getName() }), chosenFile.hashCode());
jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- choice.getParent());
+ chosenFile.getParent());
// TODO catch and handle errors for savestate
// TODO prevent user from messing with the Desktop whilst we're saving
try
{
- new Jalview2XML().saveState(choice);
+ BackupFiles backupfiles = new BackupFiles(chosenFile);
+
+ new Jalview2XML().saveState(backupfiles.getTempFile());
+
+ backupfiles.setWriteSuccess(true);
+ backupfiles.rollBackupsAndRenameTempFile();
} catch (OutOfMemoryError oom)
{
- new OOMWarning(
- "Whilst saving current state to " + choice.getName(),
- oom);
+ new OOMWarning("Whilst saving current state to "
+ + chosenFile.getName(), oom);
} catch (Exception ex)
{
- Cache.log.error(
- "Problems whilst trying to save to " + choice.getName(),
- ex);
+ Cache.log.error("Problems whilst trying to save to "
+ + chosenFile.getName(), ex);
JvOptionPane.showMessageDialog(me,
MessageManager.formatMessage(
"label.error_whilst_saving_current_state_to",
new Object[]
- { choice.getName() }),
+ { chosenFile.getName() }),
MessageManager.getString("label.couldnt_save_project"),
JvOptionPane.WARNING_MESSAGE);
}
- setProgressBar(null, choice.hashCode());
+ setProgressBar(null, chosenFile.hashCode());
}
}).start();
}
}
+ @Override
+ public void saveAsState_actionPerformed(ActionEvent e)
+ {
+ saveState_actionPerformed(true);
+ }
+
private void setProjectFile(File choice)
{
this.projectFile = choice;
"Jalview Project (old)" };
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
- "Jalview Project");
+ "Jalview Project", true, true); // last two booleans: allFiles,
+ // allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
import jalview.api.FeatureSettingsControllerI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcher;
import jalview.datamodel.features.FeatureMatcherI;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
import javax.swing.Icon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
-import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JDialog;
import javax.swing.JInternalFrame;
import javax.swing.JTable;
import javax.swing.ListSelectionModel;
import javax.swing.SwingConstants;
+import javax.swing.border.Border;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.table.AbstractTableModel;
+import javax.swing.table.JTableHeader;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumn;
private static final int MIN_HEIGHT = 400;
+ private final static String BASE_TOOLTIP = MessageManager.getString("label.click_to_edit");
+
final FeatureRenderer fr;
public final AlignFrame af;
int selectedRow = -1;
- JButton fetchDAS = new JButton();
-
- JButton saveDAS = new JButton();
-
- JButton cancelDAS = new JButton();
-
boolean resettingTable = false;
/*
{
String tip = null;
int column = table.columnAtPoint(e.getPoint());
+ int row = table.rowAtPoint(e.getPoint());
+
switch (column)
{
case TYPE_COLUMN:
tip = JvSwingUtils.wrapTooltip(true, MessageManager
.getString("label.feature_settings_click_drag"));
break;
+ case COLOUR_COLUMN:
+ FeatureColourI colour = (FeatureColourI) table.getValueAt(row,
+ column);
+ tip = getColorTooltip(colour, true);
+ break;
case FILTER_COLUMN:
- int row = table.rowAtPoint(e.getPoint());
FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row,
column);
tip = o.isEmpty()
- ? MessageManager.getString("label.filters_tooltip")
+ ? MessageManager
+ .getString("label.configure_feature_tooltip")
: o.toString();
break;
default:
break;
}
+
return tip;
}
+
+ /**
+ * Position the tooltip near the bottom edge of, and half way across, the
+ * current cell
+ */
+ @Override
+ public Point getToolTipLocation(MouseEvent e)
+ {
+ Point point = e.getPoint();
+ int column = table.columnAtPoint(point);
+ int row = table.rowAtPoint(point);
+ Rectangle r = getCellRect(row, column, false);
+ Point loc = new Point(r.x + r.width / 2, r.y + r.height - 3);
+ return loc;
+ }
};
- table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
+ JTableHeader tableHeader = table.getTableHeader();
+ tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12));
+ tableHeader.setReorderingAllowed(false);
table.setFont(new Font("Verdana", Font.PLAIN, 12));
- // table.setDefaultRenderer(Color.class, new ColorRenderer());
- // table.setDefaultEditor(Color.class, new ColorEditor(this));
- //
table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
});
men.add(dens);
- /*
- * variable colour options include colour by label, by score,
- * by selected attribute text, or attribute value
- */
- final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
- MessageManager.getString("label.variable_colour"));
- mxcol.setSelected(!featureColour.isSimpleColour());
- men.add(mxcol);
- mxcol.addActionListener(new ActionListener()
- {
- JColorChooser colorChooser;
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (e.getSource() == mxcol)
- {
- if (featureColour.isSimpleColour())
- {
- FeatureTypeSettings fc = new FeatureTypeSettings(me.fr, type);
- fc.addActionListener(this);
- }
- else
- {
- // bring up simple color chooser
- colorChooser = new JColorChooser();
- String title = MessageManager
- .getString("label.select_colour");
- JDialog dialog = JColorChooser.createDialog(me,
- title, true, // modal
- colorChooser, this, // OK button handler
- null); // no CANCEL button handler
- colorChooser.setColor(featureColour.getMaxColour());
- dialog.setVisible(true);
- }
- }
- 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, 1);
- table.validate();
- }
- else
- {
- // probably the color chooser!
- table.setValueAt(new FeatureColour(colorChooser.getColor()),
- rowSelected, 1);
- table.validate();
- me.updateFeatureRenderer(
- ((FeatureTableModel) table.getModel()).getData(),
- false);
- }
- }
- }
-
- });
-
JMenuItem selCols = new JMenuItem(
MessageManager.getString("label.select_columns_containing"));
selCols.addActionListener(new ActionListener()
}
}
});
- help.setFont(JvSwingUtils.getLabelFont());
- help.setText(MessageManager.getString("action.help"));
- help.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- try
- {
- Help.showHelpWindow(HelpId.SequenceFeatureSettings);
- } catch (HelpSetException e1)
- {
- e1.printStackTrace();
- }
- }
- });
JButton cancel = new JButton(MessageManager.getString("action.cancel"));
cancel.setFont(JvSwingUtils.getLabelFont());
this.add(settingsPane);
}
+ /**
+ * Answers a suitable tooltip to show on the colour cell of the table
+ *
+ * @param fcol
+ * @param withHint
+ * if true include 'click to edit' and similar text
+ * @return
+ */
+ public static String getColorTooltip(FeatureColourI fcol,
+ boolean withHint)
+ {
+ if (fcol == null)
+ {
+ return null;
+ }
+ if (fcol.isSimpleColour())
+ {
+ return withHint ? BASE_TOOLTIP : null;
+ }
+ String description = fcol.getDescription();
+ description = description.replaceAll("<", "<");
+ description = description.replaceAll(">", ">");
+ StringBuilder tt = new StringBuilder(description);
+ if (withHint)
+ {
+ tt.append("<br>").append(BASE_TOOLTIP).append("</br>");
+ }
+ return JvSwingUtils.wrapTooltip(true, tt.toString());
+ }
+
+ public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
+ int w, int h)
+ {
+ boolean thr = false;
+ StringBuilder tx = new StringBuilder();
+
+ if (gcol.isColourByAttribute())
+ {
+ tx.append(FeatureMatcher
+ .toAttributeDisplayName(gcol.getAttributeName()));
+ }
+ else if (!gcol.isColourByLabel())
+ {
+ tx.append(MessageManager.getString("label.score"));
+ }
+ tx.append(" ");
+ if (gcol.isAboveThreshold())
+ {
+ thr = true;
+ tx.append(">");
+ }
+ if (gcol.isBelowThreshold())
+ {
+ thr = true;
+ tx.append("<");
+ }
+ if (gcol.isColourByLabel())
+ {
+ if (thr)
+ {
+ tx.append(" ");
+ }
+ if (!gcol.isColourByAttribute())
+ {
+ tx.append("Label");
+ }
+ comp.setIcon(null);
+ }
+ else
+ {
+ Color newColor = gcol.getMaxColour();
+ comp.setBackground(newColor);
+ // System.err.println("Width is " + w / 2);
+ Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
+ comp.setIcon(ficon);
+ // tt+="RGB value: Max (" + newColor.getRed() + ", "
+ // + newColor.getGreen() + ", " + newColor.getBlue()
+ // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
+ // + ", " + minCol.getBlue() + ")");
+ }
+ comp.setHorizontalAlignment(SwingConstants.CENTER);
+ comp.setText(tx.toString());
+ }
+
// ///////////////////////////////////////////////////////////////////////
// http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
// ///////////////////////////////////////////////////////////////////////
private String[] columnNames = {
MessageManager.getString("label.feature_type"),
MessageManager.getString("action.colour"),
- MessageManager.getString("label.filter"),
+ MessageManager.getString("label.configuration"),
MessageManager.getString("label.show") };
private Object[][] data;
class ColorRenderer extends JLabel implements TableCellRenderer
{
- javax.swing.border.Border unselectedBorder = null;
+ Border unselectedBorder = null;
- javax.swing.border.Border selectedBorder = null;
-
- final String baseTT = "Click to edit, right/apple click for menu.";
+ Border selectedBorder = null;
public ColorRenderer()
{
{
FeatureColourI cellColour = (FeatureColourI) color;
setOpaque(true);
- setToolTipText(baseTT);
setBackground(tbl.getBackground());
if (!cellColour.isSimpleColour())
{
renderGraduatedColor(comp, gcol, w, h);
}
- public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
- int w, int h)
- {
- boolean thr = false;
- StringBuilder tt = new StringBuilder();
- StringBuilder tx = new StringBuilder();
-
- if (gcol.isColourByAttribute())
- {
- tx.append(String.join(":", gcol.getAttributeName()));
- }
- else if (!gcol.isColourByLabel())
- {
- tx.append(MessageManager.getString("label.score"));
- }
- tx.append(" ");
- if (gcol.isAboveThreshold())
- {
- thr = true;
- tx.append(">");
- tt.append("Thresholded (Above ").append(gcol.getThreshold())
- .append(") ");
- }
- if (gcol.isBelowThreshold())
- {
- thr = true;
- tx.append("<");
- tt.append("Thresholded (Below ").append(gcol.getThreshold())
- .append(") ");
- }
- if (gcol.isColourByLabel())
- {
- tt.append("Coloured by label text. ").append(tt);
- if (thr)
- {
- tx.append(" ");
- }
- if (!gcol.isColourByAttribute())
- {
- tx.append("Label");
- }
- comp.setIcon(null);
- }
- else
- {
- Color newColor = gcol.getMaxColour();
- comp.setBackground(newColor);
- // System.err.println("Width is " + w / 2);
- Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
- comp.setIcon(ficon);
- // tt+="RGB value: Max (" + newColor.getRed() + ", "
- // + newColor.getGreen() + ", " + newColor.getBlue()
- // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
- // + ", " + minCol.getBlue() + ")");
- }
- comp.setHorizontalAlignment(SwingConstants.CENTER);
- comp.setText(tx.toString());
- if (tt.length() > 0)
- {
- if (comp.getToolTipText() == null)
- {
- comp.setToolTipText(tt.toString());
- }
- else
- {
- comp.setToolTipText(
- tt.append(" ").append(comp.getToolTipText()).toString());
- }
- }
- }
-
class ColorEditor extends AbstractCellEditor
implements TableCellEditor, ActionListener
{
button.setOpaque(true);
button.setBackground(me.getBackground());
button.setText(currentFilter.toString());
- button.setToolTipText(currentFilter.toString());
button.setIcon(null);
return button;
}
String title = MessageManager
.formatMessage("label.display_settings_for", new String[]
{ theType });
- initDialogFrame(this, true, false, title, 500, 500);
-
+ initDialogFrame(this, true, false, title, 580, 500);
waitForInput();
}
: BELOW_THRESHOLD_OPTION);
slider.setEnabled(true);
slider.setValue((int) (fc.getThreshold() * scaleFactor));
- thresholdValue.setText(String.valueOf(getRoundedSliderValue()));
+ thresholdValue.setText(String.valueOf(fc.getThreshold()));
thresholdValue.setEnabled(true);
thresholdIsMin.setEnabled(true);
}
maxColour.setBorder(new LineBorder(Color.black));
/*
- * default max colour to last plain colour;
- * make min colour a pale version of max colour
+ * if not set, default max colour to last plain colour,
+ * and make min colour a pale version of max colour
*/
- FeatureColourI fc = fr.getFeatureColours().get(featureType);
- Color bg = fc.getColour() == null ? Color.BLACK : fc.getColour();
- maxColour.setBackground(bg);
- minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
+ Color max = originalColour.getMaxColour();
+ if (max == null)
+ {
+ max = originalColour.getColour();
+ minColour.setBackground(ColorUtils.bleachColour(max, 0.9f));
+ }
+ else
+ {
+ maxColour.setBackground(max);
+ minColour.setBackground(originalColour.getMinColour());
+ }
noValueCombo = new JComboBox<>();
noValueCombo.addItem(MessageManager.getString("label.no_colour"));
{
thresholdValue
.setText(String.valueOf(slider.getValue() / scaleFactor));
+ thresholdValue.setBackground(Color.white); // to reset red for invalid
sliderValueChanged();
}
}
singleColour.setFont(JvSwingUtils.getLabelFont());
singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
singleColour.setPreferredSize(new Dimension(40, 20));
- if (originalColour.isGraduatedColour())
- {
- singleColour.setBackground(originalColour.getMaxColour());
- singleColour.setForeground(originalColour.getMaxColour());
- }
- else
- {
+ // if (originalColour.isGraduatedColour())
+ // {
+ // singleColour.setBackground(originalColour.getMaxColour());
+ // singleColour.setForeground(originalColour.getMaxColour());
+ // }
+ // else
+ // {
singleColour.setBackground(originalColour.getColour());
singleColour.setForeground(originalColour.getColour());
- }
+ // }
singleColour.addMouseListener(new MouseAdapter()
{
@Override
private FeatureColourI makeColourFromInputs()
{
/*
- * easiest case - a single colour
- */
- if (simpleColour.isSelected())
- {
- return new FeatureColour(singleColour.getBackground());
- }
-
- /*
- * next easiest case - colour by Label, or attribute text
- */
- if (byCategory.isSelected())
- {
- Color c = singleColour.getBackground();
- FeatureColourI fc = new FeatureColour(c);
- fc.setColourByLabel(true);
- String byWhat = (String) colourByTextCombo.getSelectedItem();
- if (!LABEL_18N.equals(byWhat))
- {
- fc.setAttributeName(
- FeatureMatcher.fromAttributeDisplayName(byWhat));
- }
- return fc;
- }
-
- /*
- * remaining case - graduated colour by score, or attribute value
+ * min-max range is to (or from) threshold value if
+ * 'threshold is min/max' is selected
*/
- Color noColour = null;
- if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
- {
- noColour = minColour.getBackground();
- }
- else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
- {
- noColour = maxColour.getBackground();
- }
float thresh = 0f;
try
{
// invalid inputs are already handled on entry
}
-
- /*
- * min-max range is to (or from) threshold value if
- * 'threshold is min/max' is selected
- */
float minValue = min;
float maxValue = max;
final int thresholdOption = threshold.getSelectedIndex();
{
maxValue = thresh;
}
+ Color noColour = null;
+ if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
+ {
+ noColour = minColour.getBackground();
+ }
+ else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
+ {
+ noColour = maxColour.getBackground();
+ }
/*
- * make the graduated colour
+ * construct a colour that 'remembers' all the options, including
+ * those not currently selected
*/
- FeatureColourI fc = new FeatureColour(minColour.getBackground(),
- maxColour.getBackground(), noColour, minValue, maxValue);
+ FeatureColourI fc = new FeatureColour(singleColour.getBackground(),
+ minColour.getBackground(), maxColour.getBackground(), noColour,
+ minValue, maxValue);
/*
+ * easiest case - a single colour
+ */
+ if (simpleColour.isSelected())
+ {
+ ((FeatureColour) fc).setGraduatedColour(false);
+ return fc;
+ }
+
+ /*
+ * next easiest case - colour by Label, or attribute text
+ */
+ if (byCategory.isSelected())
+ {
+ fc.setColourByLabel(true);
+ String byWhat = (String) colourByTextCombo.getSelectedItem();
+ if (!LABEL_18N.equals(byWhat))
+ {
+ fc.setAttributeName(
+ FeatureMatcher.fromAttributeDisplayName(byWhat));
+ }
+ return fc;
+ }
+
+ /*
+ * remaining case - graduated colour by score, or attribute value;
* set attribute to colour by if selected
*/
String byWhat = (String) colourByRangeCombo.getSelectedItem();
{
try
{
+ /*
+ * set 'adjusting' flag while moving the slider, so it
+ * doesn't then in turn change the value (with rounding)
+ */
adjusting = true;
float f = Float.parseFloat(thresholdValue.getText());
+ f = Float.max(f, this.min);
+ f = Float.min(f, this.max);
+ thresholdValue.setText(String.valueOf(f));
slider.setValue((int) (f * scaleFactor));
threshline.value = f;
thresholdValue.setBackground(Color.white); // ok
-
- /*
- * force repaint of any Overview window or structure
- */
- ap.paintAlignment(true, true);
+ adjusting = false;
+ colourChanged(true);
} catch (NumberFormatException ex)
{
thresholdValue.setBackground(Color.red); // not ok
- } finally
- {
adjusting = false;
}
}
*/
package jalview.gui;
+import jalview.api.AlignViewportI;
+import jalview.api.FinderI;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import java.awt.event.ActionEvent;
import java.awt.event.KeyEvent;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
-import java.util.Vector;
+import java.util.Map;
import java.util.regex.Pattern;
import java.util.regex.PatternSyntaxException;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.KeyStroke;
+import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
/**
*/
public class Finder extends GFinder
{
- private static final int MY_HEIGHT = 120;
+ private static final int MIN_WIDTH = 350;
- private static final int MY_WIDTH = 400;
+ private static final int MIN_HEIGHT = 120;
- AlignmentViewport av;
+ private static final int MY_HEIGHT = 120;
- AlignmentPanel ap;
+ private static final int MY_WIDTH = 400;
- private static final int MIN_WIDTH = 350;
+ private AlignViewportI av;
- private static final int MIN_HEIGHT = 120;
+ private AlignmentPanel ap;
- JInternalFrame frame;
+ private JInternalFrame frame;
- int seqIndex = 0;
+ /*
+ * Finder agent per viewport searched
+ */
+ private Map<AlignViewportI, FinderI> finders;
- int resIndex = -1;
+ private SearchResultsI searchResults;
- SearchResultsI searchResults;
+ /*
+ * true if we only search a given alignment view
+ */
+ private boolean focusfixed;
/**
- * Creates a new Finder object with no associated viewport or panel.
+ * Creates a new Finder object with no associated viewport or panel. Each Find
+ * or Find Next action will act on whichever viewport has focus at the time.
*/
public Finder()
{
this(null, null);
- focusfixed = false;
}
/**
{
av = viewport;
ap = alignPanel;
- focusfixed = true;
+ finders = new HashMap<>();
+ focusfixed = viewport != null;
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(
- new javax.swing.event.InternalFrameAdapter()
+ new InternalFrameAdapter()
{
@Override
public void internalFrameClosing(InternalFrameEvent e)
}
/**
- * Performs the 'Find Next' action.
- *
- * @param e
+ * Performs the 'Find Next' action on the alignment panel with focus
*/
@Override
- public void findNext_actionPerformed(ActionEvent e)
+ public void findNext_actionPerformed()
{
if (getFocusedViewport())
{
}
/**
- * Performs the 'Find All' action.
- *
- * @param e
+ * Performs the 'Find All' action on the alignment panel with focus
*/
@Override
- public void findAll_actionPerformed(ActionEvent e)
+ public void findAll_actionPerformed()
{
if (getFocusedViewport())
{
- resIndex = -1;
- seqIndex = 0;
doSearch(true);
}
}
/**
- * do we only search a given alignment view ?
- */
- private boolean focusfixed;
-
- /**
* if !focusfixed and not in a desktop environment, checks that av and ap are
* valid. Otherwise, gets the topmost alignment window and sets av and ap
* accordingly
for (int f = 0; f < frames.length; f++)
{
JInternalFrame alignFrame = frames[f];
- if (alignFrame != null && alignFrame instanceof AlignFrame)
+ if (alignFrame != null && alignFrame instanceof AlignFrame
+ && !alignFrame.isIcon())
{
av = ((AlignFrame) alignFrame).viewport;
ap = ((AlignFrame) alignFrame).alignPanel;
@Override
public void createFeatures_actionPerformed()
{
- List<SequenceI> seqs = new ArrayList<SequenceI>();
- List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
String searchString = searchBox.getEditor().getItem().toString().trim();
String desc = "Search Results";
// other stuff
// TODO: add switches to control what is searched - sequences, IDS,
// descriptions, features
- jalview.analysis.Finder finder = new jalview.analysis.Finder(
- av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
- finder.setCaseSensitive(caseSensitive.isSelected());
- finder.setIncludeDescription(searchDescription.isSelected());
-
- finder.setFindAll(doFindAll);
-
- finder.find(searchString); // returns true if anything was actually found
-
- seqIndex = finder.getSeqIndex();
- resIndex = finder.getResIndex();
+ FinderI finder = finders.get(av);
+ if (finder == null)
+ {
+ /*
+ * first time we've searched this viewport
+ */
+ finder = new jalview.analysis.Finder(av);
+ finders.put(av, finder);
+ }
- searchResults = finder.getSearchResults(); // find(regex,
- // caseSensitive.isSelected(), )
- Vector<SequenceI> idMatch = finder.getIdMatch();
- boolean haveResults = false;
- // set or reset the GUI
- if ((idMatch.size() > 0))
+ boolean isCaseSensitive = caseSensitive.isSelected();
+ boolean doSearchDescription = searchDescription.isSelected();
+ if (doFindAll)
{
- haveResults = true;
- ap.getIdPanel().highlightSearchResults(idMatch);
+ finder.findAll(searchString, isCaseSensitive, doSearchDescription);
}
else
{
- ap.getIdPanel().highlightSearchResults(null);
+ finder.findNext(searchString, isCaseSensitive, doSearchDescription);
}
- if (searchResults.getSize() > 0)
+ searchResults = finder.getSearchResults();
+ List<SequenceI> idMatch = finder.getIdMatches();
+ ap.getIdPanel().highlightSearchResults(idMatch);
+
+ if (searchResults.isEmpty())
{
- haveResults = true;
- createFeatures.setEnabled(true);
+ searchResults = null;
}
else
{
- searchResults = null;
+ createFeatures.setEnabled(true);
}
- // if allResults is null, this effectively switches displaySearch flag in
- // seqCanvas
ap.highlightSearchResults(searchResults);
// TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
// 'SelectRegion' selection
- if (!haveResults)
+ if (idMatch.isEmpty() && searchResults == null)
{
JvOptionPane.showInternalMessageDialog(this,
MessageManager.getString("label.finished_searching"), null,
JvOptionPane.INFORMATION_MESSAGE);
- resIndex = -1;
- seqIndex = 0;
}
else
{
}
JvOptionPane.showInternalMessageDialog(this, message, null,
JvOptionPane.INFORMATION_MESSAGE);
- resIndex = -1;
- seqIndex = 0;
}
}
searchBox.updateCache();
*/
package jalview.gui;
+import java.awt.Point;
import java.net.URL;
import javax.help.BadIDException;
import javax.help.HelpSetException;
/**
- * Utility class to show the help documentation window.
+ * Utility class to show the help documentation window
*
* @author gmcarstairs
- *
*/
public class Help
{
public enum HelpId
{
Home("home"), SequenceFeatureSettings("seqfeatures.settings"),
- StructureViewer("viewingpdbs");
+ StructureViewer("viewingpdbs"), PdbFts("pdbfts"),
+ UniprotFts("uniprotfts");
private String id;
}
}
- private static final long HALF_A_MO = 500; // half a second
-
- private static long lastOpenedTime = 0L;
+ private static HelpBroker hb;
/**
* Not instantiable
}
/**
- * Show help text in a new window. But do nothing if within half a second of
- * the last invocation.
- *
- * This is a workaround for issue JAL-914 - both Desktop and AlignFrame
- * responding to F1 key, resulting in duplicate help windows opened.
+ * Shows the help window, at the entry specified by the given helpId
*
* @param id
- * TODO
*
* @throws HelpSetException
*/
public static void showHelpWindow(HelpId id) throws HelpSetException
{
- long timeNow = System.currentTimeMillis();
+ ClassLoader cl = Desktop.class.getClassLoader();
+ URL url = HelpSet.findHelpSet(cl, "help/help"); // $NON-NLS-$
+ HelpSet hs = new HelpSet(cl, url);
- if (timeNow - lastOpenedTime > HALF_A_MO)
+ if (hb == null)
{
- lastOpenedTime = timeNow;
- ClassLoader cl = Desktop.class.getClassLoader();
- URL url = HelpSet.findHelpSet(cl, "help/help"); // $NON-NLS-$
- HelpSet hs = new HelpSet(cl, url);
+ /*
+ * create help broker first time (only)
+ */
+ hb = hs.createHelpBroker();
+ }
- HelpBroker hb = hs.createHelpBroker();
- try
- {
- hb.setCurrentID(id.toString());
- } catch (BadIDException bad)
- {
- System.out.println("Bad help link: " + id.toString()
- + ": must match a target in help.jhm");
- throw bad;
- }
- hb.setDisplayed(true);
+ try
+ {
+ hb.setCurrentID(id.toString());
+ } catch (BadIDException bad)
+ {
+ System.out.println("Bad help link: " + id.toString()
+ + ": must match a target in help.jhm");
+ throw bad;
}
+
+ /*
+ * set Help visible - at its current location if it is already shown,
+ * else at a location as determined by the window manager
+ */
+ Point p = hb.getLocation();
+ hb.setLocation(p);
+ hb.setDisplayed(true);
}
+ /**
+ * Show the Help window at the root entry
+ *
+ * @throws HelpSetException
+ */
public static void showHelpWindow() throws HelpSetException
{
showHelpWindow(HelpId.Home);
int alignmentWidth = alignViewport.getAlignment().getWidth();
final int alheight = alignViewport.getAlignment().getHeight();
- if (alignViewport.hasHiddenColumns())
- {
- alignmentWidth = alignViewport.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(alignmentWidth) - 1;
- }
-
int annotationHeight = 0;
AnnotationLabels labels = null;
*/
package jalview.gui;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.SeqPanel.MousePos;
import jalview.io.SequenceAnnotationReport;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import java.awt.BorderLayout;
import java.awt.event.MouseEvent;
import java.util.List;
import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
}
/**
- * Respond to mouse movement by constructing tooltip text for the sequence id
- * under the mouse.
+ * Responds to mouse movement by setting tooltip text for the sequence id
+ * under the mouse (or possibly annotation label, when in wrapped mode)
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseMoved(MouseEvent e)
{
SeqPanel sp = alignPanel.getSeqPanel();
- int seq = Math.max(0, sp.findSeq(e));
- if (seq > -1 && seq < av.getAlignment().getHeight())
+ MousePos pos = sp.findMousePosition(e);
+ if (pos.isOverAnnotation())
+ {
+ /*
+ * mouse is over an annotation label in wrapped mode
+ */
+ AlignmentAnnotation[] anns = av.getAlignment()
+ .getAlignmentAnnotation();
+ AlignmentAnnotation annotation = anns[pos.annotationIndex];
+ setToolTipText(AnnotationLabels.getTooltip(annotation));
+ alignPanel.alignFrame.setStatus(
+ AnnotationLabels.getStatusMessage(annotation, anns));
+ }
+ else
{
- SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- StringBuilder tip = new StringBuilder(64);
- seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
- av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr);
- setToolTipText(JvSwingUtils.wrapTooltip(true,
- sequence.getDisplayId(true) + " " + tip.toString()));
+ int seq = Math.max(0, pos.seqIndex);
+ if (seq < av.getAlignment().getHeight())
+ {
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+ StringBuilder tip = new StringBuilder(64);
+ tip.append(sequence.getDisplayId(true)).append(" ");
+ seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
+ av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr);
+ setToolTipText(JvSwingUtils.wrapTooltip(true, tip.toString()));
+
+ StringBuilder text = new StringBuilder();
+ text.append("Sequence ").append(String.valueOf(seq + 1))
+ .append(" ID: ")
+ .append(sequence.getName());
+ alignPanel.alignFrame.setStatus(text.toString());
+ }
}
}
{
mouseDragging = true;
- int seq = Math.max(0, alignPanel.getSeqPanel().findSeq(e));
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+ if (pos.isOverAnnotation())
+ {
+ // mouse is over annotation label in wrapped mode
+ return;
+ }
+
+ int seq = Math.max(0, pos.seqIndex);
if (seq < lastid)
{
return;
}
- int seq = alignPanel.getSeqPanel().findSeq(e);
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+ int seq = pos.seqIndex;
+ if (pos.isOverAnnotation() || seq < 0)
+ {
+ return;
+ }
+
String id = av.getAlignment().getSequenceAt(seq).getName();
String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id);
{
if (scrollThread != null)
{
- scrollThread.running = false;
+ scrollThread.stopScrolling();
}
}
return;
}
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+
if (e.isPopupTrigger()) // Mac reports this in mousePressed
{
- showPopupMenu(e);
+ showPopupMenu(e, pos);
return;
}
av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
}
- int seq = alignPanel.getSeqPanel().findSeq(e);
if (e.isShiftDown() && (lastid != -1))
{
- selectSeqs(lastid, seq);
+ selectSeqs(lastid, pos.seqIndex);
}
else
{
- selectSeq(seq);
+ selectSeq(pos.seqIndex);
}
av.isSelectionGroupChanged(true);
*
* @param e
*/
- void showPopupMenu(MouseEvent e)
+ void showPopupMenu(MouseEvent e, MousePos pos)
{
- int seq2 = alignPanel.getSeqPanel().findSeq(e);
- Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
+ if (pos.isOverAnnotation())
+ {
+ showAnnotationMenu(e, pos);
+ return;
+ }
+
+ Sequence sq = (Sequence) av.getAlignment().getSequenceAt(pos.seqIndex);
/*
* build a new links menu based on the current links
* and any non-positional features
*/
+ List<SequenceFeature> features = null;
+ if (sq != null)
+ {
List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
- List<SequenceFeature> features = sq.getFeatures().getNonPositionalFeatures();
+ features = sq.getFeatures().getNonPositionalFeatures();
for (SequenceFeature sf : features)
{
if (sf.links != null)
{
- for (String link : sf.links)
- {
- nlinks.add(link);
- }
+ nlinks.addAll(sf.links);
}
}
+ }
PopupMenu pop = new PopupMenu(alignPanel, sq, features,
Preferences.getGroupURLLinks());
}
/**
+ * On right mouse click on a Consensus annotation label, shows a limited popup
+ * menu, with options to configure the consensus calculation and rendering.
+ *
+ * @param e
+ * @param pos
+ * @see AnnotationLabels#showPopupMenu(MouseEvent)
+ */
+ void showAnnotationMenu(MouseEvent e, MousePos pos)
+ {
+ if (pos.annotationIndex == -1)
+ {
+ return;
+ }
+ AlignmentAnnotation[] anns = this.av.getAlignment()
+ .getAlignmentAnnotation();
+ if (anns == null || pos.annotationIndex >= anns.length)
+ {
+ return;
+ }
+ AlignmentAnnotation ann = anns[pos.annotationIndex];
+ if (!ann.label.contains("Consensus"))
+ {
+ return;
+ }
+
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.annotations"));
+ AnnotationLabels.addConsensusMenuOptions(this.alignPanel, ann, pop);
+ pop.show(this, e.getX(), e.getY());
+ }
+
+ /**
* Toggle whether the sequence is part of the current selection group.
*
* @param seq
lastid = seq;
SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
- av.getSelectionGroup().addOrRemove(pickedSeq, true);
+ av.getSelectionGroup().addOrRemove(pickedSeq, false);
}
/**
for (int i = start; i <= end; i++)
{
av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
- i == end);
+ false);
}
}
{
if (scrollThread != null)
{
- scrollThread.running = false;
+ scrollThread.stopScrolling();
}
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
mouseDragging = false;
PaintRefresher.Refresh(this, av.getSequenceSetId());
if (e.isPopupTrigger()) // Windows reports this in mouseReleased
{
- showPopupMenu(e);
+ showPopupMenu(e, pos);
}
}
{
getIdCanvas().setHighlighted(list);
- if (list == null)
+ if (list == null || list.isEmpty())
{
return;
}
this.idCanvas = idCanvas;
}
- // this class allows scrolling off the bottom of the visible alignment
+ /**
+ * Performs scrolling of the visible alignment up or down, adding newly
+ * visible sequences to the current selection
+ */
class ScrollThread extends Thread
{
- boolean running = false;
+ private boolean running = false;
- boolean up = true;
+ private boolean up;
+ /**
+ * Constructor for a thread that scrolls either up or down
+ *
+ * @param up
+ */
public ScrollThread(boolean up)
{
this.up = up;
+ setName("IdPanel$ScrollThread$" + String.valueOf(up));
start();
}
+ /**
+ * Sets a flag to stop the scrolling
+ */
public void stopScrolling()
{
running = false;
}
+ /**
+ * Scrolls the alignment either up or down, one row at a time, adding newly
+ * visible sequences to the current selection. Speed is limited to a maximum
+ * of ten rows per second. The thread exits when the end of the alignment is
+ * reached or a flag is set to stop it.
+ */
@Override
public void run()
{
while (running)
{
- if (av.getRanges().scrollUp(up))
+ ViewportRanges ranges = IdPanel.this.av.getRanges();
+ if (ranges.scrollUp(up))
{
- // scroll was ok, so add new sequence to selection
- int seq = av.getRanges().getStartSeq();
-
- if (!up)
- {
- seq = av.getRanges().getEndSeq();
- }
-
- if (seq < lastid)
- {
- selectSeqs(lastid - 1, seq);
- }
- else if (seq > lastid)
- {
- selectSeqs(lastid + 1, seq);
- }
-
- lastid = seq;
+ int toSeq = up ? ranges.getStartSeq() : ranges.getEndSeq();
+ int fromSeq = toSeq < lastid ? lastid - 1 : lastid + 1;
+ IdPanel.this.selectSeqs(fromSeq, toSeq);
+
+ lastid = toSeq;
}
else
{
+ /*
+ * scroll did nothing - reached limit of visible alignment
+ */
running = false;
}
--- /dev/null
+package jalview.gui;
+
+import java.awt.Font;
+import java.awt.event.ActionListener;
+
+import javax.swing.AbstractButton;
+import javax.swing.ButtonGroup;
+import javax.swing.JRadioButton;
+
+public class JalviewBooleanRadioButtons extends AbstractButton
+{
+ private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
+
+ private ButtonGroup buttonGroup = new ButtonGroup();
+
+ private JRadioButton buttonTrue = new JRadioButton();
+
+ private JRadioButton buttonFalse = new JRadioButton();
+
+ public JalviewBooleanRadioButtons(boolean value, String trueLabel,
+ String falseLabel)
+ {
+ init();
+ this.setLabels(trueLabel, falseLabel);
+ }
+
+ public JalviewBooleanRadioButtons(boolean value)
+ {
+ init();
+ setSelected(value);
+ }
+
+ public JalviewBooleanRadioButtons()
+ {
+ init();
+ }
+
+ protected void init()
+ {
+ buttonTrue.setFont(LABEL_FONT);
+ buttonFalse.setFont(LABEL_FONT);
+ buttonGroup.add(buttonTrue);
+ buttonGroup.add(buttonFalse);
+ }
+
+ public void setLabels(String trueLabel, String falseLabel)
+ {
+ buttonTrue.setText(trueLabel);
+ buttonFalse.setText(falseLabel);
+ }
+
+ @Override
+ public void setSelected(boolean b)
+ {
+ buttonFalse.setSelected(!b);
+ // this should probably happen automatically, no harm in forcing the issue!
+ // setting them this way round so the last setSelected is on buttonTrue
+ buttonTrue.setSelected(b);
+ }
+
+ @Override
+ public boolean isSelected()
+ {
+ // unambiguous selection
+ return buttonTrue.isSelected() && !buttonFalse.isSelected();
+ }
+
+ @Override
+ public void setEnabled(boolean b)
+ {
+ buttonTrue.setEnabled(b);
+ buttonFalse.setEnabled(b);
+ }
+
+ @Override
+ public boolean isEnabled()
+ {
+ return buttonTrue.isEnabled() && buttonFalse.isEnabled();
+ }
+
+ public JRadioButton getTrueButton()
+ {
+ return buttonTrue;
+ }
+
+ public JRadioButton getFalseButton()
+ {
+ return buttonFalse;
+ }
+
+ @Override
+ public void addActionListener(ActionListener l)
+ {
+ buttonTrue.addActionListener(l);
+ buttonFalse.addActionListener(l);
+ }
+
+ public void addTrueActionListener(ActionListener l)
+ {
+ buttonTrue.addActionListener(l);
+ }
+
+ public void addFalseActionListener(ActionListener l)
+ {
+ buttonFalse.addActionListener(l);
+ }
+}
public void dispose()
{
dispose = true;
+ od = null;
synchronized (this)
{
restart = true;
this.ap = alPanel;
showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
- true);
+ false);
if (showHidden)
{
od = new OverviewDimensionsShowHidden(av.getRanges(),
// without this the overview window does not size to fit the overview canvas
setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
-
+
addComponentListener(new ComponentAdapter()
{
@Override
@Override
public void mouseMoved(MouseEvent evt)
{
- if (!draggingBox)
- // don't bother changing the cursor if we're dragging the box
- // as we can't have moved inside or out of the box in that case
+ if (od.isPositionInBox(evt.getX(), evt.getY()))
{
- if (od.isPositionInBox(evt.getX(), evt.getY()))
- {
- // display drag cursor at mouse position
- setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
- }
- else
- {
- // reset cursor
- setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
- }
+ /*
+ * using HAND_CURSOR rather than DRAG_CURSOR
+ * as the latter is not supported on Mac
+ */
+ getParent().setCursor(
+ Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ }
+ else
+ {
+ // reset cursor
+ getParent().setCursor(
+ Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR));
}
}
+
});
addMouseListener(new MouseAdapter()
od.updateViewportFromMouse(evt.getX(), evt.getY(),
av.getAlignment().getHiddenSequences(),
av.getAlignment().getHiddenColumns());
+ getParent().setCursor(
+ Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
}
else
{
package jalview.gui;
import jalview.analysis.scoremodels.ScoreModels;
-import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.AlignViewportI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GPCAPanel;
+import jalview.math.RotatableMatrix.Axis;
+import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.PCAModel;
import java.awt.print.PrinterJob;
import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JMenuItem;
import javax.swing.JRadioButtonMenuItem;
import javax.swing.event.InternalFrameEvent;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * The panel holding the Principal Component Analysis 3-D visualisation
*/
public class PCAPanel extends GPCAPanel
implements Runnable, IProgressIndicator
{
+ private static final int MIN_WIDTH = 470;
- private IProgressIndicator progressBar;
+ private static final int MIN_HEIGHT = 250;
- RotatableCanvas rc;
+ private RotatableCanvas rc;
AlignmentPanel ap;
AlignmentViewport av;
- PCAModel pcaModel;
+ private PCAModel pcaModel;
- private static final int MIN_WIDTH = 470;
-
- private static final int MIN_HEIGHT = 250;
+ private int top = 0;
- int top = 0;
+ private IProgressIndicator progressBar;
private boolean working;
/**
- * Creates a new PCAPanel object using default score model and parameters
- *
- * @param alignPanel
- */
- public PCAPanel(AlignmentPanel alignPanel)
- {
- this(alignPanel,
- ScoreModels.getInstance()
- .getDefaultModel(
- !alignPanel.av.getAlignment().isNucleotide())
- .getName(),
- SimilarityParams.SeqSpace);
- }
-
- /**
* Constructor given sequence data, a similarity (or distance) score model
* name, and score calculation parameters
*
ScoreModelI scoreModel = ScoreModels.getInstance()
.getScoreModel(modelName, ap);
- pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
- params);
+ setPcaModel(new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
+ params));
PaintRefresher.Register(this, av.getSequenceSetId());
- rc = new RotatableCanvas(alignPanel);
- this.getContentPane().add(rc, BorderLayout.CENTER);
- Thread worker = new Thread(this);
- worker.start();
+ setRotatableCanvas(new RotatableCanvas(alignPanel));
+ this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER);
+
+ addKeyListener(getRotatableCanvas());
+ validate();
+
+ this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
}
/**
*/
protected void close_actionPerformed()
{
- pcaModel = null;
- }
-
- /**
- * Repopulate the options and actions under the score model menu when it is
- * selected. Options will depend on whether 'nucleotide' or 'peptide'
- * modelling is selected (and also possibly on whether any additional score
- * models have been added).
- */
- @Override
- protected void scoreModel_menuSelected()
- {
- scoreModelMenu.removeAll();
- for (final ScoreModelI sm : ScoreModels.getInstance().getModels())
- {
- final String name = sm.getName();
- JCheckBoxMenuItem jm = new JCheckBoxMenuItem(name);
-
- /*
- * if the score model doesn't provide a description, try to look one
- * up in the text bundle, falling back on its name
- */
- String tooltip = sm.getDescription();
- if (tooltip == null)
- {
- tooltip = MessageManager.getStringOrReturn("label.score_model_",
- name);
- }
- jm.setToolTipText(tooltip);
- jm.setSelected(pcaModel.getScoreModelName().equals(name));
- if ((pcaModel.isNucleotide() && sm.isDNA())
- || (!pcaModel.isNucleotide() && sm.isProtein()))
- {
- jm.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (!pcaModel.getScoreModelName().equals(name))
- {
- ScoreModelI sm2 = ScoreModels.getInstance()
- .getScoreModel(name, ap);
- pcaModel.setScoreModel(sm2);
- Thread worker = new Thread(PCAPanel.this);
- worker.start();
- }
- }
- });
- scoreModelMenu.add(jm);
- }
- }
+ setPcaModel(null);
}
@Override
- public void bgcolour_actionPerformed(ActionEvent e)
+ protected void bgcolour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
MessageManager.getString("label.select_background_colour"),
- rc.bgColour);
+ getRotatableCanvas().getBgColour());
if (col != null)
{
- rc.bgColour = col;
+ getRotatableCanvas().setBgColour(col);
}
- rc.repaint();
+ getRotatableCanvas().repaint();
}
/**
- * DOCUMENT ME!
+ * Calculates the PCA and displays the results
*/
@Override
public void run()
{
+ working = true;
long progId = System.currentTimeMillis();
IProgressIndicator progress = this;
String message = MessageManager.getString("label.pca_recalculating");
message = MessageManager.getString("label.pca_calculating");
}
progress.setProgressBar(message, progId);
- working = true;
try
{
- calcSettings.setEnabled(false);
- pcaModel.run();
- // ////////////////
+ getPcaModel().calculate();
+
xCombobox.setSelectedIndex(0);
yCombobox.setSelectedIndex(1);
zCombobox.setSelectedIndex(2);
- pcaModel.updateRc(rc);
+ getPcaModel().updateRc(getRotatableCanvas());
// rc.invalidate();
- nuclSetting.setSelected(pcaModel.isNucleotide());
- protSetting.setSelected(!pcaModel.isNucleotide());
- top = pcaModel.getTop();
+ setTop(getPcaModel().getTop());
} catch (OutOfMemoryError er)
{
{
progress.setProgressBar("", progId);
}
- calcSettings.setEnabled(true);
+
repaint();
if (getParent() == null)
{
- addKeyListener(rc);
- Desktop.addInternalFrame(this, MessageManager
- .getString("label.principal_component_analysis"), 475, 450);
- this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+ Desktop.addInternalFrame(this,
+ MessageManager.formatMessage("label.calc_title", "PCA",
+ getPcaModel().getScoreModelName()),
+ 475, 450);
}
working = false;
}
- @Override
- protected void nuclSetting_actionPerfomed(ActionEvent arg0)
- {
- if (!pcaModel.isNucleotide())
- {
- pcaModel.setNucleotide(true);
- pcaModel.setScoreModel(
- ScoreModels.getInstance().getDefaultModel(false));
- Thread worker = new Thread(this);
- worker.start();
- }
-
- }
-
- @Override
- protected void protSetting_actionPerfomed(ActionEvent arg0)
- {
-
- if (pcaModel.isNucleotide())
- {
- pcaModel.setNucleotide(false);
- pcaModel.setScoreModel(
- ScoreModels.getInstance().getDefaultModel(true));
- Thread worker = new Thread(this);
- worker.start();
- }
- }
-
/**
- * DOCUMENT ME!
+ * Updates the PCA display after a change of component to use for x, y or z
+ * axis
*/
- void doDimensionChange()
+ @Override
+ protected void doDimensionChange()
{
- if (top == 0)
+ if (getTop() == 0)
{
return;
}
- int dim1 = top - xCombobox.getSelectedIndex();
- int dim2 = top - yCombobox.getSelectedIndex();
- int dim3 = top - zCombobox.getSelectedIndex();
- pcaModel.updateRcView(dim1, dim2, dim3);
- rc.img = null;
- rc.rotmat.setIdentity();
- rc.initAxes();
- rc.paint(rc.getGraphics());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void xCombobox_actionPerformed(ActionEvent e)
- {
- doDimensionChange();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void yCombobox_actionPerformed(ActionEvent e)
- {
- doDimensionChange();
+ int dim1 = getTop() - xCombobox.getSelectedIndex();
+ int dim2 = getTop() - yCombobox.getSelectedIndex();
+ int dim3 = getTop() - zCombobox.getSelectedIndex();
+ getPcaModel().updateRcView(dim1, dim2, dim3);
+ getRotatableCanvas().resetView();
}
/**
- * DOCUMENT ME!
+ * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for
+ * the given axis (X/Y/Z)
*
- * @param e
- * DOCUMENT ME!
+ * @param index
+ * @param axis
*/
- @Override
- protected void zCombobox_actionPerformed(ActionEvent e)
+ public void setSelectedDimensionIndex(int index, Axis axis)
{
- doDimensionChange();
+ switch (axis)
+ {
+ case X:
+ xCombobox.setSelectedIndex(index);
+ break;
+ case Y:
+ yCombobox.setSelectedIndex(index);
+ break;
+ case Z:
+ zCombobox.setSelectedIndex(index);
+ break;
+ default:
+ }
}
@Override
- public void outputValues_actionPerformed(ActionEvent e)
+ protected void outputValues_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
{
- cap.setText(pcaModel.getDetails());
+ cap.setText(getPcaModel().getDetails());
Desktop.addInternalFrame(cap,
MessageManager.getString("label.pca_details"), 500, 500);
} catch (OutOfMemoryError oom)
}
@Override
- public void showLabels_actionPerformed(ActionEvent e)
+ protected void showLabels_actionPerformed()
{
- rc.showLabels(showLabels.getState());
+ getRotatableCanvas().showLabels(showLabels.getState());
}
@Override
- public void print_actionPerformed(ActionEvent e)
+ protected void print_actionPerformed()
{
PCAPrinter printer = new PCAPrinter();
printer.start();
}
+ /**
+ * If available, shows the data which formed the inputs for the PCA as a new
+ * alignment
+ */
@Override
- public void originalSeqData_actionPerformed(ActionEvent e)
+ public void originalSeqData_actionPerformed()
{
- // this was cut'n'pasted from the equivalent TreePanel method - we should
- // make this an abstract function of all jalview analysis windows
- if (pcaModel.getSeqtrings() == null)
+ // JAL-2647 disabled after load from project (until save to project done)
+ if (getPcaModel().getInputData() == null)
{
- jalview.bin.Cache.log.info(
+ Cache.log.info(
"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
// decide if av alignment is sufficiently different to original data to
// warrant a new window to be created
- // create new alignmnt window with hidden regions (unhiding hidden regions
+ // create new alignment window with hidden regions (unhiding hidden regions
// yields unaligned seqs)
// or create a selection box around columns in alignment view
// test Alignment(SeqCigar[])
} catch (Exception ex)
{
}
- ;
- Object[] alAndColsel = pcaModel.getSeqtrings()
+
+ Object[] alAndColsel = getPcaModel().getInputData()
.getAlignmentAndHiddenColumns(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
- rc.drawBackground(pg, rc.bgColour);
- rc.drawScene(pg);
- if (rc.drawAxes == true)
+ getRotatableCanvas().drawBackground(pg);
+ getRotatableCanvas().drawScene(pg);
+ if (getRotatableCanvas().drawAxes)
{
- rc.drawAxes(pg);
+ getRotatableCanvas().drawAxes(pg);
}
if (pi == 0)
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Handler for 'Save as EPS' option
*/
@Override
- public void eps_actionPerformed(ActionEvent e)
+ protected void eps_actionPerformed()
{
- makePCAImage(jalview.util.ImageMaker.TYPE.EPS);
+ makePCAImage(ImageMaker.TYPE.EPS);
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Handler for 'Save as PNG' option
*/
@Override
- public void png_actionPerformed(ActionEvent e)
+ protected void png_actionPerformed()
{
- makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
+ makePCAImage(ImageMaker.TYPE.PNG);
}
- void makePCAImage(jalview.util.ImageMaker.TYPE type)
+ void makePCAImage(ImageMaker.TYPE type)
{
- int width = rc.getWidth();
- int height = rc.getHeight();
-
- jalview.util.ImageMaker im;
-
- if (type == jalview.util.ImageMaker.TYPE.PNG)
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA",
- width, height, null, null, null, 0, false);
- }
- else if (type == jalview.util.ImageMaker.TYPE.EPS)
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA",
- width, height, null, this.getTitle(), null, 0, false);
- }
- else
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
- width, height, null, this.getTitle(), null, 0, false);
-
+ int width = getRotatableCanvas().getWidth();
+ int height = getRotatableCanvas().getHeight();
+
+ ImageMaker im;
+
+ switch (type)
+ {
+ case PNG:
+ im = new ImageMaker(this, ImageMaker.TYPE.PNG,
+ "Make PNG image from PCA", width, height, null, null, null, 0,
+ false);
+ break;
+ case EPS:
+ im = new ImageMaker(this, ImageMaker.TYPE.EPS,
+ "Make EPS file from PCA", width, height, null,
+ this.getTitle(), null, 0, false);
+ break;
+ default:
+ im = new ImageMaker(this, ImageMaker.TYPE.SVG,
+ "Make SVG file from PCA", width, height, null,
+ this.getTitle(), null, 0, false);
}
if (im.getGraphics() != null)
{
- rc.drawBackground(im.getGraphics(), Color.black);
- rc.drawScene(im.getGraphics());
- if (rc.drawAxes == true)
+ getRotatableCanvas().drawBackground(im.getGraphics());
+ getRotatableCanvas().drawScene(im.getGraphics());
+ if (getRotatableCanvas().drawAxes)
{
- rc.drawAxes(im.getGraphics());
+ getRotatableCanvas().drawAxes(im.getGraphics());
}
im.writeImage();
}
}
@Override
- public void viewMenu_menuSelected()
+ protected void viewMenu_menuSelected()
{
buildAssociatedViewMenu();
}
+ /**
+ * Builds the menu showing the choice of possible views (for the associated
+ * sequence data) to which the PCA may be linked
+ */
void buildAssociatedViewMenu()
{
AlignmentPanel[] aps = PaintRefresher
.getAssociatedPanels(av.getSequenceSetId());
- if (aps.length == 1 && rc.av == aps[0].av)
+ if (aps.length == 1 && getRotatableCanvas().av == aps[0].av)
{
associateViewsMenu.setVisible(false);
return;
JRadioButtonMenuItem item;
ButtonGroup buttonGroup = new ButtonGroup();
- int i, iSize = aps.length;
- final PCAPanel thisPCAPanel = this;
- for (i = 0; i < iSize; i++)
+ int iSize = aps.length;
+
+ for (int i = 0; i < iSize; i++)
{
- final AlignmentPanel ap = aps[i];
- item = new JRadioButtonMenuItem(ap.av.getViewName(), ap.av == rc.av);
+ final AlignmentPanel panel = aps[i];
+ item = new JRadioButtonMenuItem(panel.av.getViewName(),
+ panel.av == getRotatableCanvas().av);
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent evt)
{
- rc.applyToAllViews = false;
- rc.av = ap.av;
- rc.ap = ap;
- PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
+ selectAssociatedView(panel);
}
});
buttonGroup.add(itemf);
- itemf.setSelected(rc.applyToAllViews);
+ itemf.setSelected(getRotatableCanvas().isApplyToAllViews());
itemf.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent evt)
{
- rc.applyToAllViews = itemf.isSelected();
+ getRotatableCanvas().setApplyToAllViews(itemf.isSelected());
}
});
associateViewsMenu.add(itemf);
* )
*/
@Override
- protected void outputPoints_actionPerformed(ActionEvent e)
+ protected void outputPoints_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
{
- cap.setText(pcaModel.getPointsasCsv(false,
+ cap.setText(getPcaModel().getPointsasCsv(false,
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
Desktop.addInternalFrame(cap, MessageManager
* .ActionEvent)
*/
@Override
- protected void outputProjPoints_actionPerformed(ActionEvent e)
+ protected void outputProjPoints_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
{
- cap.setText(pcaModel.getPointsasCsv(true,
+ cap.setText(getPcaModel().getPointsasCsv(true,
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
}
@Override
- protected void resetButton_actionPerformed(ActionEvent e)
+ protected void resetButton_actionPerformed()
{
- int t = top;
- top = 0; // ugly - prevents dimensionChanged events from being processed
+ int t = getTop();
+ setTop(0); // ugly - prevents dimensionChanged events from being processed
xCombobox.setSelectedIndex(0);
yCombobox.setSelectedIndex(1);
- top = t;
+ setTop(t);
zCombobox.setSelectedIndex(2);
}
{
return working;
}
+
+ /**
+ * Answers the selected checkbox item index for PCA dimension for the X, Y or
+ * Z axis of the display
+ *
+ * @param axis
+ * @return
+ */
+ public int getSelectedDimensionIndex(Axis axis)
+ {
+ switch (axis)
+ {
+ case X:
+ return xCombobox.getSelectedIndex();
+ case Y:
+ return yCombobox.getSelectedIndex();
+ default:
+ return zCombobox.getSelectedIndex();
+ }
+ }
+
+ public void setShowLabels(boolean show)
+ {
+ showLabels.setSelected(show);
+ }
+
+ /**
+ * Sets the input data used to calculate the PCA. This is provided for
+ * 'restore from project', which does not currently support this (AL-2647), so
+ * sets the value to null, and hides the menu option for "Input Data...". J
+ *
+ * @param data
+ */
+ public void setInputData(AlignmentView data)
+ {
+ getPcaModel().setInputData(data);
+ originalSeqData.setVisible(data != null);
+ }
+
+ public AlignViewportI getAlignViewport()
+ {
+ return av;
+ }
+
+ public PCAModel getPcaModel()
+ {
+ return pcaModel;
+ }
+
+ public void setPcaModel(PCAModel pcaModel)
+ {
+ this.pcaModel = pcaModel;
+ }
+
+ public RotatableCanvas getRotatableCanvas()
+ {
+ return rc;
+ }
+
+ public void setRotatableCanvas(RotatableCanvas rc)
+ {
+ this.rc = rc;
+ }
+
+ public int getTop()
+ {
+ return top;
+ }
+
+ public void setTop(int top)
+ {
+ this.top = top;
+ }
+
+ /**
+ * set the associated view for this PCA.
+ *
+ * @param panel
+ */
+ public void selectAssociatedView(AlignmentPanel panel)
+ {
+ getRotatableCanvas().setApplyToAllViews(false);
+
+ ap = panel;
+ av = panel.av;
+
+ getRotatableCanvas().av = panel.av;
+ getRotatableCanvas().ap = panel;
+ PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId());
+ }
}
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
import jalview.schemes.PIDColourScheme;
+import jalview.schemes.ResidueColourScheme;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.MessageManager;
import java.util.TreeMap;
import java.util.Vector;
+import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
/**
* DOCUMENT ME!
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+ protected JRadioButtonMenuItem annotationColour;
+
protected JMenuItem modifyConservation = new JMenuItem();
AlignmentPanel ap;
}
}
}
- // for the case when no sequences are even visible
+
+ /*
+ * offer 'Reveal All'
+ * - in the IdPanel (seq not null) if any sequence is hidden
+ * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null)
+ */
if (alignPanel.av.hasHiddenRows())
{
+ boolean addOption = seq != null;
+ if (!addOption && alignPanel.av.getAlignment().getHeight() == 0)
+ {
+ addOption = true;
+ }
+ if (addOption)
{
menuItem = new JMenuItem(
MessageManager.getString("action.reveal_all"));
}
}
});
-
add(menuItem);
}
}
}
});
+ annotationColour = new JRadioButtonMenuItem(
+ MessageManager.getString("action.by_annotation"));
+ annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
+ annotationColour.setEnabled(false);
+ annotationColour.setToolTipText(
+ MessageManager.getString("label.by_annotation_tooltip"));
+
modifyConservation.setText(MessageManager
.getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(new ActionListener()
colourMenu.add(textColour);
colourMenu.addSeparator();
- ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
+ ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
+ false);
+ bg.add(annotationColour);
+ colourMenu.add(annotationColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
* switch to the chosen colour scheme (or null for None)
*/
ColourSchemeI colourScheme = ColourSchemes.getInstance()
- .getColourScheme(colourSchemeName, sg,
+ .getColourScheme(colourSchemeName, ap.av, sg,
ap.av.getHiddenRepSequences());
sg.setColourScheme(colourScheme);
if (colourScheme instanceof Blosum62ColourScheme
import jalview.bin.Cache;
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.BackupFiles;
import jalview.io.FileFormatI;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
gapLabel.setEnabled(!useLegacyGap.isSelected());
gapColour.setEnabled(!useLegacyGap.isSelected());
showHiddenAtStart
- .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
+ .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
/*
* Set Structure tab defaults.
annotations_actionPerformed(null); // update the display of the annotation
// settings
+
+
+ /*
+ * Set Backups tab defaults
+ */
+ loadLastSavedBackupsOptions();
}
/**
Boolean.toString(padGaps.isSelected()));
wsPrefs.updateAndRefreshWsMenuConfig(false);
+
+ /*
+ * Save Backups settings
+ */
+ Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
+ Boolean.toString(backupfilesConfirmDelete.isSelected()));
+ Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
+ Boolean.toString(enableBackupFiles.isSelected()));
+ Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
+ Boolean.toString(backupfilesKeepAll.isSelected()));
+ Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
+ Boolean.toString(suffixReverse.isSelected()));
+ Cache.applicationProperties.setProperty(BackupFiles.SUFFIX,
+ suffixTemplate.getText());
+ Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
+ Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
+ Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
+ Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
+ Cache.applicationProperties.setProperty(BackupFiles.NS+"_PRESET",
+ Integer.toString(getComboIntStringKey(backupfilesPresetsCombo)));
+
Cache.saveProperties();
Desktop.instance.doConfigureStructurePrefs();
try
{
useLegacyGap.setSelected(false);
useLegacyGaps_actionPerformed(null);
- showHiddenAtStart.setSelected(true);
+ showHiddenAtStart.setSelected(false);
hiddenColour.setBackground(
jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
}
package jalview.gui;
import jalview.api.RotatableCanvasI;
+import jalview.datamodel.Point;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
import jalview.math.RotatableMatrix;
+import jalview.math.RotatableMatrix.Axis;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import java.awt.event.MouseMotionListener;
import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
-import java.util.Vector;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
import javax.swing.JPanel;
import javax.swing.ToolTipManager;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * Models a Panel on which a set of points, and optionally x/y/z axes, can be
+ * drawn, and rotated or zoomed with the mouse
*/
public class RotatableCanvas extends JPanel implements MouseListener,
- MouseMotionListener, KeyListener, RotatableCanvasI
+ MouseMotionListener, KeyListener, RotatableCanvasI,
+ MouseWheelListener
{
- RotatableMatrix idmat = new RotatableMatrix(3, 3);
+ private static final float ZOOM_OUT = 0.9f;
- RotatableMatrix objmat = new RotatableMatrix(3, 3);
+ private static final float ZOOM_IN = 1.1f;
- RotatableMatrix rotmat = new RotatableMatrix(3, 3);
+ /*
+ * pixels distance within which tooltip shows sequence name
+ */
+ private static final int NEARBY = 3;
- // RubberbandRectangle rubberband;
- boolean drawAxes = true;
+ private static final List<String> AXES = Arrays.asList("x", "y", "z");
- int omx = 0;
+ private static final Color AXIS_COLOUR = Color.yellow;
- int mx = 0;
+ private static final int DIMS = 3;
- int omy = 0;
+ boolean drawAxes = true;
+
+ int mouseX;
- int my = 0;
+ int mouseY;
Image img;
Graphics ig;
- Dimension prefsize;
-
- float[] centre = new float[3];
+ Dimension prefSize;
- float[] width = new float[3];
-
- float[] max = new float[3];
-
- float[] min = new float[3];
+ /*
+ * the min-max [x, y, z] values of sequence points when the points
+ * were set on the object, or when the view is reset;
+ * x and y ranges are not recomputed as points are rotated, as this
+ * would make scaling (zoom) unstable, but z ranges are (for correct
+ * graduated colour brightness based on z-coordinate)
+ */
+ float[] seqMin;
- float maxwidth;
+ float[] seqMax;
- float scale;
+ /*
+ * a scale factor used in drawing; when equal to 1, the points span
+ * half the available width or height (whichever is less); increase this
+ * factor to zoom in, decrease it to zoom out
+ */
+ private float scaleFactor;
int npoint;
- Vector points;
-
- float[][] orig;
-
- float[][] axes;
-
- int startx;
-
- int starty;
-
- int lastx;
-
- int lasty;
-
- int rectx1;
-
- int recty1;
-
- int rectx2;
+ /*
+ * sequences and their (x, y, z) PCA dimension values
+ */
+ List<SequencePoint> sequencePoints;
- int recty2;
+ /*
+ * x, y, z axis end points (PCA dimension values)
+ */
+ private Point[] axisEndPoints;
- float scalefactor = 1;
+ // fields for 'select rectangle' (JAL-1124)
+ // int rectx1;
+ // int recty1;
+ // int rectx2;
+ // int recty2;
AlignmentViewport av;
AlignmentPanel ap;
- boolean showLabels = false;
+ private boolean showLabels;
- Color bgColour = Color.black;
+ private Color bgColour;
- boolean applyToAllViews = false;
+ private boolean applyToAllViews;
- public RotatableCanvas(AlignmentPanel ap)
+ /**
+ * Constructor
+ *
+ * @param panel
+ */
+ public RotatableCanvas(AlignmentPanel panel)
{
- this.av = ap.av;
- this.ap = ap;
-
- addMouseWheelListener(new MouseWheelListener()
- {
- @Override
- public void mouseWheelMoved(MouseWheelEvent e)
- {
- double wheelRotation = e.getPreciseWheelRotation();
- if (wheelRotation > 0)
- {
- /*
- * zoom in
- */
- scale = (float) (scale * 1.1);
- repaint();
- }
- else if (wheelRotation < 0)
- {
- /*
- * zoom out
- */
- scale = (float) (scale * 0.9);
- repaint();
- }
- }
- });
-
+ this.av = panel.av;
+ this.ap = panel;
+ setAxisEndPoints(new Point[DIMS]);
+ setShowLabels(false);
+ setApplyToAllViews(false);
+ setBgColour(Color.BLACK);
+ resetAxes();
+
+ ToolTipManager.sharedInstance().registerComponent(this);
+
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ addMouseWheelListener(this);
}
- public void showLabels(boolean b)
+ /**
+ * Refreshes the display with labels shown (or not)
+ *
+ * @param show
+ */
+ public void showLabels(boolean show)
{
- showLabels = b;
+ setShowLabels(show);
repaint();
}
- boolean first = true;
-
@Override
- public void setPoints(Vector points, int npoint)
+ public void setPoints(List<SequencePoint> points, int np)
{
- this.points = points;
- this.npoint = npoint;
- if (first)
- {
- ToolTipManager.sharedInstance().registerComponent(this);
- ToolTipManager.sharedInstance().setInitialDelay(0);
- ToolTipManager.sharedInstance().setDismissDelay(10000);
- }
- prefsize = getPreferredSize();
- orig = new float[npoint][3];
+ this.sequencePoints = points;
+ this.npoint = np;
+ prefSize = getPreferredSize();
- for (int i = 0; i < npoint; i++)
- {
- SequencePoint sp = (SequencePoint) points.elementAt(i);
+ findWidths();
- for (int j = 0; j < 3; j++)
- {
- orig[i][j] = sp.coord[j];
- }
- }
-
- // Initialize the matrices to identity
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- if (i != j)
- {
- idmat.addElement(i, j, 0);
- objmat.addElement(i, j, 0);
- rotmat.addElement(i, j, 0);
- }
- else
- {
- idmat.addElement(i, j, 0);
- objmat.addElement(i, j, 0);
- rotmat.addElement(i, j, 0);
- }
- }
- }
-
- axes = new float[3][3];
- initAxes();
-
- findCentre();
- findWidth();
-
- scale = findScale();
- if (first)
- {
-
- addMouseListener(this);
-
- addMouseMotionListener(this);
- }
- first = false;
- }
-
- public void initAxes()
- {
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- if (i != j)
- {
- axes[i][j] = 0;
- }
- else
- {
- axes[i][j] = 1;
- }
- }
- }
+ setScaleFactor(1f);
}
/**
- * DOCUMENT ME!
+ * Resets axes to the initial state: x-axis to the right, y-axis up, z-axis to
+ * back (so obscured in a 2-D display)
*/
- public void findWidth()
+ protected void resetAxes()
{
- max = new float[3];
- min = new float[3];
-
- max[0] = (float) -1e30;
- max[1] = (float) -1e30;
- max[2] = (float) -1e30;
-
- min[0] = (float) 1e30;
- min[1] = (float) 1e30;
- min[2] = (float) 1e30;
-
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < npoint; j++)
- {
- SequencePoint sp = (SequencePoint) points.elementAt(j);
-
- if (sp.coord[i] >= max[i])
- {
- max[i] = sp.coord[i];
- }
-
- if (sp.coord[i] <= min[i])
- {
- min[i] = sp.coord[i];
- }
- }
- }
-
- // System.out.println("xmax " + max[0] + " min " + min[0]);
- // System.out.println("ymax " + max[1] + " min " + min[1]);
- // System.out.println("zmax " + max[2] + " min " + min[2]);
- width[0] = Math.abs(max[0] - min[0]);
- width[1] = Math.abs(max[1] - min[1]);
- width[2] = Math.abs(max[2] - min[2]);
-
- maxwidth = width[0];
-
- if (width[1] > width[0])
- {
- maxwidth = width[1];
- }
-
- if (width[2] > width[1])
- {
- maxwidth = width[2];
- }
-
- // System.out.println("Maxwidth = " + maxwidth);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public float findScale()
- {
- int dim;
- int width;
- int height;
-
- if (getWidth() != 0)
- {
- width = getWidth();
- height = getHeight();
- }
- else
- {
- width = prefsize.width;
- height = prefsize.height;
- }
-
- if (width < height)
- {
- dim = width;
- }
- else
- {
- dim = height;
- }
-
- return (dim * scalefactor) / (2 * maxwidth);
+ getAxisEndPoints()[0] = new Point(1f, 0f, 0f);
+ getAxisEndPoints()[1] = new Point(0f, 1f, 0f);
+ getAxisEndPoints()[2] = new Point(0f, 0f, 1f);
}
/**
- * DOCUMENT ME!
+ * Computes and saves the min-max ranges of x/y/z positions of the sequence
+ * points
*/
- public void findCentre()
+ protected void findWidths()
{
- // Find centre coordinate
- findWidth();
-
- centre[0] = (max[0] + min[0]) / 2;
- centre[1] = (max[1] + min[1]) / 2;
- centre[2] = (max[2] + min[2]) / 2;
-
- // System.out.println("Centre x " + centre[0]);
- // System.out.println("Centre y " + centre[1]);
- // System.out.println("Centre z " + centre[2]);
+ float[] max = new float[DIMS];
+ float[] min = new float[DIMS];
+
+ max[0] = -Float.MAX_VALUE;
+ max[1] = -Float.MAX_VALUE;
+ max[2] = -Float.MAX_VALUE;
+
+ min[0] = Float.MAX_VALUE;
+ min[1] = Float.MAX_VALUE;
+ min[2] = Float.MAX_VALUE;
+
+ for (SequencePoint sp : sequencePoints)
+ {
+ max[0] = Math.max(max[0], sp.coord.x);
+ max[1] = Math.max(max[1], sp.coord.y);
+ max[2] = Math.max(max[2], sp.coord.z);
+ min[0] = Math.min(min[0], sp.coord.x);
+ min[1] = Math.min(min[1], sp.coord.y);
+ min[2] = Math.min(min[2], sp.coord.z);
+ }
+
+ seqMin = min;
+ seqMax = max;
}
/**
- * DOCUMENT ME!
+ * Answers the preferred size if it has been set, else 400 x 400
*
- * @return DOCUMENT ME!
+ * @return
*/
@Override
public Dimension getPreferredSize()
{
- if (prefsize != null)
+ if (prefSize != null)
{
- return prefsize;
+ return prefSize;
}
else
{
}
/**
- * DOCUMENT ME!
+ * Answers the preferred size
*
- * @return DOCUMENT ME!
+ * @return
+ * @see RotatableCanvas#getPreferredSize()
*/
@Override
public Dimension getMinimumSize()
}
/**
- * DOCUMENT ME!
+ * Repaints the panel
*
* @param g
- * DOCUMENT ME!
*/
@Override
public void paintComponent(Graphics g1)
g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
- if (points == null)
+ if (sequencePoints == null)
{
g.setFont(new Font("Verdana", Font.PLAIN, 18));
g.drawString(
}
else
{
- // Only create the image at the beginning -
- if ((img == null) || (prefsize.width != getWidth())
- || (prefsize.height != getHeight()))
+ /*
+ * create the image at the beginning or after a resize
+ */
+ boolean resized = prefSize.width != getWidth()
+ || prefSize.height != getHeight();
+ if (img == null || resized)
{
- prefsize.width = getWidth();
- prefsize.height = getHeight();
+ prefSize.width = getWidth();
+ prefSize.height = getHeight();
- scale = findScale();
-
- // System.out.println("New scale = " + scale);
img = createImage(getWidth(), getHeight());
ig = img.getGraphics();
}
- drawBackground(ig, bgColour);
+ drawBackground(ig);
drawScene(ig);
- if (drawAxes == true)
+ if (drawAxes)
{
drawAxes(ig);
}
}
/**
- * DOCUMENT ME!
+ * Resets the rotation and choice of axes to the initial state (without change
+ * of scale factor)
+ */
+ public void resetView()
+ {
+ img = null;
+ findWidths();
+ resetAxes();
+ repaint();
+ }
+
+ /**
+ * Draws lines for the x, y, z axes
*
* @param g
- * DOCUMENT ME!
*/
public void drawAxes(Graphics g)
{
+ g.setColor(AXIS_COLOUR);
- g.setColor(Color.yellow);
+ int midX = getWidth() / 2;
+ int midY = getHeight() / 2;
+ float maxWidth = Math.max(Math.abs(seqMax[0] - seqMin[0]),
+ Math.abs(seqMax[1] - seqMin[1]));
+ int pix = Math.min(getWidth(), getHeight());
+ float scaleBy = pix * getScaleFactor() / (2f * maxWidth);
- for (int i = 0; i < 3; i++)
+ for (int i = 0; i < DIMS; i++)
{
- g.drawLine(getWidth() / 2, getHeight() / 2,
- (int) ((axes[i][0] * scale * max[0]) + (getWidth() / 2)),
- (int) ((axes[i][1] * scale * max[1]) + (getHeight() / 2)));
+ g.drawLine(midX, midY,
+ midX + (int) (getAxisEndPoints()[i].x * scaleBy * seqMax[0]),
+ midY + (int) (getAxisEndPoints()[i].y * scaleBy * seqMax[1]));
}
}
/**
- * DOCUMENT ME!
+ * Fills the background with the currently configured background colour
*
* @param g
- * DOCUMENT ME!
- * @param col
- * DOCUMENT ME!
*/
- public void drawBackground(Graphics g, Color col)
+ public void drawBackground(Graphics g)
{
- g.setColor(col);
- g.fillRect(0, 0, prefsize.width, prefsize.height);
+ g.setColor(getBgColour());
+ g.fillRect(0, 0, prefSize.width, prefSize.height);
}
/**
- * DOCUMENT ME!
+ * Draws points (6x6 squares) for the sequences of the PCA, and labels
+ * (sequence names) if configured to do so. The sequence points colours are
+ * taken from the sequence ids in the alignment (converting black to white).
+ * Sequences 'at the back' (z-coordinate is negative) are shaded slightly
+ * darker to help give a 3-D sensation.
*
* @param g
- * DOCUMENT ME!
*/
public void drawScene(Graphics g1)
{
-
Graphics2D g = (Graphics2D) g1;
g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
+ int pix = Math.min(getWidth(), getHeight());
+ float xWidth = Math.abs(seqMax[0] - seqMin[0]);
+ float yWidth = Math.abs(seqMax[1] - seqMin[1]);
+ float maxWidth = Math.max(xWidth, yWidth);
+ float scaleBy = pix * getScaleFactor() / (2f * maxWidth);
- int halfwidth = getWidth() / 2;
- int halfheight = getHeight() / 2;
+ float[] centre = getCentre();
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int x = (int) ((sp.coord[0] - centre[0]) * scale) + halfwidth;
- int y = (int) ((sp.coord[1] - centre[1]) * scale)
- + halfheight;
- float z = sp.coord[1] - centre[2];
-
- if (av.getSequenceColour(sp.sequence) == Color.black)
- {
- g.setColor(Color.white);
- }
- else
- {
- g.setColor(av.getSequenceColour(sp.sequence));
- }
-
- if (av.getSelectionGroup() != null)
- {
- if (av.getSelectionGroup().getSequences(null)
- .contains(((SequencePoint) points.elementAt(i)).sequence))
- {
- g.setColor(Color.gray);
- }
- }
+ /*
+ * sequence point colour as sequence id, but
+ * gray if sequence is currently selected
+ */
+ SequencePoint sp = sequencePoints.get(i);
+ Color sequenceColour = getSequencePointColour(sp);
+ g.setColor(sequenceColour);
+
+ int halfwidth = getWidth() / 2;
+ int halfheight = getHeight() / 2;
+ int x = (int) ((sp.coord.x - centre[0]) * scaleBy) + halfwidth;
+ int y = (int) ((sp.coord.y - centre[1]) * scaleBy) + halfheight;
+ g.fillRect(x - 3, y - 3, 6, 6);
- if (z < 0)
+ if (isShowLabels())
{
- g.setColor(g.getColor().darker());
+ g.setColor(Color.red);
+ g.drawString(sp.getSequence().getName(), x - 3, y - 4);
}
-
- g.fillRect(x - 3, y - 3, 6, 6);
- if (showLabels)
+ }
+ if (isShowLabels())
+ {
+ g.setColor(AXIS_COLOUR);
+ int midX = getWidth() / 2;
+ int midY = getHeight() / 2;
+ Iterator<String> axes = AXES.iterator();
+ for (Point p : getAxisEndPoints())
{
- g.setColor(Color.red);
- g.drawString(
- ((SequencePoint) points.elementAt(i)).sequence.getName(),
- x - 3, y - 4);
+ int x = midX + (int) (p.x * scaleBy * seqMax[0]);
+ int y = midY + (int) (p.y * scaleBy * seqMax[1]);
+ g.drawString(axes.next(), x - 3, y - 4);
}
}
-
// //Now the rectangle
// if (rectx2 != -1 && recty2 != -1) {
// g.setColor(Color.white);
}
/**
- * DOCUMENT ME!
+ * Determines the colour to use when drawing a sequence point. The colour is
+ * taken from the sequence id, with black converted to white, and then
+ * graduated from darker (at the back) to brighter (at the front) based on the
+ * z-axis coordinate of the point.
*
- * @return DOCUMENT ME!
+ * @param sp
+ * @return
*/
- public Dimension minimumsize()
+ protected Color getSequencePointColour(SequencePoint sp)
{
- return prefsize;
- }
+ SequenceI sequence = sp.getSequence();
+ Color sequenceColour = av.getSequenceColour(sequence);
+ if (sequenceColour == Color.black)
+ {
+ sequenceColour = Color.white;
+ }
+ if (av.getSelectionGroup() != null)
+ {
+ if (av.getSelectionGroup().getSequences(null).contains(sequence))
+ {
+ sequenceColour = Color.gray;
+ }
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Dimension preferredsize()
- {
- return prefsize;
+ /*
+ * graduate brighter for point in front of centre, darker if behind centre
+ */
+ float zCentre = (seqMin[2] + seqMax[2]) / 2f;
+ if (sp.coord.z > zCentre)
+ {
+ sequenceColour = ColorUtils.getGraduatedColour(sp.coord.z, 0,
+ sequenceColour, seqMax[2], sequenceColour.brighter());
+ }
+ else if (sp.coord.z < zCentre)
+ {
+ sequenceColour = ColorUtils.getGraduatedColour(sp.coord.z, seqMin[2],
+ sequenceColour.darker(), 0, sequenceColour);
+ }
+
+ return sequenceColour;
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
@Override
public void keyTyped(KeyEvent evt)
{
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
@Override
public void keyReleased(KeyEvent evt)
{
}
/**
- * DOCUMENT ME!
+ * Responds to up or down arrow key by zooming in or out, respectively
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void keyPressed(KeyEvent evt)
{
- if (evt.getKeyCode() == KeyEvent.VK_UP)
+ int keyCode = evt.getKeyCode();
+ boolean shiftDown = evt.isShiftDown();
+
+ if (keyCode == KeyEvent.VK_UP)
+ {
+ if (shiftDown)
+ {
+ rotate(0f, -1f);
+ }
+ else
+ {
+ zoom(ZOOM_IN);
+ }
+ }
+ else if (keyCode == KeyEvent.VK_DOWN)
+ {
+ if (shiftDown)
+ {
+ rotate(0f, 1f);
+ }
+ else
+ {
+ zoom(ZOOM_OUT);
+ }
+ }
+ else if (shiftDown && keyCode == KeyEvent.VK_LEFT)
{
- scalefactor = (float) (scalefactor * 1.1);
- scale = findScale();
+ rotate(1f, 0f);
}
- else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+ else if (shiftDown && keyCode == KeyEvent.VK_RIGHT)
{
- scalefactor = (float) (scalefactor * 0.9);
- scale = findScale();
+ rotate(-1f, 0f);
}
else if (evt.getKeyChar() == 's')
{
- System.err.println("DEBUG: Rectangle selection"); // log.debug
-
- if ((rectx2 != -1) && (recty2 != -1))
- {
- rectSelect(rectx1, recty1, rectx2, recty2);
- }
+ // Cache.log.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))
+ // {
+ // rectSelect(rectx1, recty1, rectx2, recty2);
+ // }
}
repaint();
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
+ @Override
+ public void zoom(float factor)
+ {
+ if (factor > 0f)
+ {
+ setScaleFactor(getScaleFactor() * factor);
+ }
+ }
+
@Override
public void mouseClicked(MouseEvent evt)
{
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
@Override
public void mouseEntered(MouseEvent evt)
{
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
@Override
public void mouseExited(MouseEvent evt)
{
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
@Override
public void mouseReleased(MouseEvent evt)
{
}
/**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
+ * If the mouse press is at (within 2 pixels of) a sequence point, toggles
+ * (adds or removes) the corresponding sequence as a member of the viewport
+ * selection group. This supports configuring a group in the alignment by
+ * clicking on points in the PCA display.
*/
@Override
public void mousePressed(MouseEvent evt)
int x = evt.getX();
int y = evt.getY();
- mx = x;
- my = y;
-
- omx = mx;
- omy = my;
-
- startx = x;
- starty = y;
+ mouseX = x;
+ mouseY = y;
- rectx1 = x;
- recty1 = y;
+ // rectx1 = x;
+ // recty1 = y;
+ // rectx2 = -1;
+ // recty2 = -1;
- rectx2 = -1;
- recty2 = -1;
-
- SequenceI found = findPoint(x, y);
+ SequenceI found = findSequenceAtPoint(x, y);
if (found != null)
{
repaint();
}
- // private void fireSequenceSelectionEvent(Selection sel) {
- // controller.handleSequenceSelectionEvent(new
- // SequenceSelectionEvent(this,sel));
- // }
+ /**
+ * Sets the tooltip to the name of the sequence within 2 pixels of the mouse
+ * position, or clears the tooltip if none found
+ */
@Override
public void mouseMoved(MouseEvent evt)
{
- SequenceI found = findPoint(evt.getX(), evt.getY());
+ SequenceI found = findSequenceAtPoint(evt.getX(), evt.getY());
- if (found != null)
- {
- this.setToolTipText(found.getName());
- }
- else
- {
- this.setToolTipText(null);
- }
+ this.setToolTipText(found == null ? null : found.getName());
}
/**
- * DOCUMENT ME!
+ * Action handler for a mouse drag. Rotates the display around the X axis (for
+ * up/down mouse movement) and/or the Y axis (for left/right mouse movement).
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void mouseDragged(MouseEvent evt)
{
- mx = evt.getX();
- my = evt.getY();
+ int xPos = evt.getX();
+ int yPos = evt.getY();
+
+ if (xPos == mouseX && yPos == mouseY)
+ {
+ return;
+ }
+
+ int xDelta = xPos - mouseX;
+ int yDelta = yPos - mouseY;
// Check if this is a rectangle drawing drag
if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
}
else
{
- rotmat.setIdentity();
+ rotate(xDelta, yDelta);
- rotmat.rotate(my - omy, 'x');
- rotmat.rotate(mx - omx, 'y');
+ mouseX = xPos;
+ mouseY = yPos;
- for (int i = 0; i < npoint; i++)
- {
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- sp.coord[0] -= centre[0];
- sp.coord[1] -= centre[1];
- sp.coord[2] -= centre[2];
-
- // Now apply the rotation matrix
- sp.coord = rotmat.vectorMultiply(sp.coord);
-
- // Now translate back again
- sp.coord[0] += centre[0];
- sp.coord[1] += centre[1];
- sp.coord[2] += centre[2];
- }
+ // findWidths();
- for (int i = 0; i < 3; i++)
- {
- axes[i] = rotmat.vectorMultiply(axes[i]);
- }
+ repaint();
+ }
+ }
+
+ @Override
+ public void rotate(float x, float y)
+ {
+ if (x == 0f && y == 0f)
+ {
+ return;
+ }
+
+ /*
+ * get the identity transformation...
+ */
+ RotatableMatrix rotmat = new RotatableMatrix();
+
+ /*
+ * rotate around the X axis for change in Y
+ * (mouse movement up/down); note we are equating a
+ * number of pixels with degrees of rotation here!
+ */
+ if (y != 0)
+ {
+ rotmat.rotate(y, Axis.X);
+ }
+
+ /*
+ * rotate around the Y axis for change in X
+ * (mouse movement left/right)
+ */
+ if (x != 0)
+ {
+ rotmat.rotate(x, Axis.Y);
+ }
+
+ /*
+ * apply the composite transformation to sequence points;
+ * update z min-max range (affects colour graduation), but not
+ * x or y min-max (as this would affect axis scaling)
+ */
+ float[] centre = getCentre();
+ float zMin = Float.MAX_VALUE;
+ float zMax = -Float.MAX_VALUE;
+
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = sequencePoints.get(i);
+ sp.translate(-centre[0], -centre[1], -centre[2]);
+
+ // Now apply the rotation matrix
+ sp.coord = rotmat.vectorMultiply(sp.coord);
+
+ // Now translate back again
+ sp.translate(centre[0], centre[1], centre[2]);
+
+ zMin = Math.min(zMin, sp.coord.z);
+ zMax = Math.max(zMax, sp.coord.z);
+ }
- omx = mx;
- omy = my;
+ seqMin[2] = zMin;
+ seqMax[2] = zMax;
- paint(this.getGraphics());
+ /*
+ * rotate the x/y/z axis positions
+ */
+ for (int i = 0; i < DIMS; i++)
+ {
+ getAxisEndPoints()[i] = rotmat.vectorMultiply(getAxisEndPoints()[i]);
}
}
/**
- * DOCUMENT ME!
+ * Answers the x/y/z coordinates that are midway between the maximum and
+ * minimum sequence point values
+ *
+ * @return
+ */
+ private float[] getCentre()
+ {
+ float xCentre = (seqMin[0] + seqMax[0]) / 2f;
+ float yCentre = (seqMin[1] + seqMax[1]) / 2f;
+ float zCentre = (seqMin[2] + seqMax[2]) / 2f;
+
+ return new float[] { xCentre, yCentre, zCentre };
+ }
+
+ /**
+ * Adds any sequences whose displayed points are within the given rectangle to
+ * the viewport's current selection. Intended for key 's' after dragging to
+ * select a region of the PCA.
*
* @param x1
- * DOCUMENT ME!
* @param y1
- * DOCUMENT ME!
* @param x2
- * DOCUMENT ME!
* @param y2
- * DOCUMENT ME!
*/
- public void rectSelect(int x1, int y1, int x2, int y2)
+ protected void rectSelect(int x1, int y1, int x2, int y2)
{
+ float[] centre = getCentre();
+
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int tmp1 = (int) (((sp.coord[0] - centre[0]) * scale)
+ SequencePoint sp = sequencePoints.get(i);
+ int tmp1 = (int) (((sp.coord.x - centre[0]) * getScaleFactor())
+ (getWidth() / 2.0));
- int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale)
+ int tmp2 = (int) (((sp.coord.y - centre[1]) * getScaleFactor())
+ (getHeight() / 2.0));
if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
{
if (av != null)
{
+ SequenceI sequence = sp.getSequence();
if (!av.getSelectionGroup().getSequences(null)
- .contains(sp.sequence))
+ .contains(sequence))
{
- av.getSelectionGroup().addSequence(sp.sequence, true);
+ av.getSelectionGroup().addSequence(sequence, true);
}
}
}
}
-
- // if (changedSel) {
- // fireSequenceSelectionEvent(av.getSelection());
- // }
}
/**
- * DOCUMENT ME!
+ * Answers the first sequence found whose point on the display is within 2
+ * pixels of the given coordinates, or null if none is found
*
* @param x
- * DOCUMENT ME!
* @param y
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @return
*/
- public SequenceI findPoint(int x, int y)
+ protected SequenceI findSequenceAtPoint(int x, int y)
{
int halfwidth = getWidth() / 2;
int halfheight = getHeight() / 2;
int found = -1;
+ int pix = Math.min(getWidth(), getHeight());
+ float xWidth = Math.abs(seqMax[0] - seqMin[0]);
+ float yWidth = Math.abs(seqMax[1] - seqMin[1]);
+ float maxWidth = Math.max(xWidth, yWidth);
+ float scaleBy = pix * getScaleFactor() / (2f * maxWidth);
+
+ float[] centre = getCentre();
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int px = (int) ((sp.coord[0] - centre[0]) * scale)
+ SequencePoint sp = sequencePoints.get(i);
+ int px = (int) ((sp.coord.x - centre[0]) * scaleBy)
+ halfwidth;
- int py = (int) ((sp.coord[1] - centre[1]) * scale)
+ int py = (int) ((sp.coord.y - centre[1]) * scaleBy)
+ halfheight;
- if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
+ if ((Math.abs(px - x) < NEARBY) && (Math.abs(py - y) < NEARBY))
{
found = i;
+ break;
}
}
if (found != -1)
{
- return ((SequencePoint) points.elementAt(found)).sequence;
+ return sequencePoints.get(found).getSequence();
}
else
{
}
}
+ /**
+ * Answers the panel the PCA is associated with (all panels for this alignment
+ * if 'associate with all panels' is selected).
+ *
+ * @return
+ */
AlignmentPanel[] getAssociatedPanels()
{
- if (applyToAllViews)
+ if (isApplyToAllViews())
{
return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
}
}
}
+ public Color getBackgroundColour()
+ {
+ return getBgColour();
+ }
+
+ /**
+ * Zooms in or out in response to mouse wheel movement
+ */
+ @Override
+ public void mouseWheelMoved(MouseWheelEvent e)
+ {
+ double wheelRotation = e.getPreciseWheelRotation();
+ if (wheelRotation > 0)
+ {
+ zoom(ZOOM_IN);
+ repaint();
+ }
+ else if (wheelRotation < 0)
+ {
+ zoom(ZOOM_OUT);
+ repaint();
+ }
+ }
+
+ /**
+ * Answers the sequence point minimum [x, y, z] values. Note these are derived
+ * when sequence points are set, but x and y values are not updated on
+ * rotation (because this would result in changes to scaling).
+ *
+ * @return
+ */
+ public float[] getSeqMin()
+ {
+ return seqMin;
+ }
+
+ /**
+ * Answers the sequence point maximum [x, y, z] values. Note these are derived
+ * when sequence points are set, but x and y values are not updated on
+ * rotation (because this would result in changes to scaling).
+ *
+ * @return
+ */
+ public float[] getSeqMax()
+ {
+ return seqMax;
+ }
+
/**
+ * Sets the minimum and maximum [x, y, z] positions for sequence points. For
+ * use when restoring a saved PCA from state data.
*
- * @return x,y,z positions of point s (index into points) under current
- * transform.
+ * @param min
+ * @param max
*/
- public double[] getPointPosition(int s)
+ public void setSeqMinMax(float[] min, float[] max)
+ {
+ seqMin = min;
+ seqMax = max;
+ }
+
+ public float getScaleFactor()
+ {
+ return scaleFactor;
+ }
+
+ public void setScaleFactor(float scaleFactor)
+ {
+ this.scaleFactor = scaleFactor;
+ }
+
+ public boolean isShowLabels()
{
- double pts[] = new double[3];
- float[] p = ((SequencePoint) points.elementAt(s)).coord;
- pts[0] = p[0];
- pts[1] = p[1];
- pts[2] = p[2];
- return pts;
+ return showLabels;
}
+ public void setShowLabels(boolean showLabels)
+ {
+ this.showLabels = showLabels;
+ }
+
+ public boolean isApplyToAllViews()
+ {
+ return applyToAllViews;
+ }
+
+ public void setApplyToAllViews(boolean applyToAllViews)
+ {
+ this.applyToAllViews = applyToAllViews;
+ }
+
+ public Point[] getAxisEndPoints()
+ {
+ return axisEndPoints;
+ }
+
+ public void setAxisEndPoints(Point[] axisEndPoints)
+ {
+ this.axisEndPoints = axisEndPoints;
+ }
+
+ public Color getBgColour()
+ {
+ return bgColour;
+ }
+
+ public void setBgColour(Color bgColour)
+ {
+ this.bgColour = bgColour;
+ }
}
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
import jalview.renderer.ScaleRenderer;
import jalview.renderer.ScaleRenderer.ScaleMark;
import jalview.util.MessageManager;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
+import java.awt.Point;
import java.awt.RenderingHints;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
protected void rightMouseButtonPressed(MouseEvent evt, final int res)
{
JPopupMenu pop = new JPopupMenu();
- if (reveal != null)
+
+ /*
+ * grab the hidden range in case mouseMoved nulls it
+ */
+ final int[] hiddenRange = reveal;
+ if (hiddenRange != null)
{
JMenuItem item = new JMenuItem(
MessageManager.getString("label.reveal"));
@Override
public void actionPerformed(ActionEvent e)
{
- av.showColumn(reveal[0]);
+ av.showColumn(hiddenRange[0]);
reveal = null;
+ ap.updateLayout();
ap.paintAlignment(true, true);
av.sendSelection();
}
{
av.showAllHiddenColumns();
reveal = null;
+ ap.updateLayout();
ap.paintAlignment(true, true);
av.sendSelection();
}
av.setSelectionGroup(null);
}
+ ap.updateLayout();
ap.paintAlignment(true, true);
av.sendSelection();
}
}
av.getColumnSelection().addElement(res);
- SequenceGroup sg = new SequenceGroup();
- // try to be as quick as possible
- SequenceI[] iVec = av.getAlignment().getSequencesArray();
- for (int i = 0; i < iVec.length; i++)
- {
- sg.addSequence(iVec[i], false);
- iVec[i] = null;
- }
- iVec = null;
+ SequenceGroup sg = new SequenceGroup(av.getAlignment().getSequences());
sg.setStartRes(res);
sg.setEndRes(res);
}
/**
- * DOCUMENT ME!
+ * Action on mouseUp is to set the limit of the current selection group (if
+ * there is one) and broadcast the selection
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void mouseReleased(MouseEvent evt)
{
+ boolean wasDragging = mouseDragging;
mouseDragging = false;
+ ap.getSeqPanel().stopScrolling();
- int res = (evt.getX() / av.getCharWidth())
+ int xCords = Math.max(0, evt.getX()); // prevent negative X coordinates
+ int res = (xCords / av.getCharWidth())
+ av.getRanges().getStartRes();
-
if (av.hasHiddenColumns())
{
res = av.getAlignment().getHiddenColumns()
.visibleToAbsoluteColumn(res);
}
-
- if (res >= av.getAlignment().getWidth())
- {
- res = av.getAlignment().getWidth() - 1;
- }
+ res = Math.min(res, av.getRanges().getEndRes());
+ res = Math.max(0, res);
if (!stretchingGroup)
{
{
sg.setStartRes(res);
}
+ if (wasDragging)
+ {
+ min = Math.min(res, min);
+ max = Math.max(res, max);
+ av.getColumnSelection().stretchGroup(res, sg, min, max);
+ }
}
stretchingGroup = false;
ap.paintAlignment(false, false);
+ av.isSelectionGroupChanged(true);
+ av.isColSelChanged(true);
av.sendSelection();
}
/**
* Action on dragging the mouse in the scale panel is to expand or shrink the
- * selection group range (including any hidden columns that it spans)
+ * selection group range (including any hidden columns that it spans). Note
+ * that the selection is only broadcast at the start of the drag (on
+ * mousePressed) and at the end (on mouseReleased), to avoid overload
+ * redrawing of other views.
*
* @param evt
*/
{
if (mouseDragging)
{
- ap.getSeqPanel().scrollCanvas(null);
+ ap.getSeqPanel().stopScrolling();
}
}
+ /**
+ * Action on leaving the panel bounds with mouse drag in progress is to start
+ * scrolling the alignment in the direction of the mouse. To restrict
+ * scrolling to left-right (not up-down), the y-value of the mouse position is
+ * replaced with zero.
+ */
@Override
public void mouseExited(MouseEvent evt)
{
if (mouseDragging)
{
- ap.getSeqPanel().scrollCanvas(evt);
+ ap.getSeqPanel().startScrolling(new Point(evt.getX(), 0));
}
}
*/
public class SeqCanvas extends JComponent implements ViewportListenerI
{
+ /*
+ * pixels gap between sequences and annotations when in wrapped mode
+ */
+ static final int SEQS_ANNOTATION_GAP = 3;
+
private static final String ZEROS = "0000000000";
final FeatureRenderer fr;
private int labelWidthWest; // label left width in pixels if shown
- private int wrappedSpaceAboveAlignment; // gap between widths
+ int wrappedSpaceAboveAlignment; // gap between widths
- private int wrappedRepeatHeightPx; // height in pixels of wrapped width
+ int wrappedRepeatHeightPx; // height in pixels of wrapped width
private int wrappedVisibleWidths; // number of wrapped widths displayed
calculateWrappedGeometry(canvasWidth, canvasHeight);
/*
- * draw one width at a time (excluding any scales or annotation shown),
+ * draw one width at a time (excluding any scales shown),
* until we have run out of either alignment or vertical space available
*/
int ypos = wrappedSpaceAboveAlignment;
* (av.getScaleAboveWrapped() ? 2 : 1);
/*
- * height in pixels of the wrapped widths
+ * compute height in pixels of the wrapped widths
+ * - start with space above plus sequences
*/
wrappedRepeatHeightPx = wrappedSpaceAboveAlignment;
- // add sequences
wrappedRepeatHeightPx += av.getAlignment().getHeight()
* charHeight;
- // add annotations panel height if shown
- wrappedRepeatHeightPx += getAnnotationHeight();
+
+ /*
+ * add annotations panel height if shown
+ * also gap between sequences and annotations
+ */
+ if (av.isShowAnnotation())
+ {
+ wrappedRepeatHeightPx += getAnnotationHeight();
+ wrappedRepeatHeightPx += SEQS_ANNOTATION_GAP; // 3px
+ }
/*
* number of visible widths (the last one may be part height),
* @param endColumn
* @param canvasHeight
*/
- protected void drawWrappedWidth(Graphics g, int ypos, int startColumn,
- int endColumn, int canvasHeight)
+ protected void drawWrappedWidth(Graphics g, final int ypos,
+ final int startColumn, final int endColumn,
+ final int canvasHeight)
{
ViewportRanges ranges = av.getRanges();
int viewportWidth = ranges.getViewportWidth();
if (av.isShowAnnotation())
{
- g.translate(0, cHeight + ypos + 3);
+ final int yShift = cHeight + ypos + SEQS_ANNOTATION_GAP;
+ g.translate(0, yShift);
if (annotations == null)
{
annotations = new AnnotationPanel(av);
annotations.renderer.drawComponent(annotations, av, g, -1,
startColumn, endx + 1);
- g.translate(0, -cHeight - ypos - 3);
+ g.translate(0, -yShift);
}
g.setClip(clip);
g.translate(-xOffset, 0);
int startx = startRes;
int endx;
int ypos = hgap; // vertical offset
- int maxwidth = av.getAlignment().getWidth();
-
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth);
- }
+ int maxwidth = av.getAlignment().getVisibleWidth();
// chop the wrapped alignment extent up into panel-sized blocks and treat
// each block as if it were a block from an unwrapped alignment
}
ViewportRanges vpRanges = av.getRanges();
- int range = vpRanges.getEndRes() - vpRanges.getStartRes();
+ int range = vpRanges.getEndRes() - vpRanges.getStartRes() + 1;
if (scrollX > range)
{
scrollX = range;
{
ViewportRanges ranges = av.getRanges();
- if (Math.abs(scrollX) > ranges.getViewportWidth())
+ if (Math.abs(scrollX) >= ranges.getViewportWidth())
{
/*
- * shift of more than one view width is
+ * shift of one view width or more is
* overcomplicated to handle in this method
*/
fastPaint = false;
while (y >= 0)
{
+ /*
+ * shift 'widthToCopy' residues by 'positions' places to the right
+ */
gg.copyArea(copyFromLeftStart, y, widthToCopy, heightToCopy,
positions * charWidth, 0);
if (y > 0)
{
+ /*
+ * copy 'positions' residue from the row above (right hand end)
+ * to this row's left hand end
+ */
gg.copyArea(copyFromRightStart, y - wrappedRepeatHeightPx,
positions * charWidth, heightToCopy, -widthToCopy,
wrappedRepeatHeightPx);
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import java.awt.BorderLayout;
import java.awt.Color;
implements MouseListener, MouseMotionListener, MouseWheelListener,
SequenceListener, SelectionListener
{
+ /*
+ * a class that holds computed mouse position
+ * - column of the alignment (0...)
+ * - sequence offset (0...)
+ * - annotation row offset (0...)
+ * where annotation offset is -1 unless the alignment is shown
+ * in wrapped mode, annotations are shown, and the mouse is
+ * over an annnotation row
+ */
+ static class MousePos
+ {
+ /*
+ * alignment column position of cursor (0...)
+ */
+ final int column;
+
+ /*
+ * index in alignment of sequence under cursor,
+ * or nearest above if cursor is not over a sequence
+ */
+ final int seqIndex;
+
+ /*
+ * index in annotations array of annotation under the cursor
+ * (only possible in wrapped mode with annotations shown),
+ * or -1 if cursor is not over an annotation row
+ */
+ final int annotationIndex;
+
+ MousePos(int col, int seq, int ann)
+ {
+ column = col;
+ seqIndex = seq;
+ annotationIndex = ann;
+ }
+
+ boolean isOverAnnotation()
+ {
+ return annotationIndex != -1;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == null || !(obj instanceof MousePos))
+ {
+ return false;
+ }
+ MousePos o = (MousePos) obj;
+ boolean b = (column == o.column && seqIndex == o.seqIndex
+ && annotationIndex == o.annotationIndex);
+ // System.out.println(obj + (b ? "= " : "!= ") + this);
+ return b;
+ }
+
+ /**
+ * A simple hashCode that ensures that instances that satisfy equals() have
+ * the same hashCode
+ */
+ @Override
+ public int hashCode()
+ {
+ return column + seqIndex + annotationIndex;
+ }
+
+ /**
+ * toString method for debug output purposes only
+ */
+ @Override
+ public String toString()
+ {
+ return String.format("c%d:s%d:a%d", column, seqIndex,
+ annotationIndex);
+ }
+ }
+
private static final int MAX_TOOLTIP_LENGTH = 300;
public SeqCanvas seqCanvas;
public AlignmentPanel ap;
/*
- * last column position for mouseMoved event
+ * last position for mouseMoved event
*/
- private int lastMouseColumn;
+ private MousePos lastMousePosition;
- /*
- * last sequence offset for mouseMoved event
- */
- private int lastMouseSeq;
-
- protected int lastres;
+ protected int editLastRes;
- protected int startseq;
+ protected int editStartSeq;
protected AlignViewport av;
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
-
- lastMouseColumn = -1;
- lastMouseSeq = -1;
}
int startWrapBlock = -1;
int wrappedBlock = -1;
/**
+ * Computes the column and sequence row (and possibly annotation row when in
+ * wrapped mode) for the given mouse position
+ *
+ * @param evt
+ * @return
+ */
+ MousePos findMousePosition(MouseEvent evt)
+ {
+ int col = findColumn(evt);
+ int seqIndex = -1;
+ int annIndex = -1;
+ int y = evt.getY();
+
+ int charHeight = av.getCharHeight();
+ int alignmentHeight = av.getAlignment().getHeight();
+ if (av.getWrapAlignment())
+ {
+ seqCanvas.calculateWrappedGeometry(seqCanvas.getWidth(),
+ seqCanvas.getHeight());
+
+ /*
+ * yPos modulo height of repeating width
+ */
+ int yOffsetPx = y % seqCanvas.wrappedRepeatHeightPx;
+
+ /*
+ * height of sequences plus space / scale above,
+ * plus gap between sequences and annotations
+ */
+ int alignmentHeightPixels = seqCanvas.wrappedSpaceAboveAlignment
+ + alignmentHeight * charHeight
+ + SeqCanvas.SEQS_ANNOTATION_GAP;
+ if (yOffsetPx >= alignmentHeightPixels)
+ {
+ /*
+ * mouse is over annotations; find annotation index, also set
+ * last sequence above (for backwards compatible behaviour)
+ */
+ AlignmentAnnotation[] anns = av.getAlignment()
+ .getAlignmentAnnotation();
+ int rowOffsetPx = yOffsetPx - alignmentHeightPixels;
+ annIndex = AnnotationPanel.getRowIndex(rowOffsetPx, anns);
+ seqIndex = alignmentHeight - 1;
+ }
+ else
+ {
+ /*
+ * mouse is over sequence (or the space above sequences)
+ */
+ yOffsetPx -= seqCanvas.wrappedSpaceAboveAlignment;
+ if (yOffsetPx >= 0)
+ {
+ seqIndex = Math.min(yOffsetPx / charHeight, alignmentHeight - 1);
+ }
+ }
+ }
+ else
+ {
+ seqIndex = Math.min((y / charHeight) + av.getRanges().getStartSeq(),
+ alignmentHeight - 1);
+ }
+
+ return new MousePos(col, seqIndex, annIndex);
+ }
+ /**
* Returns the aligned sequence position (base 0) at the mouse position, or
* the closest visible one
*
int res = 0;
int x = evt.getX();
- int startRes = av.getRanges().getStartRes();
+ final int startRes = av.getRanges().getStartRes();
+ final int charWidth = av.getCharWidth();
+
if (av.getWrapAlignment())
{
-
int hgap = av.getCharHeight();
if (av.getScaleAboveWrapped())
{
int y = evt.getY();
y = Math.max(0, y - hgap);
- x = Math.max(0, x - seqCanvas.getLabelWidthWest());
+ x -= seqCanvas.getLabelWidthWest();
+ if (x < 0)
+ {
+ // mouse is over left scale
+ return -1;
+ }
int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
if (cwidth < 1)
{
return 0;
}
+ if (x >= cwidth * charWidth)
+ {
+ // mouse is over right scale
+ return -1;
+ }
wrappedBlock = y / cHeight;
wrappedBlock += startRes / cwidth;
// allow for wrapped view scrolled right (possible from Overview)
int startOffset = startRes % cwidth;
res = wrappedBlock * cwidth + startOffset
- + +Math.min(cwidth - 1, x / av.getCharWidth());
+ + Math.min(cwidth - 1, x / charWidth);
}
else
{
- if (x > seqCanvas.getX() + seqCanvas.getWidth())
- {
- // make sure we calculate relative to visible alignment, rather than
- // right-hand gutter
- x = seqCanvas.getX() + seqCanvas.getWidth();
- }
- res = (x / av.getCharWidth()) + startRes;
- if (res > av.getRanges().getEndRes())
- {
- // moused off right
- res = av.getRanges().getEndRes();
- }
+ /*
+ * make sure we calculate relative to visible alignment,
+ * rather than right-hand gutter
+ */
+ x = Math.min(x, seqCanvas.getX() + seqCanvas.getWidth());
+ res = (x / charWidth) + startRes;
+ res = Math.min(res, av.getRanges().getEndRes());
}
if (av.hasHiddenColumns())
}
return res;
-
- }
-
- int findSeq(MouseEvent evt)
- {
- int seq = 0;
- int y = evt.getY();
-
- if (av.getWrapAlignment())
- {
- int hgap = av.getCharHeight();
- if (av.getScaleAboveWrapped())
- {
- hgap += av.getCharHeight();
- }
-
- int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
- + hgap + seqCanvas.getAnnotationHeight();
-
- y -= hgap;
-
- seq = Math.min((y % cHeight) / av.getCharHeight(),
- av.getAlignment().getHeight() - 1);
- }
- else
- {
- seq = Math.min(
- (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
- av.getAlignment().getHeight() - 1);
- }
-
- return seq;
}
/**
/*
* Tidy up come what may...
*/
- startseq = -1;
- lastres = -1;
+ editStartSeq = -1;
+ editLastRes = -1;
editingSeqs = false;
groupEditing = false;
keyboardNo1 = null;
void insertGapAtCursor(boolean group)
{
groupEditing = group;
- startseq = seqCanvas.cursorY;
- lastres = seqCanvas.cursorX;
+ editStartSeq = seqCanvas.cursorY;
+ editLastRes = seqCanvas.cursorX;
editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
endEditing();
}
void deleteGapAtCursor(boolean group)
{
groupEditing = group;
- startseq = seqCanvas.cursorY;
- lastres = seqCanvas.cursorX + getKeyboardNo1();
+ editStartSeq = seqCanvas.cursorY;
+ editLastRes = seqCanvas.cursorX + getKeyboardNo1();
editSequence(false, false, seqCanvas.cursorX);
endEditing();
}
{
// TODO not called - delete?
groupEditing = group;
- startseq = seqCanvas.cursorY;
- lastres = seqCanvas.cursorX;
+ editStartSeq = seqCanvas.cursorY;
+ editLastRes = seqCanvas.cursorX;
editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
endEditing();
}
@Override
public void mouseReleased(MouseEvent evt)
{
+ MousePos pos = findMousePosition(evt);
+ if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1)
+ {
+ return;
+ }
+
boolean didDrag = mouseDragging; // did we come here after a drag
mouseDragging = false;
mouseWheelPressed = false;
if (evt.isPopupTrigger()) // Windows: mouseReleased
{
- showPopupMenu(evt);
+ showPopupMenu(evt, pos);
evt.consume();
return;
}
- if (!editingSeqs)
+ if (editingSeqs)
+ {
+ endEditing();
+ }
+ else
{
doMouseReleasedDefineMode(evt, didDrag);
- return;
}
-
- endEditing();
}
/**
public void mousePressed(MouseEvent evt)
{
lastMousePress = evt.getPoint();
+ MousePos pos = findMousePosition(evt);
+ if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1)
+ {
+ return;
+ }
if (SwingUtilities.isMiddleMouseButton(evt))
{
}
else
{
- doMousePressedDefineMode(evt);
+ doMousePressedDefineMode(evt, pos);
return;
}
- int seq = findSeq(evt);
- int res = findColumn(evt);
-
- if (seq < 0 || res < 0)
- {
- return;
- }
+ int seq = pos.seqIndex;
+ int res = pos.column;
if ((seq < av.getAlignment().getHeight())
&& (res < av.getAlignment().getSequenceAt(seq).getLength()))
{
- startseq = seq;
- lastres = res;
+ editStartSeq = seq;
+ editLastRes = res;
}
else
{
- startseq = -1;
- lastres = -1;
+ editStartSeq = -1;
+ editLastRes = -1;
}
return;
// over residue to change abruptly, causing highlighted residue in panel 2
// to change, causing a scroll in panel 1 etc)
ap.setToScrollComplementPanel(false);
- wasScrolled = ap.scrollToPosition(results, false);
+ wasScrolled = ap.scrollToPosition(results);
if (wasScrolled)
{
seqCanvas.revalidate();
mouseDragged(evt);
}
- final int column = findColumn(evt);
- final int seq = findSeq(evt);
+ final MousePos mousePos = findMousePosition(evt);
+ if (mousePos.equals(lastMousePosition))
+ {
+ /*
+ * just a pixel move without change of 'cell'
+ */
+ return;
+ }
+ lastMousePosition = mousePos;
- if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
+ if (mousePos.isOverAnnotation())
{
- lastMouseSeq = -1;
+ mouseMovedOverAnnotation(mousePos);
return;
}
- if (column == lastMouseColumn && seq == lastMouseSeq)
+ final int seq = mousePos.seqIndex;
+
+ final int column = mousePos.column;
+ if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
{
- /*
- * just a pixel move without change of residue
- */
+ lastMousePosition = null;
+ setToolTipText(null);
+ lastTooltip = null;
+ ap.alignFrame.setStatus("");
return;
}
- lastMouseColumn = column;
- lastMouseSeq = seq;
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
}
}
+ /**
+ * When the view is in wrapped mode, and the mouse is over an annotation row,
+ * shows the corresponding tooltip and status message (if any)
+ *
+ * @param pos
+ * @param column
+ */
+ protected void mouseMovedOverAnnotation(MousePos pos)
+ {
+ final int column = pos.column;
+ final int rowIndex = pos.annotationIndex;
+
+ if (column < 0 || !av.getWrapAlignment() || !av.isShowAnnotation()
+ || rowIndex < 0)
+ {
+ return;
+ }
+ AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+
+ String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column,
+ anns);
+ setToolTipText(tooltip);
+ lastTooltip = tooltip;
+
+ String msg = AnnotationPanel.getStatusMessage(av.getAlignment(), column,
+ anns[rowIndex]);
+ ap.alignFrame.setStatus(msg);
+ }
+
private Point lastp = null;
/*
@Override
public Point getToolTipLocation(MouseEvent event)
{
- int x = event.getX(), w = getWidth();
- int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
- // close to edge
+ if (tooltipText == null || tooltipText.length() <= 6)
+ {
+ lastp = null;
+ return null;
+ }
+
+ int x = event.getX();
+ int w = getWidth();
+ // switch sides when tooltip is too close to edge
+ int wdth = (w - x < 200) ? -(w / 2) : 5;
Point p = lastp;
if (!event.isShiftDown() || p == null)
{
- p = (tooltipText != null && tooltipText.length() > 6)
- ? new Point(event.getX() + wdth, event.getY() - 20)
- : null;
+ p = new Point(event.getX() + wdth, event.getY() - 20);
+ lastp = p;
}
/*
- * TODO: try to modify position region is not obcured by tooltip
+ * TODO: try to set position so region is not obscured by tooltip
*/
- return lastp = p;
+ return p;
}
String lastTooltip;
text.append(" (").append(Integer.toString(residuePos)).append(")");
}
- ap.alignFrame.statusBar.setText(text.toString());
+ ap.alignFrame.setStatus(text.toString());
}
/**
@Override
public void mouseDragged(MouseEvent evt)
{
+ MousePos pos = findMousePosition(evt);
+ if (pos.isOverAnnotation() || pos.column == -1)
+ {
+ return;
+ }
+
if (mouseWheelPressed)
{
boolean inSplitFrame = ap.av.getCodingComplement() != null;
if (!editingSeqs)
{
- doMouseDraggedDefineMode(evt);
+ dragStretchGroup(evt);
return;
}
- int res = findColumn(evt);
+ int res = pos.column;
if (res < 0)
{
res = 0;
}
- if ((lastres == -1) || (lastres == res))
+ if ((editLastRes == -1) || (editLastRes == res))
{
return;
}
- if ((res < av.getAlignment().getWidth()) && (res < lastres))
+ if ((res < av.getAlignment().getWidth()) && (res < editLastRes))
{
// dragLeft, delete gap
editSequence(false, false, res);
}
mouseDragging = true;
- if ((scrollThread != null) && (scrollThread.isRunning()))
+ if (scrollThread != null)
{
- scrollThread.setEvent(evt);
+ scrollThread.setMousePosition(evt.getPoint());
}
}
- // TODO: Make it more clever than many booleans
+ /**
+ * Edits the sequence to insert or delete one or more gaps, in response to a
+ * mouse drag or cursor mode command. The number of inserts/deletes may be
+ * specified with the cursor command, or else depends on the mouse event
+ * (normally one column, but potentially more for a fast mouse drag).
+ * <p>
+ * Delete gaps is limited to the number of gaps left of the cursor position
+ * (mouse drag), or at or right of the cursor position (cursor mode).
+ * <p>
+ * In group editing mode (Ctrl or Cmd down), the edit acts on all sequences in
+ * the current selection group.
+ * <p>
+ * In locked editing mode (with a selection group present), inserts/deletions
+ * within the selection group are limited to its boundaries (and edits outside
+ * the group stop at its border).
+ *
+ * @param insertGap
+ * true to insert gaps, false to delete gaps
+ * @param editSeq
+ * (unused parameter)
+ * @param startres
+ * the column at which to perform the action; the number of columns
+ * affected depends on <code>this.editLastRes</code> (cursor column
+ * position)
+ */
synchronized void editSequence(boolean insertGap, boolean editSeq,
- int startres)
+ final int startres)
{
int fixedLeft = -1;
int fixedRight = -1;
boolean fixedColumns = false;
SequenceGroup sg = av.getSelectionGroup();
- SequenceI seq = av.getAlignment().getSequenceAt(startseq);
+ final SequenceI seq = av.getAlignment().getSequenceAt(editStartSeq);
// No group, but the sequence may represent a group
if (!groupEditing && av.hasHiddenRows())
}
}
- StringBuilder message = new StringBuilder(64);
+ StringBuilder message = new StringBuilder(64); // for status bar
+
+ /*
+ * make a name for the edit action, for
+ * status bar message and Undo/Redo menu
+ */
+ String label = null;
if (groupEditing)
{
- message.append("Edit group:");
- if (editCommand == null)
- {
- editCommand = new EditCommand(
- MessageManager.getString("action.edit_group"));
- }
+ message.append("Edit group:");
+ label = MessageManager.getString("action.edit_group");
}
else
{
- message.append("Edit sequence: " + seq.getName());
- String label = seq.getName();
+ message.append("Edit sequence: " + seq.getName());
+ label = seq.getName();
if (label.length() > 10)
{
label = label.substring(0, 10);
}
- if (editCommand == null)
- {
- editCommand = new EditCommand(MessageManager
- .formatMessage("label.edit_params", new String[]
- { label }));
- }
+ label = MessageManager.formatMessage("label.edit_params",
+ new String[]
+ { label });
+ }
+
+ /*
+ * initialise the edit command if there is not
+ * already one being extended
+ */
+ if (editCommand == null)
+ {
+ editCommand = new EditCommand(label);
}
if (insertGap)
message.append(" delete ");
}
- message.append(Math.abs(startres - lastres) + " gaps.");
- ap.alignFrame.statusBar.setText(message.toString());
+ message.append(Math.abs(startres - editLastRes) + " gaps.");
+ ap.alignFrame.setStatus(message.toString());
- // Are we editing within a selection group?
- if (groupEditing || (sg != null
- && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
+ /*
+ * is there a selection group containing the sequence being edited?
+ * if so the boundary of the group is the limit of the edit
+ * (but the edit may be inside or outside the selection group)
+ */
+ boolean inSelectionGroup = sg != null
+ && sg.getSequences(av.getHiddenRepSequences()).contains(seq);
+ if (groupEditing || inSelectionGroup)
{
fixedColumns = true;
fixedLeft = sg.getStartRes();
fixedRight = sg.getEndRes();
- if ((startres < fixedLeft && lastres >= fixedLeft)
- || (startres >= fixedLeft && lastres < fixedLeft)
- || (startres > fixedRight && lastres <= fixedRight)
- || (startres <= fixedRight && lastres > fixedRight))
+ if ((startres < fixedLeft && editLastRes >= fixedLeft)
+ || (startres >= fixedLeft && editLastRes < fixedLeft)
+ || (startres > fixedRight && editLastRes <= fixedRight)
+ || (startres <= fixedRight && editLastRes > fixedRight))
{
endEditing();
return;
int y2 = av.getAlignment().getHiddenColumns()
.getNextHiddenBoundary(false, startres);
- if ((insertGap && startres > y1 && lastres < y1)
- || (!insertGap && startres < y2 && lastres > y2))
+ if ((insertGap && startres > y1 && editLastRes < y1)
+ || (!insertGap && startres < y2 && editLastRes > y2))
{
endEditing();
return;
}
}
+ boolean success = doEditSequence(insertGap, editSeq, startres,
+ fixedRight, fixedColumns, sg);
+
+ /*
+ * report what actually happened (might be less than
+ * what was requested), by inspecting the edit commands added
+ */
+ String msg = getEditStatusMessage(editCommand);
+ ap.alignFrame.setStatus(msg == null ? " " : msg);
+ if (!success)
+ {
+ endEditing();
+ }
+
+ editLastRes = startres;
+ seqCanvas.repaint();
+ }
+
+ /**
+ * A helper method that performs the requested editing to insert or delete
+ * gaps (if possible). Answers true if the edit was successful, false if could
+ * only be performed in part or not at all. Failure may occur in 'locked edit'
+ * mode, when an insertion requires a matching gapped position (or column) to
+ * delete, and deletion requires an adjacent gapped position (or column) to
+ * remove.
+ *
+ * @param insertGap
+ * true if inserting gap(s), false if deleting
+ * @param editSeq
+ * (unused parameter, currently always false)
+ * @param startres
+ * the column at which to perform the edit
+ * @param fixedRight
+ * fixed right boundary column of a locked edit (within or to the
+ * left of a selection group)
+ * @param fixedColumns
+ * true if this is a locked edit
+ * @param sg
+ * the sequence group (if group edit is being performed)
+ * @return
+ */
+ protected boolean doEditSequence(final boolean insertGap,
+ final boolean editSeq, final int startres, int fixedRight,
+ final boolean fixedColumns, final SequenceGroup sg)
+ {
+ final SequenceI seq = av.getAlignment().getSequenceAt(editStartSeq);
+ SequenceI[] seqs = new SequenceI[] { seq };
+
if (groupEditing)
{
List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
&& sg.getEndRes() == av.getAlignment().getWidth() - 1)
{
- sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
+ sg.setEndRes(
+ av.getAlignment().getWidth() + startres - editLastRes);
fixedRight = sg.getEndRes();
}
// Find the next gap before the end
// of the visible region boundary
boolean blank = false;
- for (; fixedRight > lastres; fixedRight--)
+ for (; fixedRight > editLastRes; fixedRight--)
{
blank = true;
for (g = 0; g < groupSize; g++)
{
- for (int j = 0; j < startres - lastres; j++)
+ for (int j = 0; j < startres - editLastRes; j++)
{
- if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
+ if (!Comparison
+ .isGap(groupSeqs[g].getCharAt(fixedRight - j)))
{
blank = false;
break;
{
if (sg.getSize() == av.getAlignment().getHeight())
{
- if ((av.hasHiddenColumns() && startres < av.getAlignment()
- .getHiddenColumns()
- .getNextHiddenBoundary(false, startres)))
+ if ((av.hasHiddenColumns()
+ && startres < av.getAlignment().getHiddenColumns()
+ .getNextHiddenBoundary(false, startres)))
{
- endEditing();
- return;
+ return false;
}
int alWidth = av.getAlignment().getWidth();
}
// We can still insert gaps if the selectionGroup
// contains all the sequences
- sg.setEndRes(sg.getEndRes() + startres - lastres);
- fixedRight = alWidth + startres - lastres;
+ sg.setEndRes(sg.getEndRes() + startres - editLastRes);
+ fixedRight = alWidth + startres - editLastRes;
}
else
{
- endEditing();
- return;
+ return false;
}
}
}
for (g = 0; g < groupSize; g++)
{
- for (int j = startres; j < lastres; j++)
+ for (int j = startres; j < editLastRes; j++)
{
if (groupSeqs[g].getLength() <= j)
{
if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
{
// Not a gap, block edit not valid
- endEditing();
- return;
+ return false;
}
}
}
// dragging to the right
if (fixedColumns && fixedRight != -1)
{
- for (int j = lastres; j < startres; j++)
+ for (int j = editLastRes; j < startres; j++)
{
- insertChar(j, groupSeqs, fixedRight);
+ insertGap(j, groupSeqs, fixedRight);
}
}
else
{
appendEdit(Action.INSERT_GAP, groupSeqs, startres,
- startres - lastres);
+ startres - editLastRes, false);
}
}
else
// dragging to the left
if (fixedColumns && fixedRight != -1)
{
- for (int j = lastres; j > startres; j--)
+ for (int j = editLastRes; j > startres; j--)
{
deleteChar(startres, groupSeqs, fixedRight);
}
else
{
appendEdit(Action.DELETE_GAP, groupSeqs, startres,
- lastres - startres);
+ editLastRes - startres, false);
}
-
}
}
else
- // ///Editing a single sequence///////////
{
+ /*
+ * editing a single sequence
+ */
if (insertGap)
{
// dragging to the right
if (fixedColumns && fixedRight != -1)
{
- for (int j = lastres; j < startres; j++)
+ for (int j = editLastRes; j < startres; j++)
{
- insertChar(j, new SequenceI[] { seq }, fixedRight);
+ if (!insertGap(j, seqs, fixedRight))
+ {
+ /*
+ * e.g. cursor mode command specified
+ * more inserts than are possible
+ */
+ return false;
+ }
}
}
else
{
- appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
- startres - lastres);
+ appendEdit(Action.INSERT_GAP, seqs, editLastRes,
+ startres - editLastRes, false);
}
}
else
// dragging to the left
if (fixedColumns && fixedRight != -1)
{
- for (int j = lastres; j > startres; j--)
+ for (int j = editLastRes; j > startres; j--)
{
if (!Comparison.isGap(seq.getCharAt(startres)))
{
- endEditing();
- break;
+ return false;
}
- deleteChar(startres, new SequenceI[] { seq }, fixedRight);
+ deleteChar(startres, seqs, fixedRight);
}
}
else
{
// could be a keyboard edit trying to delete none gaps
int max = 0;
- for (int m = startres; m < lastres; m++)
+ for (int m = startres; m < editLastRes; m++)
{
if (!Comparison.isGap(seq.getCharAt(m)))
{
}
max++;
}
-
if (max > 0)
{
- appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
- startres, max);
+ appendEdit(Action.DELETE_GAP, seqs, startres, max, false);
}
}
}
{// insertGap==false AND editSeq==TRUE;
if (fixedColumns && fixedRight != -1)
{
- for (int j = lastres; j < startres; j++)
+ for (int j = editLastRes; j < startres; j++)
{
- insertChar(j, new SequenceI[] { seq }, fixedRight);
+ insertGap(j, seqs, fixedRight);
}
}
else
{
- appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
- startres - lastres);
+ appendEdit(Action.INSERT_NUC, seqs, editLastRes,
+ startres - editLastRes, false);
}
}
}
}
- lastres = startres;
- seqCanvas.repaint();
+ return true;
}
- void insertChar(int j, SequenceI[] seq, int fixedColumn)
+ /**
+ * Constructs an informative status bar message while dragging to insert or
+ * delete gaps. Answers null if inserts and deletes cancel out.
+ *
+ * @param editCommand
+ * a command containing the list of individual edits
+ * @return
+ */
+ protected static String getEditStatusMessage(EditCommand editCommand)
+ {
+ if (editCommand == null)
+ {
+ return null;
+ }
+
+ /*
+ * add any inserts, and subtract any deletes,
+ * not counting those auto-inserted when doing a 'locked edit'
+ * (so only counting edits 'under the cursor')
+ */
+ int count = 0;
+ for (Edit cmd : editCommand.getEdits())
+ {
+ if (!cmd.isSystemGenerated())
+ {
+ count += cmd.getAction() == Action.INSERT_GAP ? cmd.getNumber()
+ : -cmd.getNumber();
+ }
+ }
+
+ if (count == 0)
+ {
+ /*
+ * inserts and deletes cancel out
+ */
+ return null;
+ }
+
+ String msgKey = count > 1 ? "label.insert_gaps"
+ : (count == 1 ? "label.insert_gap"
+ : (count == -1 ? "label.delete_gap"
+ : "label.delete_gaps"));
+ count = Math.abs(count);
+
+ return MessageManager.formatMessage(msgKey, String.valueOf(count));
+ }
+
+ /**
+ * Inserts one gap at column j, deleting the right-most gapped column up to
+ * (and including) fixedColumn. Returns true if the edit is successful, false
+ * if no blank column is available to allow the insertion to be balanced by a
+ * deletion.
+ *
+ * @param j
+ * @param seq
+ * @param fixedColumn
+ * @return
+ */
+ boolean insertGap(int j, SequenceI[] seq, int fixedColumn)
{
int blankColumn = fixedColumn;
for (int s = 0; s < seq.length; s++)
{
blankColumn = fixedColumn;
endEditing();
- return;
+ return false;
}
}
- appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
+ appendEdit(Action.DELETE_GAP, seq, blankColumn, 1, true);
- appendEdit(Action.INSERT_GAP, seq, j, 1);
+ appendEdit(Action.INSERT_GAP, seq, j, 1, false);
+ return true;
}
/**
- * Helper method to add and perform one edit action.
+ * Helper method to add and perform one edit action
*
* @param action
* @param seq
* @param pos
* @param count
+ * @param systemGenerated
+ * true if the edit is a 'balancing' delete (or insert) to match a
+ * user's insert (or delete) in a locked editing region
*/
protected void appendEdit(Action action, SequenceI[] seq, int pos,
- int count)
+ int count, boolean systemGenerated)
{
final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
av.getAlignment().getGapCharacter());
+ edit.setSystemGenerated(systemGenerated);
editCommand.appendEdit(edit, av.getAlignment(), true, null);
}
- void deleteChar(int j, SequenceI[] seq, int fixedColumn)
+ /**
+ * Deletes the character at column j, and inserts a gap at fixedColumn, in
+ * each of the given sequences. The caller should ensure that all sequences
+ * are gapped in column j.
+ *
+ * @param j
+ * @param seqs
+ * @param fixedColumn
+ */
+ void deleteChar(int j, SequenceI[] seqs, int fixedColumn)
{
+ appendEdit(Action.DELETE_GAP, seqs, j, 1, false);
- appendEdit(Action.DELETE_GAP, seq, j, 1);
-
- appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
+ appendEdit(Action.INSERT_GAP, seqs, fixedColumn, 1, true);
}
/**
- * DOCUMENT ME!
+ * On reentering the panel, stops any scrolling that was started on dragging
+ * out of the panel
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseEntered(MouseEvent e)
{
oldSeq = 0;
}
-
- if ((scrollThread != null) && (scrollThread.isRunning()))
- {
- scrollThread.stopScrolling();
- scrollThread = null;
- }
+ stopScrolling();
}
/**
- * DOCUMENT ME!
+ * On leaving the panel, if the mouse is being dragged, starts a thread to
+ * scroll it until the mouse is released (in unwrapped mode only)
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseExited(MouseEvent e)
{
+ ap.alignFrame.setStatus(" ");
if (av.getWrapAlignment())
{
return;
public void mouseClicked(MouseEvent evt)
{
SequenceGroup sg = null;
- SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
+ MousePos pos = findMousePosition(evt);
+ if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1)
+ {
+ return;
+ }
+
if (evt.getClickCount() > 1)
{
sg = av.getSelectionGroup();
av.setSelectionGroup(null);
}
- int column = findColumn(evt);
+ int column = pos.column;
/*
* find features at the position (if not gapped), or straddling
* the position (if at a gap)
*/
+ SequenceI sequence = av.getAlignment().getSequenceAt(pos.seqIndex);
List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
.findFeaturesAtColumn(sequence, column + 1);
/**
* DOCUMENT ME!
*
- * @param evt
+ * @param pos
* DOCUMENT ME!
*/
- public void doMousePressedDefineMode(MouseEvent evt)
+ protected void doMousePressedDefineMode(MouseEvent evt, MousePos pos)
{
- final int res = findColumn(evt);
- final int seq = findSeq(evt);
- oldSeq = seq;
- updateOverviewAndStructs = false;
-
- startWrapBlock = wrappedBlock;
-
- if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
+ if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString(
- "label.cannot_edit_annotations_in_wrapped_view"),
- MessageManager.getString("label.wrapped_view_no_edit"),
- JvOptionPane.WARNING_MESSAGE);
return;
}
- if (seq < 0 || res < 0)
- {
- return;
- }
+ final int res = pos.column;
+ final int seq = pos.seqIndex;
+ oldSeq = seq;
+ updateOverviewAndStructs = false;
+
+ startWrapBlock = wrappedBlock;
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
if (evt.isPopupTrigger()) // Mac: mousePressed
{
- showPopupMenu(evt);
+ showPopupMenu(evt, pos);
return;
}
if (av.cursorMode)
{
- seqCanvas.cursorX = findColumn(evt);
- seqCanvas.cursorY = findSeq(evt);
+ seqCanvas.cursorX = res;
+ seqCanvas.cursorY = seq;
seqCanvas.repaint();
return;
}
/**
* Build and show a pop-up menu at the right-click mouse position
- *
+ *
* @param evt
- * @param res
- * @param sequences
+ * @param pos
*/
- void showPopupMenu(MouseEvent evt)
+ void showPopupMenu(MouseEvent evt, MousePos pos)
{
- final int column = findColumn(evt);
- final int seq = findSeq(evt);
+ final int column = pos.column;
+ final int seq = pos.seqIndex;
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
List<SequenceFeature> features = ap.getFeatureRenderer()
.findFeaturesAtColumn(sequence, column + 1);
* true if this event is happening after a mouse drag (rather than a
* mouse down)
*/
- public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
+ protected void doMouseReleasedDefineMode(MouseEvent evt,
+ boolean afterDrag)
{
if (stretchGroup == null)
{
&& afterDrag;
if (stretchGroup.cs != null)
{
- stretchGroup.cs.alignmentChanged(stretchGroup,
- av.getHiddenRepSequences());
+ if (afterDrag)
+ {
+ stretchGroup.cs.alignmentChanged(stretchGroup,
+ av.getHiddenRepSequences());
+ }
ResidueShaderI groupColourScheme = stretchGroup
.getGroupColourScheme();
}
/**
- * DOCUMENT ME!
+ * Resizes the borders of a selection group depending on the direction of
+ * mouse drag
*
* @param evt
- * DOCUMENT ME!
*/
- public void doMouseDraggedDefineMode(MouseEvent evt)
+ protected void dragStretchGroup(MouseEvent evt)
{
- int res = findColumn(evt);
- int y = findSeq(evt);
-
- if (wrappedBlock != startWrapBlock)
+ if (stretchGroup == null)
{
return;
}
- if (stretchGroup == null)
+ MousePos pos = findMousePosition(evt);
+ if (pos.isOverAnnotation() || pos.column == -1 || pos.seqIndex == -1)
{
return;
}
- if (res >= av.getAlignment().getWidth())
+ int res = pos.column;
+ int y = pos.seqIndex;
+
+ if (wrappedBlock != startWrapBlock)
{
- res = av.getAlignment().getWidth() - 1;
+ return;
}
+ res = Math.min(res, av.getAlignment().getWidth()-1);
+
if (stretchGroup.getEndRes() == res)
{
// Edit end res position of selected group
mouseDragging = true;
- if ((scrollThread != null) && (scrollThread.isRunning()))
+ if (scrollThread != null)
{
- scrollThread.setEvent(evt);
+ scrollThread.setMousePosition(evt.getPoint());
}
+
+ /*
+ * construct a status message showing the range of the selection
+ */
+ StringBuilder status = new StringBuilder(64);
+ List<SequenceI> seqs = stretchGroup.getSequences();
+ String name = seqs.get(0).getName();
+ if (name.length() > 20)
+ {
+ name = name.substring(0, 20);
+ }
+ status.append(name).append(" - ");
+ name = seqs.get(seqs.size() - 1).getName();
+ if (name.length() > 20)
+ {
+ name = name.substring(0, 20);
+ }
+ status.append(name).append(" ");
+ int startRes = stretchGroup.getStartRes();
+ status.append(" cols ").append(String.valueOf(startRes + 1))
+ .append("-");
+ int endRes = stretchGroup.getEndRes();
+ status.append(String.valueOf(endRes + 1));
+ status.append(" (").append(String.valueOf(seqs.size())).append(" x ")
+ .append(String.valueOf(endRes - startRes + 1)).append(")");
+ ap.alignFrame.setStatus(status.toString());
}
- void scrollCanvas(MouseEvent evt)
+ /**
+ * Stops the scroll thread if it is running
+ */
+ void stopScrolling()
{
- if (evt == null)
+ if (scrollThread != null)
{
- if ((scrollThread != null) && (scrollThread.isRunning()))
- {
- scrollThread.stopScrolling();
- scrollThread = null;
- }
- mouseDragging = false;
+ scrollThread.stopScrolling();
+ scrollThread = null;
}
- else
- {
- if (scrollThread == null)
- {
- scrollThread = new ScrollThread();
- }
+ mouseDragging = false;
+ }
- mouseDragging = true;
- scrollThread.setEvent(evt);
+ /**
+ * Starts a thread to scroll the alignment, towards a given mouse position
+ * outside the panel bounds
+ *
+ * @param mousePos
+ */
+ void startScrolling(Point mousePos)
+ {
+ if (scrollThread == null)
+ {
+ scrollThread = new ScrollThread();
}
+ mouseDragging = true;
+ scrollThread.setMousePosition(mousePos);
}
- // this class allows scrolling off the bottom of the visible alignment
+ /**
+ * Performs scrolling of the visible alignment left, right, up or down
+ */
class ScrollThread extends Thread
{
- MouseEvent evt;
+ private Point mousePos;
private volatile boolean threadRunning = true;
+ /**
+ * Constructor
+ */
public ScrollThread()
{
+ setName("SeqPanel$ScrollThread");
start();
}
- public void setEvent(MouseEvent e)
+ /**
+ * Sets the position of the mouse that determines the direction of the
+ * scroll to perform
+ *
+ * @param p
+ */
+ public void setMousePosition(Point p)
{
- evt = e;
+ mousePos = p;
}
+ /**
+ * Sets a flag that will cause the thread to exit
+ */
public void stopScrolling()
{
threadRunning = false;
}
- public boolean isRunning()
- {
- return threadRunning;
- }
-
+ /**
+ * Scrolls the alignment left or right, and/or up or down, depending on the
+ * last notified mouse position, until the limit of the alignment is
+ * reached, or a flag is set to stop the scroll
+ */
@Override
public void run()
{
- while (threadRunning)
+ while (threadRunning && mouseDragging)
{
- if (evt != null)
+ if (mousePos != null)
{
- if (mouseDragging && (evt.getY() < 0)
- && (av.getRanges().getStartSeq() > 0))
+ boolean scrolled = false;
+ ViewportRanges ranges = SeqPanel.this.av.getRanges();
+
+ /*
+ * scroll up or down
+ */
+ if (mousePos.y < 0)
{
- av.getRanges().scrollUp(true);
+ // mouse is above this panel - try scroll up
+ scrolled = ranges.scrollUp(true);
}
-
- if (mouseDragging && (evt.getY() >= getHeight()) && (av
- .getAlignment().getHeight() > av.getRanges().getEndSeq()))
+ else if (mousePos.y >= getHeight())
{
- av.getRanges().scrollUp(false);
+ // mouse is below this panel - try scroll down
+ scrolled = ranges.scrollUp(false);
}
- if (mouseDragging && (evt.getX() < 0))
+ /*
+ * scroll left or right
+ */
+ if (mousePos.x < 0)
{
- av.getRanges().scrollRight(false);
+ scrolled |= ranges.scrollRight(false);
}
- else if (mouseDragging && (evt.getX() >= getWidth()))
+ else if (mousePos.x >= getWidth())
{
- av.getRanges().scrollRight(true);
+ scrolled |= ranges.scrollRight(true);
+ }
+ if (!scrolled)
+ {
+ /*
+ * we have reached the limit of the visible alignment - quit
+ */
+ threadRunning = false;
+ SeqPanel.this.ap.repaint();
}
}
HiddenColumns hs = new HiddenColumns();
MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
av.setColumnSelection(cs);
- av.getAlignment().setHiddenColumns(hs);
+ boolean hiddenChanged = av.getAlignment().setHiddenColumns(hs);
// lastly, update any dependent dialogs
if (ap.getCalculationDialog() != null)
ap.getCalculationDialog().validateCalcTypes();
}
- PaintRefresher.Refresh(this, av.getSequenceSetId());
+ /*
+ * repaint alignment, and also Overview or Structure
+ * if hidden column selection has changed
+ */
+ ap.paintAlignment(hiddenChanged, hiddenChanged);
return true;
}
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- af.statusBar.setText(MessageManager
+ af.setStatus(MessageManager
.getString("label.successfully_pasted_alignment_file"));
try
import jalview.renderer.ResidueShaderI;
import jalview.util.MessageManager;
+import java.awt.event.ActionEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.beans.PropertyVetoException;
public void setAllGroupsCheckEnabled(boolean b)
{
allGroupsCheck.setEnabled(b);
- allGroupsCheck.setSelected(ap.av.getColourAppliesToAllGroups());
}
/**
}
return title;
}
+
+ @Override
+ protected void allGroupsCheck_actionPerformed(ActionEvent e)
+ {
+ if (allGroupsCheck.isSelected())
+ {
+ valueChanged(slider.getValue());
+ }
+ }
}
{
AlignmentI al = getAlignmentPanel().av.getAlignment();
ColourSchemeI cs = ColourSchemes.getInstance()
- .getColourScheme(colourSchemeName, al, null);
+ .getColourScheme(colourSchemeName, getAlignmentPanel().av, al,
+ null);
getBinding().setJalviewColourScheme(cs);
}
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
import jalview.structure.SelectionSource;
import jalview.util.Format;
-import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import java.awt.Color;
return;
}
- if ((node.left() == null) && (node.right() == null)) // TODO: internal node
+ node.color = c;
+ if (node.element() instanceof SequenceI)
{
- node.color = c;
-
- if (node.element() instanceof SequenceI)
+ final SequenceI seq = (SequenceI) node.element();
+ AlignmentPanel[] aps = getAssociatedPanels();
+ if (aps != null)
{
- AlignmentPanel[] aps = getAssociatedPanels();
- if (aps != null)
+ for (int a = 0; a < aps.length; a++)
{
- for (int a = 0; a < aps.length; a++)
- {
- final SequenceI seq = (SequenceI) node.element();
- aps[a].av.setSequenceColour(seq, c);
- }
+ aps[a].av.setSequenceColour(seq, c);
}
}
}
- else
- {
- node.color = c;
- setColor((SequenceNode) node.left(), c);
- setColor((SequenceNode) node.right(), c);
- }
+ setColor((SequenceNode) node.left(), c);
+ setColor((SequenceNode) node.right(), c);
}
/**
.deleteAllGroups();
aps[a].av.getCodingComplement().clearSequenceColours();
}
+ aps[a].av.setUpdateStructures(true);
}
colourGroups(groups);
}
ColourSchemeI cs = null;
- SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
+ SequenceGroup _sg = new SequenceGroup(sequences, null, cs, true, true,
false, 0, av.getAlignment().getWidth() - 1);
- if (av.getGlobalColourScheme() != null)
- {
- if (av.getGlobalColourScheme() instanceof UserColourScheme)
- {
- cs = new UserColourScheme(
- ((UserColourScheme) av.getGlobalColourScheme())
- .getColours());
-
- }
- else
- {
- cs = ColourSchemeProperty.getColourScheme(sg, ColourSchemeProperty
- .getColourName(av.getGlobalColourScheme()));
- }
- // cs is null if shading is an annotationColourGradient
- // if (cs != null)
- // {
- // cs.setThreshold(av.getViewportColourScheme().getThreshold(),
- // av.isIgnoreGapsConsensus());
- // }
- }
- sg.setColourScheme(cs);
- sg.getGroupColourScheme().setThreshold(
- av.getResidueShading().getThreshold(),
- av.isIgnoreGapsConsensus());
- // sg.recalcConservation();
- sg.setName("JTreeGroup:" + sg.hashCode());
- sg.setIdColour(col);
+ _sg.setName("JTreeGroup:" + _sg.hashCode());
+ _sg.setIdColour(col);
for (int a = 0; a < aps.length; a++)
{
- if (aps[a].av.getGlobalColourScheme() != null
- && aps[a].av.getResidueShading().conservationApplied())
- {
- Conservation c = new Conservation("Group", sg.getSequences(null),
- sg.getStartRes(), sg.getEndRes());
- c.calculate();
- c.verdict(false, aps[a].av.getConsPercGaps());
- sg.cs.setConservation(c);
- }
+ SequenceGroup sg = new SequenceGroup(_sg);
+ AlignViewport viewport = aps[a].av;
- aps[a].av.getAlignment().addGroup(new SequenceGroup(sg));
- // TODO can we push all of the below into AlignViewportI?
- final AlignViewportI codingComplement = aps[a].av
- .getCodingComplement();
- if (codingComplement != null)
+ // Propagate group colours in each view
+ if (viewport.getGlobalColourScheme() != null)
{
- SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,
- codingComplement);
- if (mappedGroup.getSequences().size() > 0)
+ cs = viewport.getGlobalColourScheme().getInstance(viewport, sg);
+ sg.setColourScheme(cs);
+ sg.getGroupColourScheme().setThreshold(
+ viewport.getResidueShading().getThreshold(),
+ viewport.isIgnoreGapsConsensus());
+
+ if (viewport.getResidueShading().conservationApplied())
{
- codingComplement.getAlignment().addGroup(mappedGroup);
- for (SequenceI seq : mappedGroup.getSequences())
- {
- codingComplement.setSequenceColour(seq, col.brighter());
- }
+ Conservation c = new Conservation("Group",
+ sg.getSequences(null), sg.getStartRes(),
+ sg.getEndRes());
+ c.calculate();
+ c.verdict(false, viewport.getConsPercGaps());
+ sg.cs.setConservation(c);
}
}
+ // indicate that associated structure views will need an update
+ viewport.setUpdateStructures(true);
+ // propagate structure view update and sequence group to complement view
+ viewport.addSequenceGroup(sg);
}
}
- // notify the panel(s) to redo any group specific stuff.
+ // notify the panel(s) to redo any group specific stuff
+ // also updates structure views if necessary
for (int a = 0; a < aps.length; a++)
{
aps[a].updateAnnotation();
- // TODO: JAL-868 - need to ensure view colour change message is broadcast
- // to any Jmols listening in
final AlignViewportI codingComplement = aps[a].av
.getCodingComplement();
if (codingComplement != null)
{
this.threshold = threshold;
}
+
+ public boolean isApplyToAllViews()
+ {
+ return this.applyToAllViews;
+ }
+
+ public void setApplyToAllViews(boolean applyToAllViews)
+ {
+ this.applyToAllViews = applyToAllViews;
+ }
}
/*
* put them together as <method> Using <model>
*/
- final String ttl = MessageManager.formatMessage("label.treecalc_title",
+ final String ttl = MessageManager.formatMessage("label.calc_title",
treecalcnm, smn);
return ttl;
}
}
else if (key.equalsIgnoreCase("colour"))
{
+ // TODO need to notify colourscheme of view reference once it is
+ // available
sg.cs.setColourScheme(
- ColourSchemeProperty.getColourScheme(al, value));
+ ColourSchemeProperty.getColourScheme(null, al, value));
}
else if (key.equalsIgnoreCase("pidThreshold"))
{
--- /dev/null
+package jalview.io;
+
+import java.io.File;
+import java.io.FilenameFilter;
+import java.io.IOException;
+
+public class BackupFilenameFilter implements FilenameFilter
+{
+
+ public String base;
+
+ public String template;
+
+ public int digits;
+
+ public BackupFilenameFilter(String base, String template, int digits)
+ {
+ this.base = base;
+ this.template = template;
+ this.digits = digits;
+ }
+
+ @Override
+ public boolean accept(File dir, String filename)
+ {
+ try
+ {
+ File file = new File(
+ dir.getCanonicalPath() + File.separatorChar + filename);
+ if (file.isDirectory())
+ {
+ // backup files aren't dirs!
+ return false;
+ }
+ } catch (IOException e)
+ {
+ System.out.println("IOException when checking file '" + filename
+ + "' is a backupfile");
+ }
+
+ BackupFilenameParts bffp = new BackupFilenameParts(filename, base,
+ template, digits);
+ return bffp.isBackupFile();
+ }
+
+}
--- /dev/null
+package jalview.io;
+
+import jalview.bin.Cache;
+
+import java.io.File;
+
+public class BackupFilenameParts
+{
+ private String base;
+
+ private String templateStart;
+
+ private int num;
+
+ private int digits;
+
+ private String templateEnd;
+
+ private boolean isBackupFile;
+
+ private BackupFilenameParts()
+ {
+ this.isBackupFile = false;
+ }
+
+ public BackupFilenameParts(File file, String base, String template,
+ int digits)
+ {
+ this(file.getName(), base, template, digits);
+ }
+
+ public BackupFilenameParts(String filename, String base, String template,
+ int suggesteddigits)
+ {
+ this(filename, base, template, suggesteddigits, false);
+ }
+
+ public BackupFilenameParts(String filename, String base, String template,
+ int suggesteddigits, boolean extensionMatch)
+ {
+ this.isBackupFile = false;
+
+ int numcharstart = template.indexOf(BackupFiles.NUM_PLACEHOLDER);
+ int digits = 0;
+ String templateStart = template;
+ String templateEnd = "";
+ if (numcharstart > -1)
+ {
+ templateStart = template.substring(0, numcharstart);
+ templateEnd = template.substring(
+ numcharstart + BackupFiles.NUM_PLACEHOLDER.length());
+ digits = suggesteddigits;
+ }
+
+ String savedFilename = "";
+ // if extensionOnly is set then reset the filename to the last occurrence of the extension+templateStart and try the match
+ if (extensionMatch)
+ {
+ // only trying to match from extension onwards
+
+ int extensioncharstart = filename
+ .lastIndexOf('.' + base + templateStart);
+ if (extensioncharstart == -1)
+ {
+ return;
+ }
+
+ savedFilename = filename.substring(0, extensioncharstart + 1); // include
+ // the "."
+ filename = filename.substring(extensioncharstart + 1);
+ }
+
+ // full filename match
+
+ // calculate minimum length of a backup filename
+ int minlength = base.length() + template.length()
+ - BackupFiles.NUM_PLACEHOLDER.length() + digits;
+
+ if (!(filename.startsWith(base + templateStart)
+ && filename.endsWith(templateEnd)
+ && filename.length() >= minlength))
+ {
+ // non-starter
+ return;
+ }
+
+ int startLength = base.length() + templateStart.length();
+ int endLength = templateEnd.length();
+ String numString = numcharstart > -1
+ ? filename.substring(startLength, filename.length() - endLength)
+ : "";
+
+ if (filename.length() >= startLength + digits + endLength
+ && filename.startsWith(base + templateStart)
+ && filename.endsWith(templateEnd)
+ // match exactly digits number of number-characters (numString
+ // should be all digits and at least the right length), or more than
+ // digits long with proviso it's not zero-leading.
+ && (numString.matches("[0-9]{" + digits + "}")
+ || numString.matches("[1-9][0-9]{" + digits + ",}")))
+ {
+ this.base = extensionMatch ? savedFilename + base : base;
+ this.templateStart = templateStart;
+ this.num = numString.length() > 0 ? Integer.parseInt(numString) : 0;
+ this.digits = digits;
+ this.templateEnd = templateEnd;
+ this.isBackupFile = true;
+ }
+
+ }
+
+ public static BackupFilenameParts currentBackupFilenameParts(
+ String filename, String base, boolean extensionMatch)
+ {
+ BackupFilenameParts bfp = new BackupFilenameParts();
+ String template = Cache.getDefault(BackupFiles.SUFFIX, null);
+ if (template == null)
+ {
+ return bfp;
+ }
+ int digits;
+ try
+ {
+ digits = Integer
+ .parseInt(Cache.getDefault(BackupFiles.SUFFIX_DIGITS, null));
+ } catch (Exception e)
+ {
+ return bfp;
+ }
+ return new BackupFilenameParts(filename, base, template, digits,
+ extensionMatch);
+ }
+
+ public boolean isBackupFile()
+ {
+ return this.isBackupFile;
+ }
+
+ public int indexNum()
+ {
+ return this.num;
+ }
+
+ public static String getBackupFilename(int index, String base,
+ String template, int digits)
+ {
+ String numString = String.format("%0" + digits + "d", index);
+ String backupSuffix = template.replaceFirst(BackupFiles.NUM_PLACEHOLDER,
+ numString);
+ String backupfilename = base + backupSuffix;
+ return backupfilename;
+ }
+}
--- /dev/null
+package jalview.io;
+
+import jalview.bin.Cache;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
+
+import java.io.File;
+import java.io.IOException;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.TreeMap;
+
+/*
+ * BackupFiles used for manipulating (naming rolling/deleting) backup/version files when an alignment or project file is saved.
+ * User configurable options are:
+ * BACKUPFILES_ENABLED - boolean flag as to whether to use this mechanism or act as before, including overwriting files as saved.
+ * BACKUPFILES_SUFFIX - a template to insert after the file extension. Use '%n' to be replaced by a 0-led SUFFIX_DIGITS long integer.
+ * BACKUPFILES_NO_MAX - flag to turn off setting a maximum number of backup files to keep.
+ * BACKUPFILES_ROLL_MAX - the maximum number of backupfiles to keep for any one alignment or project file.
+ * BACKUPFILES_SUFFIX_DIGITS - the number of digits to insert replace %n with (e.g. BACKUPFILES_SUFFIX_DIGITS = 3 would make "001", "002", etc)
+ * BACKUPFILES_REVERSE_ORDER - if true then "logfile" style numbering and file rolling will occur. If false then ever-increasing version numbering will occur, but old files will still be deleted if there are more than ROLL_MAX backup files.
+ * BACKUPFILES_CONFIRM_DELETE_OLD - if true then prompt/confirm with the user when deleting older backup/version files.
+ */
+
+public class BackupFiles
+{
+
+ // labels for saved params in Cache and .jalview_properties
+ public static final String NS = "BACKUPFILES";
+
+ public static final String ENABLED = NS + "_ENABLED";
+
+ public static final String SUFFIX = NS + "_SUFFIX";
+
+ public static final String NO_MAX = NS + "_NO_MAX";
+
+ public static final String ROLL_MAX = NS + "_ROLL_MAX";
+
+ public static final String SUFFIX_DIGITS = NS + "_SUFFIX_DIGITS";
+
+ public static final String NUM_PLACEHOLDER = "%n";
+
+ public static final String REVERSE_ORDER = NS + "_REVERSE_ORDER";
+
+ public static final String CONFIRM_DELETE_OLD = NS
+ + "_CONFIRM_DELETE_OLD";
+
+ private static final String DEFAULT_TEMP_FILE = "jalview_temp_file_" + NS;
+
+ private static final String TEMP_FILE_EXT = ".tmp";
+
+ // file - File object to be backed up and then updated (written over)
+ private File file;
+
+ // enabled - default flag as to whether to do the backup file roll (if not
+ // defined in preferences)
+ private static boolean enabled;
+
+ // confirmDelete - default flag as to whether to confirm with the user before
+ // deleting old backup/version files
+ private static boolean confirmDelete;
+
+ // defaultSuffix - default template to use to append to basename of file
+ private String suffix;
+
+ // noMax - flag to turn off a maximum number of files
+ private boolean noMax;
+
+ // defaultMax - default max number of backup files
+ private int max;
+
+ // defaultDigits - number of zero-led digits to use in the filename
+ private int digits;
+
+ // reverseOrder - set to true to make newest (latest) files lowest number
+ // (like rolled log files)
+ private boolean reverseOrder;
+
+ // temp saved file to become new saved file
+ private File tempFile;
+
+ // flag set to see if file save to temp file was successful
+ private boolean tempFileWriteSuccess;
+
+ // array of files to be deleted, with extra information
+ private ArrayList<File> deleteFiles = new ArrayList<>();
+
+ // date formatting for modification times
+ private static final SimpleDateFormat sdf = new SimpleDateFormat(
+ "yyyy-MM-dd HH:mm:ss");
+
+ public BackupFiles(String filename)
+ {
+ this(new File(filename));
+ }
+
+ // first time defaults for SUFFIX, NO_MAX, ROLL_MAX, SUFFIX_DIGITS and
+ // REVERSE_ORDER
+ public BackupFiles(File file)
+ {
+ this(file, ".bak" + NUM_PLACEHOLDER, false, 3, 3, false);
+ }
+
+ public BackupFiles(File file, String defaultSuffix, boolean defaultNoMax,
+ int defaultMax, int defaultDigits, boolean defaultReverseOrder)
+ {
+ classInit();
+ this.file = file;
+ this.suffix = Cache.getDefault(SUFFIX, defaultSuffix);
+ this.noMax = Cache.getDefault(NO_MAX, defaultNoMax);
+ this.max = Cache.getDefault(ROLL_MAX, defaultMax);
+ this.digits = Cache.getDefault(SUFFIX_DIGITS, defaultDigits);
+ this.reverseOrder = Cache.getDefault(REVERSE_ORDER,
+ defaultReverseOrder);
+
+ // create a temp file to save new data in
+ File temp = null;
+ try
+ {
+ if (file != null)
+ {
+ String tempfilename = file.getName();
+ File tempdir = file.getParentFile();
+ temp = File.createTempFile(tempfilename, TEMP_FILE_EXT + "_newfile",
+ tempdir);
+ }
+ else
+ {
+ temp = File.createTempFile(DEFAULT_TEMP_FILE, TEMP_FILE_EXT);
+ }
+ } catch (IOException e)
+ {
+ System.out.println(
+ "Could not create temp file to save into (IOException)");
+ } catch (Exception e)
+ {
+ System.out.println("Exception ctreating temp file for saving");
+ }
+ this.setTempFile(temp);
+ }
+
+ public static void classInit()
+ {
+ setEnabled(Cache.getDefault(ENABLED, true));
+ setConfirmDelete(Cache.getDefault(CONFIRM_DELETE_OLD, true));
+ }
+
+ public static void setEnabled(boolean flag)
+ {
+ enabled = flag;
+ }
+
+ public static boolean getEnabled()
+ {
+ classInit();
+ return enabled;
+ }
+
+ public static void setConfirmDelete(boolean flag)
+ {
+ confirmDelete = flag;
+ }
+
+ public static boolean getConfirmDelete()
+ {
+ classInit();
+ return confirmDelete;
+ }
+
+ // set, get and rename temp file into place
+ public void setTempFile(File temp)
+ {
+ this.tempFile = temp;
+ }
+
+ public File getTempFile()
+ {
+ return tempFile;
+ }
+
+ public String getTempFilePath()
+ {
+ String path = null;
+ try
+ {
+ path = this.getTempFile().getCanonicalPath();
+ } catch (IOException e)
+ {
+ System.out.println(
+ "IOException when getting Canonical Path of temp file '"
+ + this.getTempFile().getName() + "'");
+ }
+ return path;
+ }
+
+ public boolean setWriteSuccess(boolean flag)
+ {
+ boolean old = this.tempFileWriteSuccess;
+ this.tempFileWriteSuccess = flag;
+ return old;
+ }
+
+ public boolean getWriteSuccess()
+ {
+ return this.tempFileWriteSuccess;
+ }
+
+ public boolean renameTempFile()
+ {
+ return tempFile.renameTo(file);
+ }
+
+ // roll the backupfiles
+ public boolean rollBackupFiles()
+ {
+ return this.rollBackupFiles(true);
+ }
+
+ public boolean rollBackupFiles(boolean tidyUp)
+ {
+ // file doesn't yet exist or backups are not enabled or template is null or
+ // empty
+ if ((!file.exists()) || (!enabled) || max < 0 || suffix == null
+ || suffix.length() == 0)
+ {
+ // nothing to do
+ return true;
+ }
+
+ String dir = "";
+ File dirFile;
+ try
+ {
+ dirFile = file.getParentFile();
+ dir = dirFile.getCanonicalPath();
+ } catch (Exception e)
+ {
+ System.out.println(
+ "Could not get canonical path for file '" + file + "'");
+ return false;
+ }
+ String filename = file.getName();
+ String basename = filename;
+
+ boolean ret = true;
+ // Create/move backups up one
+
+ deleteFiles.clear();
+
+ // find existing backup files
+ BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix,
+ digits);
+ File[] backupFiles = dirFile.listFiles(bff);
+ int nextIndexNum = 0;
+
+ if (backupFiles.length == 0)
+ {
+ // No other backup files. Just need to move existing file to backupfile_1
+ nextIndexNum = 1;
+ }
+ else
+ {
+ TreeMap<Integer, File> bfTreeMap = sortBackupFilesAsTreeMap(
+ backupFiles, basename);
+ // bfTreeMap now a sorted list of <Integer index>,<File backupfile>
+ // mappings
+
+ if (reverseOrder)
+ {
+ // backup style numbering
+
+
+ int tempMax = noMax ? -1 : max;
+ // noMax == true means no limits
+ // look for first "gap" in backupFiles
+ // if tempMax is -1 at this stage just keep going until there's a gap,
+ // then hopefully tempMax gets set to the right index (a positive
+ // integer so the loop breaks)...
+ // why do I feel a little uneasy about this loop?..
+ for (int i = 1; tempMax < 0 || i <= max; i++)
+ {
+ if (!bfTreeMap.containsKey(i)) // first index without existent
+ // backupfile
+ {
+ tempMax = i;
+ }
+ }
+
+ File previousFile = null;
+ File fileToBeDeleted = null;
+ for (int n = tempMax; n > 0; n--)
+ {
+ String backupfilename = dir + File.separatorChar
+ + BackupFilenameParts.getBackupFilename(n, basename,
+ suffix, digits);
+ File backupfile_n = new File(backupfilename);
+
+ if (!backupfile_n.exists())
+ {
+ // no "oldest" file to delete
+ previousFile = backupfile_n;
+ fileToBeDeleted = null;
+ continue;
+ }
+
+ // check the modification time of this (backupfile_n) and the previous
+ // file (fileToBeDeleted) if the previous file is going to be deleted
+ if (fileToBeDeleted != null)
+ {
+ File replacementFile = backupfile_n;
+ long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
+ long replacementFileLMT = replacementFile.lastModified();
+
+ try
+ {
+ File oldestTempFile = nextTempFile(fileToBeDeleted.getName(),
+ dirFile);
+
+ if (fileToBeDeletedLMT > replacementFileLMT)
+ {
+ String fileToBeDeletedLMTString = sdf
+ .format(fileToBeDeletedLMT);
+ String replacementFileLMTString = sdf
+ .format(replacementFileLMT);
+ System.out.println("WARNING! I am set to delete backupfile "
+ + fileToBeDeleted.getName()
+ + " has modification time "
+ + fileToBeDeletedLMTString
+ + " which is newer than its replacement "
+ + replacementFile.getName()
+ + " with modification time "
+ + replacementFileLMTString);
+
+ boolean delete = confirmNewerDeleteFile(fileToBeDeleted,
+ replacementFile, true);
+
+ if (delete)
+ {
+ // User has confirmed delete -- no need to add it to the list
+ fileToBeDeleted.delete();
+ }
+ else
+ {
+ fileToBeDeleted.renameTo(oldestTempFile);
+ }
+ }
+ else
+ {
+ fileToBeDeleted.renameTo(oldestTempFile);
+ addDeleteFile(oldestTempFile);
+ }
+
+ } catch (Exception e)
+ {
+ System.out.println(
+ "Error occurred, probably making new temp file for '"
+ + fileToBeDeleted.getName() + "'");
+ e.printStackTrace();
+ }
+
+ // reset
+ fileToBeDeleted = null;
+ }
+
+ if (!noMax && n == tempMax && backupfile_n.exists())
+ {
+ fileToBeDeleted = backupfile_n;
+ }
+ else
+ {
+ if (previousFile != null)
+ {
+ ret = ret && backupfile_n.renameTo(previousFile);
+ }
+ }
+
+ previousFile = backupfile_n;
+ }
+
+ // index to use for the latest backup
+ nextIndexNum = 1;
+ }
+ else
+ {
+ // version style numbering (with earliest file deletion if max files
+ // reached)
+
+ bfTreeMap.values().toArray(backupFiles);
+
+ // noMax == true means keep all backup files
+ if ((!noMax) && bfTreeMap.size() >= max)
+ {
+ // need to delete some files to keep number of backups to designated
+ // max
+ int numToDelete = bfTreeMap.size() - max + 1;
+ // the "replacement" file is the latest backup file being kept (it's
+ // not replacing though)
+ File replacementFile = numToDelete < backupFiles.length
+ ? backupFiles[numToDelete]
+ : null;
+ for (int i = 0; i < numToDelete; i++)
+ {
+ // check the deletion files for modification time of the last
+ // backupfile being saved
+ File fileToBeDeleted = backupFiles[i];
+ boolean delete = true;
+
+ boolean newer = false;
+ if (replacementFile != null)
+ {
+ long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
+ long replacementFileLMT = replacementFile != null
+ ? replacementFile.lastModified()
+ : Long.MAX_VALUE;
+ if (fileToBeDeletedLMT > replacementFileLMT)
+ {
+ String fileToBeDeletedLMTString = sdf
+ .format(fileToBeDeletedLMT);
+ String replacementFileLMTString = sdf
+ .format(replacementFileLMT);
+
+ System.out
+ .println("WARNING! I am set to delete backupfile '"
+ + fileToBeDeleted.getName()
+ + "' has modification time "
+ + fileToBeDeletedLMTString
+ + " which is newer than the oldest backupfile being kept '"
+ + replacementFile.getName()
+ + "' with modification time "
+ + replacementFileLMTString);
+
+ delete = confirmNewerDeleteFile(fileToBeDeleted,
+ replacementFile, false);
+ if (delete)
+ {
+ // User has confirmed delete -- no need to add it to the list
+ fileToBeDeleted.delete();
+ delete = false;
+ }
+ else
+ {
+ // keeping file, nothing to do!
+ }
+ }
+ }
+ if (delete)
+ {
+ addDeleteFile(fileToBeDeleted);
+ }
+
+ }
+
+ }
+
+ nextIndexNum = bfTreeMap.lastKey() + 1;
+ }
+ }
+
+ // Let's make the new backup file!! yay, got there at last!
+ String latestBackupFilename = dir + File.separatorChar
+ + BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
+ suffix, digits);
+ ret |= file.renameTo(new File(latestBackupFilename));
+
+ if (tidyUp)
+ {
+ tidyUpFiles();
+ }
+
+ return ret;
+ }
+
+ private static File nextTempFile(String filename, File dirFile)
+ throws IOException
+ {
+ File temp = null;
+ COUNT: for (int i = 1; i < 1000; i++)
+ {
+ File trythis = new File(dirFile,
+ filename + '~' + Integer.toString(i));
+ if (!trythis.exists())
+ {
+ temp = trythis;
+ break COUNT;
+ }
+
+ }
+ if (temp == null)
+ {
+ temp = File.createTempFile(filename, TEMP_FILE_EXT, dirFile);
+ }
+ return temp;
+ }
+
+ private void tidyUpFiles()
+ {
+ deleteOldFiles();
+ }
+
+ private static boolean confirmNewerDeleteFile(File fileToBeDeleted,
+ File replacementFile, boolean replace)
+ {
+ StringBuilder messageSB = new StringBuilder();
+
+ File ftbd = fileToBeDeleted;
+ String ftbdLMT = sdf.format(ftbd.lastModified());
+ String ftbdSize = Long.toString(ftbd.length());
+
+ File rf = replacementFile;
+ String rfLMT = sdf.format(rf.lastModified());
+ String rfSize = Long.toString(rf.length());
+
+ int confirmButton = JvOptionPane.NO_OPTION;
+ if (replace)
+ {
+ File saveFile = null;
+ try
+ {
+ saveFile = nextTempFile(ftbd.getName(), ftbd.getParentFile());
+ } catch (Exception e)
+ {
+ System.out.println(
+ "Error when confirming to keep backup file newer than other backup files.");
+ e.printStackTrace();
+ }
+ messageSB.append(MessageManager.formatMessage(
+ "label.newerdelete_replacement_line", new String[]
+ { ftbd.getName(), rf.getName(), ftbdLMT, rfLMT, ftbdSize,
+ rfSize }));
+ messageSB.append("\n\n");
+ messageSB.append(MessageManager.formatMessage(
+ "label.confirm_deletion_or_rename", new String[]
+ { ftbd.getName(), saveFile.getName() }));
+ String[] options = new String[] {
+ MessageManager.getString("label.delete"),
+ MessageManager.getString("label.rename") };
+
+ confirmButton = JvOptionPane.showOptionDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager.getString("label.backupfiles_confirm_delete"),
+ JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
+ null, options, options[0]);
+ }
+ else
+ {
+ messageSB.append(MessageManager
+ .formatMessage("label.newerdelete_line", new String[]
+ { ftbd.getName(), rf.getName(), ftbdLMT, rfLMT, ftbdSize,
+ rfSize }));
+ messageSB.append("\n\n");
+ messageSB.append(MessageManager
+ .formatMessage("label.confirm_deletion", new String[]
+ { ftbd.getName() }));
+ String[] options = new String[] {
+ MessageManager.getString("label.delete"),
+ MessageManager.getString("label.keep") };
+
+ confirmButton = JvOptionPane.showOptionDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager.getString("label.backupfiles_confirm_delete"),
+ JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
+ null, options, options[0]);
+ }
+
+
+ // return should be TRUE if file is to be deleted
+ return (confirmButton == JvOptionPane.YES_OPTION);
+ }
+
+ private void deleteOldFiles()
+ {
+ if (deleteFiles != null && !deleteFiles.isEmpty())
+ {
+ boolean doDelete = false;
+ StringBuilder messageSB = null;
+ if (confirmDelete && deleteFiles.size() > 0)
+ {
+ messageSB = new StringBuilder();
+ messageSB.append(MessageManager
+ .getString("label.backupfiles_confirm_delete_old_files"));
+ for (int i = 0; i < deleteFiles.size(); i++)
+ {
+ File df = deleteFiles.get(i);
+ messageSB.append("\n");
+ messageSB.append(df.getName());
+ messageSB.append(" ");
+ messageSB.append(MessageManager.formatMessage("label.file_info",
+ new String[]
+ { sdf.format(df.lastModified()),
+ Long.toString(df.length()) }));
+ }
+
+ int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager
+ .getString("label.backupfiles_confirm_delete"),
+ JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
+
+ doDelete = (confirmButton == JvOptionPane.YES_OPTION);
+ }
+ else
+ {
+ doDelete = true;
+ }
+
+ if (doDelete)
+ {
+ for (int i = 0; i < deleteFiles.size(); i++)
+ {
+ File fileToDelete = deleteFiles.get(i);
+ fileToDelete.delete();
+ System.out.println("DELETING '" + fileToDelete.getName() + "'");
+ }
+ }
+
+ }
+
+ deleteFiles.clear();
+ }
+
+ private TreeMap<Integer, File> sortBackupFilesAsTreeMap(
+ File[] backupFiles,
+ String basename)
+ {
+ // sort the backup files (based on integer found in the suffix) using a
+ // precomputed Hashmap for speed
+ Map<Integer, File> bfHashMap = new HashMap<>();
+ for (int i = 0; i < backupFiles.length; i++)
+ {
+ File f = backupFiles[i];
+ BackupFilenameParts bfp = new BackupFilenameParts(f, basename, suffix,
+ digits);
+ bfHashMap.put(bfp.indexNum(), f);
+ }
+ TreeMap<Integer, File> bfTreeMap = new TreeMap<>();
+ bfTreeMap.putAll(bfHashMap);
+ return bfTreeMap;
+ }
+
+ public boolean rollBackupsAndRenameTempFile()
+ {
+ boolean write = this.getWriteSuccess();
+
+ boolean roll = false;
+ boolean rename = false;
+ if (write)
+ {
+ roll = this.rollBackupFiles(false);
+ rename = this.renameTempFile();
+ }
+
+ /*
+ * Not sure that this confirmation is desirable. By this stage the new file is
+ * already written successfully, but something (e.g. disk full) has happened while
+ * trying to roll the backup files, and most likely the filename needed will already
+ * be vacant so renaming the temp file is nearly always correct!
+ */
+ boolean okay = roll && rename;
+ if (!okay)
+ {
+ StringBuilder messageSB = new StringBuilder();
+ messageSB.append(MessageManager.getString( "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
+ if (rename)
+ {
+ if (messageSB.length() > 0)
+ {
+ messageSB.append("\n");
+ }
+ messageSB.append(MessageManager.getString(
+ "label.backupfiles_confirm_save_new_saved_file_ok"));
+ }
+ else
+ {
+ if (messageSB.length() > 0)
+ {
+ messageSB.append("\n");
+ }
+ messageSB.append(MessageManager.getString(
+ "label.backupfiles_confirm_save_new_saved_file_not_ok"));
+ }
+
+ int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager
+ .getString("label.backupfiles_confirm_save_file"),
+ JvOptionPane.OK_OPTION, JvOptionPane.WARNING_MESSAGE);
+ okay = confirmButton == JvOptionPane.OK_OPTION;
+ }
+ if (okay)
+ {
+ tidyUpFiles();
+ }
+
+ return rename;
+ }
+
+ public static TreeMap<Integer, File> getBackupFilesAsTreeMap(
+ String fileName, String suffix, int digits)
+ {
+ File[] backupFiles = null;
+
+ File file = new File(fileName);
+
+ File dirFile;
+ try
+ {
+ dirFile = file.getParentFile();
+ } catch (Exception e)
+ {
+ System.out.println(
+ "Could not get canonical path for file '" + file + "'");
+ return new TreeMap<>();
+ }
+
+ String filename = file.getName();
+ String basename = filename;
+
+ // find existing backup files
+ BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix,
+ digits);
+ backupFiles = dirFile.listFiles(bff); // is clone needed?
+
+ // sort the backup files (based on integer found in the suffix) using a
+ // precomputed Hashmap for speed
+ Map<Integer, File> bfHashMap = new HashMap<>();
+ for (int i = 0; i < backupFiles.length; i++)
+ {
+ File f = backupFiles[i];
+ BackupFilenameParts bfp = new BackupFilenameParts(f, basename, suffix,
+ digits);
+ bfHashMap.put(bfp.indexNum(), f);
+ }
+ TreeMap<Integer, File> bfTreeMap = new TreeMap<>();
+ bfTreeMap.putAll(bfHashMap);
+
+ return bfTreeMap;
+ }
+
+ /*
+ private boolean addDeleteFile(File fileToBeDeleted, File originalFile,
+ boolean delete, boolean newer)
+ {
+ return addDeleteFile(fileToBeDeleted, originalFile, null, delete, newer);
+ }
+ */
+ private boolean addDeleteFile(File fileToBeDeleted)
+ {
+ boolean ret = false;
+ int pos = deleteFiles.indexOf(fileToBeDeleted);
+ if (pos > -1)
+ {
+ return true;
+ }
+ else
+ {
+ deleteFiles.add(fileToBeDeleted);
+ }
+ return ret;
+ }
+
+}
import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
+import jalview.api.FeatureRenderer;
import jalview.api.FeaturesSourceI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
}
/**
- * Returns contents of a Jalview format features file, for visible features, as
- * filtered by type and group. Features with a null group are displayed if their
- * feature type is visible. Non-positional features may optionally be included
- * (with no check on type or group).
+ * Returns contents of a Jalview format features file, for visible features,
+ * as filtered by type and group. Features with a null group are displayed if
+ * their feature type is visible. Non-positional features may optionally be
+ * included (with no check on type or group).
*
* @param sequences
- * source of features
- * @param visible
- * map of colour for each visible feature type
- * @param featureFilters
- * @param visibleFeatureGroups
+ * @param fr
* @param includeNonPositional
* if true, include non-positional features (regardless of group or
* type)
* @return
*/
public String printJalviewFormat(SequenceI[] sequences,
- Map<String, FeatureColourI> visible,
- Map<String, FeatureMatcherSetI> featureFilters,
- List<String> visibleFeatureGroups, boolean includeNonPositional)
+ FeatureRenderer fr, boolean includeNonPositional)
{
- if (!includeNonPositional && (visible == null || visible.isEmpty()))
+ Map<String, FeatureColourI> visibleColours = fr
+ .getDisplayedFeatureCols();
+ Map<String, FeatureMatcherSetI> featureFilters = fr.getFeatureFilters();
+
+ if (!includeNonPositional
+ && (visibleColours == null || visibleColours.isEmpty()))
{
// no point continuing.
return "No Features Visible";
*/
// TODO: decide if feature links should also be written here ?
StringBuilder out = new StringBuilder(256);
- if (visible != null)
+ if (visibleColours != null)
{
- for (Entry<String, FeatureColourI> featureColour : visible.entrySet())
+ for (Entry<String, FeatureColourI> featureColour : visibleColours
+ .entrySet())
{
FeatureColourI colour = featureColour.getValue();
out.append(colour.toJalviewFormat(featureColour.getKey())).append(
}
}
- String[] types = visible == null ? new String[0] : visible.keySet()
- .toArray(new String[visible.keySet().size()]);
+ String[] types = visibleColours == null ? new String[0]
+ : visibleColours.keySet()
+ .toArray(new String[visibleColours.keySet().size()]);
/*
* feature filters if any
*/
- outputFeatureFilters(out, visible, featureFilters);
-
- /*
- * sort groups alphabetically, and ensure that features with a
- * null or empty group are output after those in named groups
- */
- List<String> sortedGroups = new ArrayList<>(visibleFeatureGroups);
- sortedGroups.remove(null);
- sortedGroups.remove("");
- Collections.sort(sortedGroups);
- sortedGroups.add(null);
- sortedGroups.add("");
-
- boolean foundSome = false;
-
- /*
- * first output any non-positional features
- */
- if (includeNonPositional)
- {
- for (int i = 0; i < sequences.length; i++)
- {
- String sequenceName = sequences[i].getName();
- for (SequenceFeature feature : sequences[i].getFeatures()
- .getNonPositionalFeatures())
- {
- foundSome = true;
- out.append(formatJalviewFeature(sequenceName, feature));
- }
- }
- }
+ outputFeatureFilters(out, visibleColours, featureFilters);
/*
- * positional features within groups
+ * output features within groups
*/
- foundSome |= outputFeaturesByGroup(out, sortedGroups, types, sequences);
+ int count = outputFeaturesByGroup(out, fr, types, sequences,
+ includeNonPositional);
- return foundSome ? out.toString() : "No Features Visible";
+ return count > 0 ? out.toString() : "No Features Visible";
}
/**
}
if (!first)
{
- out.append(ENDFILTERS).append(newline).append(newline);
+ out.append(ENDFILTERS).append(newline);
}
}
/**
- * Appends output of sequence features within feature groups to the output
- * buffer. Groups other than the null or empty group are sandwiched by
- * STARTGROUP and ENDGROUP lines.
+ * Appends output of visible sequence features within feature groups to the
+ * output buffer. Groups other than the null or empty group are sandwiched by
+ * STARTGROUP and ENDGROUP lines. Answers the number of features written.
*
* @param out
- * @param groups
+ * @param fr
* @param featureTypes
* @param sequences
+ * @param includeNonPositional
* @return
*/
- private boolean outputFeaturesByGroup(StringBuilder out,
- List<String> groups, String[] featureTypes, SequenceI[] sequences)
+ private int outputFeaturesByGroup(StringBuilder out,
+ FeatureRenderer fr, String[] featureTypes,
+ SequenceI[] sequences, boolean includeNonPositional)
{
- boolean foundSome = false;
- for (String group : groups)
+ List<String> featureGroups = fr.getFeatureGroups();
+
+ /*
+ * sort groups alphabetically, and ensure that features with a
+ * null or empty group are output after those in named groups
+ */
+ List<String> sortedGroups = new ArrayList<>(featureGroups);
+ sortedGroups.remove(null);
+ sortedGroups.remove("");
+ Collections.sort(sortedGroups);
+ sortedGroups.add(null);
+ sortedGroups.add("");
+
+ int count = 0;
+ List<String> visibleGroups = fr.getDisplayedFeatureGroups();
+
+ /*
+ * loop over all groups (may be visible or not);
+ * non-positional features are output even if group is not visible
+ */
+ for (String group : sortedGroups)
{
- boolean isNamedGroup = (group != null && !"".equals(group));
- if (isNamedGroup)
- {
- out.append(newline);
- out.append(STARTGROUP).append(TAB);
- out.append(group);
- out.append(newline);
- }
+ boolean firstInGroup = true;
+ boolean isNullGroup = group == null || "".equals(group);
- /*
- * output positional features within groups
- */
for (int i = 0; i < sequences.length; i++)
{
String sequenceName = sequences[i].getName();
List<SequenceFeature> features = new ArrayList<>();
- if (featureTypes.length > 0)
+
+ /*
+ * get any non-positional features in this group, if wanted
+ * (for any feature type, whether visible or not)
+ */
+ if (includeNonPositional)
+ {
+ features.addAll(sequences[i].getFeatures()
+ .getFeaturesForGroup(false, group));
+ }
+
+ /*
+ * add positional features for visible feature types, but
+ * (for named groups) only if feature group is visible
+ */
+ if (featureTypes.length > 0
+ && (isNullGroup || visibleGroups.contains(group)))
{
features.addAll(sequences[i].getFeatures().getFeaturesForGroup(
true, group, featureTypes));
}
- for (SequenceFeature sequenceFeature : features)
+ for (SequenceFeature sf : features)
{
- foundSome = true;
- out.append(formatJalviewFeature(sequenceName, sequenceFeature));
+ if (sf.isNonPositional() || fr.isVisible(sf))
+ {
+ count++;
+ if (firstInGroup)
+ {
+ out.append(newline);
+ if (!isNullGroup)
+ {
+ out.append(STARTGROUP).append(TAB).append(group)
+ .append(newline);
+ }
+ }
+ firstInGroup = false;
+ out.append(formatJalviewFeature(sequenceName, sf));
+ }
}
}
- if (isNamedGroup)
+ if (!isNullGroup && !firstInGroup)
{
- out.append(ENDGROUP).append(TAB);
- out.append(group);
- out.append(newline);
+ out.append(ENDGROUP).append(TAB).append(group).append(newline);
}
}
- return foundSome;
+ return count;
}
/**
* @return
*/
public String printGffFormat(SequenceI[] sequences,
- Map<String, FeatureColourI> visible,
- List<String> visibleFeatureGroups,
- boolean includeNonPositionalFeatures)
+ FeatureRenderer fr, boolean includeNonPositionalFeatures)
{
+ Map<String, FeatureColourI> visibleColours = fr.getDisplayedFeatureCols();
+
StringBuilder out = new StringBuilder(256);
out.append(String.format("%s %d\n", GFF_VERSION, gffVersion == 0 ? 2 : gffVersion));
if (!includeNonPositionalFeatures
- && (visible == null || visible.isEmpty()))
+ && (visibleColours == null || visibleColours.isEmpty()))
{
return out.toString();
}
- String[] types = visible == null ? new String[0] : visible.keySet()
- .toArray(
- new String[visible.keySet().size()]);
+ String[] types = visibleColours == null ? new String[0]
+ : visibleColours.keySet()
+ .toArray(new String[visibleColours.keySet().size()]);
for (SequenceI seq : sequences)
{
{
features.addAll(seq.getFeatures().getNonPositionalFeatures());
}
- if (visible != null && !visible.isEmpty())
+ if (visibleColours != null && !visibleColours.isEmpty())
{
features.addAll(seq.getFeatures().getPositionalFeatures(types));
}
for (SequenceFeature sf : features)
{
- String source = sf.featureGroup;
- if (!sf.isNonPositional() && source != null
- && !visibleFeatureGroups.contains(source))
+ if (!sf.isNonPositional() && !fr.isVisible(sf))
{
- // group is not visible
+ /*
+ * feature hidden by group visibility, colour threshold,
+ * or feature filter condition
+ */
continue;
}
+ String source = sf.featureGroup;
if (source == null)
{
source = sf.getDescription();
alignFrame.getViewport()
.applyFeaturesStyle(proxyColourScheme);
}
- alignFrame.statusBar.setText(MessageManager.formatMessage(
+ alignFrame.setStatus(MessageManager.formatMessage(
"label.successfully_loaded_file", new String[]
{ title }));
import java.awt.Dimension;
import java.awt.EventQueue;
import java.awt.HeadlessException;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.io.File;
import java.util.StringTokenizer;
import java.util.Vector;
+import javax.swing.BoxLayout;
import javax.swing.DefaultListCellRenderer;
+import javax.swing.JCheckBox;
import javax.swing.JFileChooser;
import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.SpringLayout;
+import javax.swing.SwingUtilities;
+import javax.swing.border.TitledBorder;
+import javax.swing.filechooser.FileFilter;
import javax.swing.plaf.basic.BasicFileChooserUI;
/**
public class JalviewFileChooser extends JFileChooser
{
/**
+ * backupfilesCheckBox = "Include backup files" checkbox includeBackupfiles =
+ * flag set by checkbox
+ */
+ private JCheckBox backupfilesCheckBox = null;
+
+ protected boolean includeBackupFiles = false;
+
+ /**
* Factory method to return a file chooser that offers readable alignment file
* formats
*
public static JalviewFileChooser forRead(String directory,
String selected)
{
+ return JalviewFileChooser.forRead(directory, selected, false);
+ }
+
+ public static JalviewFileChooser forRead(String directory,
+ String selected, boolean allowBackupFiles)
+ {
List<String> extensions = new ArrayList<>();
List<String> descs = new ArrayList<>();
for (FileFormatI format : FileFormats.getInstance().getFormats())
descs.add(format.getName());
}
}
+
return new JalviewFileChooser(directory,
extensions.toArray(new String[extensions.size()]),
- descs.toArray(new String[descs.size()]), selected, true);
+ descs.toArray(new String[descs.size()]), selected, true,
+ allowBackupFiles);
}
/**
JalviewFileChooser(String dir, String[] extensions, String[] descs,
String selected, boolean allFiles)
{
+ this(dir, extensions, descs, selected, allFiles, false);
+ }
+
+ public JalviewFileChooser(String dir, String[] extensions, String[] descs,
+ String selected, boolean allFiles, boolean allowBackupFiles)
+ {
super(safePath(dir));
if (extensions.length == descs.length)
{
{
formats.add(new String[] { extensions[i], descs[i] });
}
- init(formats, selected, allFiles);
+ init(formats, selected, allFiles, allowBackupFiles);
}
else
{
*/
void init(List<String[]> formats, String selected, boolean allFiles)
{
+ init(formats, selected, allFiles, false);
+ }
+
+ void init(List<String[]> formats, String selected, boolean allFiles,
+ boolean allowBackupFiles)
+ {
JalviewFileFilter chosen = null;
for (String[] format : formats)
{
JalviewFileFilter jvf = new JalviewFileFilter(format[0], format[1]);
+ if (allowBackupFiles)
+ {
+ jvf.setParentJFC(this);
+ }
addChoosableFileFilter(jvf);
if ((selected != null) && selected.equalsIgnoreCase(format[1]))
{
setFileFilter(chosen);
}
- setAccessory(new RecentlyOpened());
+ if (allowBackupFiles)
+ {
+ JPanel multi = new JPanel();
+ multi.setLayout(new BoxLayout(multi, BoxLayout.PAGE_AXIS));
+ if (backupfilesCheckBox == null)
+ {
+ try {
+ includeBackupFiles = Boolean.parseBoolean(
+ Cache.getProperty(BackupFiles.NS + "_FC_INCLUDE"));
+ } catch (Exception e)
+ {
+ includeBackupFiles = false;
+ }
+ backupfilesCheckBox = new JCheckBox(
+ MessageManager.getString("label.include_backup_files"),
+ includeBackupFiles);
+ backupfilesCheckBox.setAlignmentX(Component.CENTER_ALIGNMENT);
+ JalviewFileChooser jfc = this;
+ backupfilesCheckBox.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ includeBackupFiles = backupfilesCheckBox.isSelected();
+ Cache.setProperty(BackupFiles.NS + "_FC_INCLUDE",
+ String.valueOf(includeBackupFiles));
+
+ FileFilter f = jfc.getFileFilter();
+ // deselect the selected file if it's no longer choosable
+ File selectedFile = jfc.getSelectedFile();
+ if (selectedFile != null && !f.accept(selectedFile))
+ {
+ jfc.setSelectedFile(null);
+ }
+ // fake the OK button changing (to force it to upate)
+ String s = jfc.getApproveButtonText();
+ jfc.firePropertyChange(
+ APPROVE_BUTTON_TEXT_CHANGED_PROPERTY, null, s);
+ // fake the file filter changing (its behaviour actually has)
+ jfc.firePropertyChange(FILE_FILTER_CHANGED_PROPERTY, null, f);
+
+ jfc.rescanCurrentDirectory();
+ jfc.revalidate();
+ jfc.repaint();
+ }
+ });
+ }
+ multi.add(new RecentlyOpened());
+ multi.add(backupfilesCheckBox);
+ setAccessory(multi);
+ }
+ else
+ {
+ // set includeBackupFiles=false to avoid other file choosers from picking
+ // up backup files (Just In Case)
+ includeBackupFiles = false;
+ setAccessory(new RecentlyOpened());
+ }
}
@Override
public int showSaveDialog(Component parent) throws HeadlessException
{
this.setAccessory(null);
+ this.setSelectedFile(null);
+ return super.showSaveDialog(parent);
+ }
- setDialogType(SAVE_DIALOG);
+ /**
+ * If doing a Save, and an existing file is chosen or entered, prompt for
+ * confirmation of overwrite. Proceed if Yes, else leave the file chooser
+ * open.
+ *
+ * @see https://stackoverflow.com/questions/8581215/jfilechooser-and-checking-for-overwrite
+ */
+ @Override
+ public void approveSelection()
+ {
+ if (getDialogType() != SAVE_DIALOG)
+ {
+ super.approveSelection();
+ return;
+ }
- this.setSelectedFile(null);
- int ret = showDialog(parent, MessageManager.getString("action.save"));
ourselectedFile = getSelectedFile();
- if (getSelectedFile() == null)
+ if (ourselectedFile == null)
{
// Workaround for Java 9,10 on OSX - no selected file, but there is a
// filename typed in
"Unexpected exception when trying to get filename.");
x.printStackTrace();
}
+ // TODO: ENSURE THAT FILES SAVED WITH A ':' IN THE NAME ARE REFUSED AND
+ // THE
+ // USER PROMPTED FOR A NEW FILENAME
}
if (ourselectedFile == null)
{
- return JalviewFileChooser.CANCEL_OPTION;
+ return;
}
+
if (getFileFilter() instanceof JalviewFileFilter)
{
JalviewFileFilter jvf = (JalviewFileFilter) getFileFilter();
setSelectedFile(ourselectedFile);
}
}
- // TODO: ENSURE THAT FILES SAVED WITH A ':' IN THE NAME ARE REFUSED AND THE
- // USER PROMPTED FOR A NEW FILENAME
- if ((ret == JalviewFileChooser.APPROVE_OPTION)
- && ourselectedFile.exists())
+
+ if (ourselectedFile.exists())
{
- int confirm = JvOptionPane.showConfirmDialog(parent,
+ int confirm = JvOptionPane.showConfirmDialog(this,
MessageManager.getString("label.overwrite_existing_file"),
MessageManager.getString("label.file_already_exists"),
JvOptionPane.YES_NO_OPTION);
if (confirm != JvOptionPane.YES_OPTION)
{
- ret = JalviewFileChooser.CANCEL_OPTION;
+ return;
}
}
- return ret;
+ super.approveSelection();
}
void recentListSelectionChanged(Object selection)
}
}
+ /**
+ * A panel to set as the 'accessory' component to the file chooser dialog,
+ * holding a list of recently opened files (if any). These are held as a
+ * tab-separated list of file paths under key <code>RECENT_FILE</code> in
+ * <code>.jalview_properties</code>. A click in the list calls a method in
+ * JalviewFileChooser to set the chosen file as the selection.
+ */
class RecentlyOpened extends JPanel
{
- JList list;
+ private static final long serialVersionUID = 1L;
- public RecentlyOpened()
- {
+ private JList<String> list;
- String historyItems = jalview.bin.Cache.getProperty("RECENT_FILE");
+ RecentlyOpened()
+ {
+ String historyItems = Cache.getProperty("RECENT_FILE");
StringTokenizer st;
- Vector recent = new Vector();
+ Vector<String> recent = new Vector<>();
if (historyItems != null)
{
st = new StringTokenizer(historyItems, "\t");
-
while (st.hasMoreTokens())
{
- recent.addElement(st.nextElement());
+ recent.addElement(st.nextToken());
}
}
- list = new JList(recent);
+ list = new JList<>(recent);
DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
dlcr.setHorizontalAlignment(DefaultListCellRenderer.RIGHT);
}
});
- this.setBorder(new javax.swing.border.TitledBorder(
+ this.setBorder(new TitledBorder(
MessageManager.getString("label.recently_opened")));
final JScrollPane scroller = new JScrollPane(list);
layout.putConstraint(SpringLayout.NORTH, scroller, 5,
SpringLayout.NORTH, this);
- if (new Platform().isAMac())
+ if (Platform.isAMac())
{
scroller.setPreferredSize(new Dimension(500, 100));
}
this.add(scroller);
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
.setValue(scroller.getHorizontalScrollBar().getMaximum());
}
});
-
}
-
}
}
private boolean useExtensionsInDescription = true;
+ private JalviewFileChooser parentJFC = null;
+
public JalviewFileFilter(String extension, String description)
{
StringTokenizer st = new StringTokenizer(extension, ",");
@Override
public boolean accept(File f)
{
+
if (f != null)
{
String extension = getExtension(f);
{
return true;
}
+
}
+ if (parentJFC != null && parentJFC.includeBackupFiles)
+ {
+ Iterator<String> it = filters.keySet().iterator();
+ EXTENSION: while (it.hasNext())
+ {
+ String ext = it.next();
+
+ // quick negative test
+ if (!f.getName().contains(ext))
+ {
+ continue EXTENSION;
+ }
+
+ BackupFilenameParts bfp = BackupFilenameParts
+ .currentBackupFilenameParts(f.getName(), ext, true);
+ if (bfp.isBackupFile())
+ {
+ return true;
+ }
+ }
+ }
+
return false;
}
{
return useExtensionsInDescription;
}
+
+ protected void setParentJFC(JalviewFileChooser p)
+ {
+ this.parentJFC = p;
+ }
+
}
*/
package jalview.io;
+import jalview.util.MessageManager;
+
import java.io.File;
import java.net.URL;
import java.util.HashMap;
+import java.util.Iterator;
import java.util.Map;
import javax.swing.Icon;
public String getTypeDescription(File f)
{
String extension = getExtension(f);
+
String type = getDescriptionForExtension(extension);
+
if (extension != null)
{
if (extensions.containsKey(extension))
{
String extension = getExtension(f);
Icon icon = null;
+ String type = getDescriptionForExtension(extension);
+
+ if (type == null)
+ {
+ Iterator<String> it = extensions.keySet().iterator();
+ EXTENSION: while (it.hasNext())
+ {
+ String ext = it.next();
+
+ // quick negative test
+ if (!f.getName().contains(ext))
+ {
+ continue EXTENSION;
+ }
+
+ BackupFilenameParts bfp = BackupFilenameParts
+ .currentBackupFilenameParts(f.getName(), ext, true);
+ if (bfp.isBackupFile())
+ {
+ extension = ext;
+ type = getDescriptionForExtension(extension)
+ + MessageManager.getString("label.backup");
+ break;
+ }
+ }
+ }
- if (getDescriptionForExtension(extension) != null)
+ if (type != null)
{
icon = getImageIcon("/images/file.png");
}
}
/**
- * A convenience method to get the AF value for the given alternate allele
- * index
- *
- * @param variant
- * @param alleleIndex
- * @return
- */
- protected float getAlleleFrequency(VariantContext variant, int alleleIndex)
- {
- float score = 0f;
- String attributeValue = getAttributeValue(variant,
- ALLELE_FREQUENCY_KEY, alleleIndex);
- if (attributeValue != null)
- {
- try
- {
- score = Float.parseFloat(attributeValue);
- } catch (NumberFormatException e)
- {
- // leave as 0
- }
- }
-
- return score;
- }
-
- /**
* A convenience method to get an attribute value for an alternate allele
*
* @param variant
type = getOntologyTerm(consequence);
}
- float score = getAlleleFrequency(variant, altAlleleIndex);
-
SequenceFeature sf = new SequenceFeature(type, alleles, featureStart,
- featureEnd, score, FEATURE_GROUP_VCF);
+ featureEnd, FEATURE_GROUP_VCF);
sf.setSource(sourceId);
sf.setValue(Gff3Helper.ALLELES, alleles);
package jalview.jbgui;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.GeneticCodeI;
+import jalview.analysis.GeneticCodes;
import jalview.api.SplitContainerI;
import jalview.bin.Cache;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
import jalview.io.FileFormats;
+import jalview.schemes.ResidueColourScheme;
import jalview.util.MessageManager;
import jalview.util.Platform;
protected JMenu sortByAnnotScore = new JMenu();
- public JLabel statusBar = new JLabel();
+ protected JLabel statusBar = new JLabel();
protected JMenu outputTextboxMenu = new JMenu();
protected JMenuItem modifyPID;
- protected JMenuItem annotationColour;
+ protected JRadioButtonMenuItem annotationColour;
protected JMenu sortByTreeMenu = new JMenu();
protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
- protected JMenuItem showTranslation = new JMenuItem();
+ protected JMenu showTranslation = new JMenu();
protected JMenuItem showReverse = new JMenuItem();
private boolean showAutoCalculatedAbove = false;
- private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+ private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
private SplitContainerI splitFrame;
vamsasStore_actionPerformed(e);
}
});
- showTranslation
- .setText(MessageManager.getString("label.translate_cDNA"));
- showTranslation.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
+
+ /*
+ * Translate as cDNA with sub-menu of translation tables
+ */
+ showTranslation.setText(MessageManager
+ .getString("label.translate_cDNA"));
+ boolean first = true;
+ for (final GeneticCodeI table : GeneticCodes.getInstance()
+ .getCodeTables())
+ {
+ JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
+ showTranslation.add(item);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showTranslation_actionPerformed(table);
+ }
+ });
+ if (first)
{
- showTranslation_actionPerformed(e);
+ showTranslation.addSeparator();
}
- });
+ first = false;
+ }
+
showReverse.setText(MessageManager.getString("label.reverse"));
showReverse.addActionListener(new ActionListener()
{
}
});
- annotationColour = new JMenuItem(
+ annotationColour = new JRadioButtonMenuItem(
MessageManager.getString("action.by_annotation"));
+ annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
annotationColour.addActionListener(new ActionListener()
{
@Override
}
- public void showTranslation_actionPerformed(ActionEvent e)
+ public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
}
+++ /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.jbgui;
-
-import jalview.util.MessageManager;
-
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.FlowLayout;
-import java.awt.Font;
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.Insets;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-
-import javax.swing.BorderFactory;
-import javax.swing.JButton;
-import javax.swing.JEditorPane;
-import javax.swing.JLabel;
-import javax.swing.JList;
-import javax.swing.JPanel;
-import javax.swing.JProgressBar;
-import javax.swing.JScrollPane;
-import javax.swing.JTable;
-import javax.swing.JTextField;
-import javax.swing.SwingConstants;
-import javax.swing.border.TitledBorder;
-import javax.swing.event.HyperlinkEvent;
-import javax.swing.event.HyperlinkListener;
-
-public class GDasSourceBrowser extends JPanel
-{
- public GDasSourceBrowser()
- {
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- private void jbInit() throws Exception
- {
- this.setLayout(gridBagLayout1);
- refresh.setText(
- MessageManager.getString("label.refresh_available_sources"));
- refresh.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- refresh_actionPerformed(e);
- }
- });
- progressBar.setPreferredSize(new Dimension(450, 20));
- progressBar.setString("");
- scrollPane.setBorder(titledBorder1);
- scrollPane.setBorder(BorderFactory.createEtchedBorder());
- fullDetailsScrollpane.setBorder(BorderFactory.createEtchedBorder());
- fullDetails.addHyperlinkListener(new HyperlinkListener()
- {
- public void hyperlinkUpdate(HyperlinkEvent e)
- {
- fullDetails_hyperlinkUpdate(e);
- }
- });
- fullDetails.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- fullDetails.setEditable(false);
- registryLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- registryLabel.setHorizontalAlignment(SwingConstants.TRAILING);
- registryLabel.setText(MessageManager.getString("label.use_registry"));
- addLocal.setText(MessageManager.getString("label.add_local_source"));
- addLocal.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- amendLocal(true);
- }
- });
- jPanel1.setLayout(flowLayout1);
- jPanel1.setMinimumSize(new Dimension(596, 30));
- jPanel1.setPreferredSize(new Dimension(596, 30));
- jScrollPane2.setBorder(titledBorder3);
- jScrollPane3.setBorder(titledBorder4);
- jScrollPane4.setBorder(titledBorder5);
- titledBorder2
- .setTitleFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- titledBorder3
- .setTitleFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- titledBorder4
- .setTitleFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- filter1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- filter2.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- filter3.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- table.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- reset.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- reset.setMargin(new Insets(2, 2, 2, 2));
- reset.setText(MessageManager.getString("action.reset"));
- reset.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- reset_actionPerformed(e);
- }
- });
- jPanel2.setLayout(borderLayout1);
- borderLayout1.setHgap(5);
- registryURL.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- scrollPane.getViewport().add(table);
- fullDetailsScrollpane.getViewport().add(fullDetails);
- jScrollPane3.getViewport().add(filter2);
- jScrollPane4.getViewport().add(filter3);
- jPanel1.add(refresh, null);
- jPanel1.add(addLocal, null);
- jPanel1.add(progressBar, null);
- jScrollPane2.getViewport().add(filter1);
- this.add(jPanel1, new GridBagConstraints(0, 3, 3, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
- new Insets(0, 0, 0, 0), 0, 0));
- this.add(fullDetailsScrollpane,
- new GridBagConstraints(1, 0, 2, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH,
- new Insets(3, 0, 0, 3), 240, 130));
- this.add(scrollPane,
- new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH,
- new Insets(3, 2, 0, 0), 150, 130));
- jPanel2.add(registryLabel, java.awt.BorderLayout.WEST);
- jPanel2.add(registryURL, java.awt.BorderLayout.CENTER);
- jPanel2.add(reset, java.awt.BorderLayout.EAST);
- this.add(jPanel2, new GridBagConstraints(0, 2, 3, 1, 0.0, 0.0,
- GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
- new Insets(5, 10, 0, 10), 339, 0));
- this.add(jScrollPane2,
- new GridBagConstraints(0, 1, 1, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH,
- new Insets(0, 0, 0, 60), 80, 60));
- this.add(jScrollPane4,
- new GridBagConstraints(2, 1, 1, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH,
- new Insets(0, -80, 0, 0), 80, 60));
- this.add(jScrollPane3,
- new GridBagConstraints(1, 1, 1, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH,
- new Insets(0, -60, 0, 80), 80, 60));
- }
-
- protected JTable table = new JTable();
-
- protected JEditorPane fullDetails = new JEditorPane("text/html", "");
-
- TitledBorder titledBorder1 = new TitledBorder(
- MessageManager.getString("label.available_das_sources"));
-
- protected JButton refresh = new JButton();
-
- protected JProgressBar progressBar = new JProgressBar();
-
- protected JScrollPane scrollPane = new JScrollPane();
-
- TitledBorder titledBorder2 = new TitledBorder(
- MessageManager.getString("label.full_details"));
-
- protected JScrollPane fullDetailsScrollpane = new JScrollPane();
-
- protected JList filter1 = new JList();
-
- protected JList filter2 = new JList();
-
- protected JList filter3 = new JList();
-
- JScrollPane jScrollPane2 = new JScrollPane();
-
- JScrollPane jScrollPane3 = new JScrollPane();
-
- JScrollPane jScrollPane4 = new JScrollPane();
-
- protected JTextField registryURL = new JTextField();
-
- protected JLabel registryLabel = new JLabel();
-
- protected JButton addLocal = new JButton();
-
- JPanel jPanel1 = new JPanel();
-
- FlowLayout flowLayout1 = new FlowLayout();
-
- GridBagLayout gridBagLayout1 = new GridBagLayout();
-
- TitledBorder titledBorder3 = new TitledBorder(
- MessageManager.getString("label.authority") + ":");
-
- TitledBorder titledBorder4 = new TitledBorder(
- MessageManager.getString("label.type") + ":");
-
- TitledBorder titledBorder5 = new TitledBorder(
- MessageManager.getString("label.label") + ":");
-
- JButton reset = new JButton();
-
- JPanel jPanel2 = new JPanel();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- public void refresh_actionPerformed(ActionEvent e)
- {
-
- }
-
- public void fullDetails_hyperlinkUpdate(HyperlinkEvent e)
- {
- try
- {
-
- if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED)
- {
- jalview.util.BrowserLauncher.openURL(e.getURL().toString());
- }
- } catch (Exception ex)
- {
- System.out.println(e.getURL());
- ex.printStackTrace();
- }
- }
-
- public void amendLocal(boolean newSource)
- {
-
- }
-
- public void reset_actionPerformed(ActionEvent e)
- {
-
- }
-
-}
JMenuItem saveState = new JMenuItem();
+ JMenuItem saveAsState = new JMenuItem();
+
JMenuItem loadState = new JMenuItem();
JMenu inputMenu = new JMenu();
saveState_actionPerformed();
}
});
+ saveAsState.setText(MessageManager.getString("action.save_project_as"));
+ saveAsState.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ saveAsState_actionPerformed(e);
+ }
+ });
loadState.setText(MessageManager.getString("action.load_project"));
loadState.addActionListener(new ActionListener()
{
FileMenu.add(inputSequence);
FileMenu.addSeparator();
FileMenu.add(saveState);
+ FileMenu.add(saveAsState);
FileMenu.add(loadState);
FileMenu.addSeparator();
FileMenu.add(quit);
{
}
+ public void saveAsState_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
public void loadState_actionPerformed()
{
}
public class GFinder extends JPanel
{
- JLabel jLabelFind = new JLabel();
+ private static final java.awt.Font VERDANA_12 = new java.awt.Font("Verdana", 0,
+ 12);
- protected JButton findAll = new JButton();
-
- protected JButton findNext = new JButton();
-
- JPanel actionsPanel = new JPanel();
-
- GridLayout gridLayout1 = new GridLayout();
+ private static final String FINDER_CACHE_KEY = "CACHE.FINDER";
protected JButton createFeatures = new JButton();
- protected JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<String>(
+ protected JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
getCacheKey());
- BorderLayout mainBorderLayout = new BorderLayout();
-
- JPanel jPanel2 = new JPanel();
-
- JPanel jPanel3 = new JPanel();
-
- JPanel jPanel4 = new JPanel();
-
- BorderLayout borderLayout2 = new BorderLayout();
-
- JPanel jPanel6 = new JPanel();
-
protected JCheckBox caseSensitive = new JCheckBox();
protected JCheckBox searchDescription = new JCheckBox();
- GridLayout optionsGridLayout = new GridLayout();
-
- private static final String FINDER_CACHE_KEY = "CACHE.FINDER";
-
public GFinder()
{
try
private void jbInit() throws Exception
{
- jLabelFind.setFont(new java.awt.Font("Verdana", 0, 12));
- jLabelFind.setText(MessageManager.getString("label.find"));
+ BorderLayout mainBorderLayout = new BorderLayout();
this.setLayout(mainBorderLayout);
- findAll.setFont(new java.awt.Font("Verdana", 0, 12));
- findAll.setText(MessageManager.getString("action.find_all"));
+ mainBorderLayout.setHgap(5);
+ mainBorderLayout.setVgap(5);
+
+ JLabel jLabelFind = new JLabel(MessageManager.getString("label.find"));
+ jLabelFind.setFont(VERDANA_12);
+
+ JButton findAll = new JButton(
+ MessageManager.getString("action.find_all"));
+ findAll.setFont(VERDANA_12);
findAll.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- findAll_actionPerformed(e);
+ findAll_actionPerformed();
}
});
- findNext.setFont(new java.awt.Font("Verdana", 0, 12));
- findNext.setText(MessageManager.getString("action.find_next"));
+
+ JButton findNext = new JButton(
+ MessageManager.getString("action.find_next"));
+ findNext.setFont(VERDANA_12);
findNext.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- findNext_actionPerformed(e);
+ findNext_actionPerformed();
}
});
+
+ JPanel actionsPanel = new JPanel();
+ GridLayout gridLayout1 = new GridLayout();
actionsPanel.setLayout(gridLayout1);
gridLayout1.setHgap(0);
gridLayout1.setRows(3);
gridLayout1.setVgap(2);
+
createFeatures.setEnabled(false);
- createFeatures.setFont(new java.awt.Font("Verdana", 0, 12));
+ createFeatures.setFont(VERDANA_12);
createFeatures.setMargin(new Insets(0, 0, 0, 0));
createFeatures.setText(MessageManager.getString("label.new_feature"));
createFeatures.addActionListener(new java.awt.event.ActionListener()
@Override
public void caretUpdate(CaretEvent e)
{
- textfield_caretUpdate(e);
+ textfield_caretUpdate();
}
});
searchBox.getEditor().getEditorComponent()
textfield_keyPressed(e);
}
});
- mainBorderLayout.setHgap(5);
- mainBorderLayout.setVgap(5);
- jPanel4.setLayout(borderLayout2);
- jPanel2.setPreferredSize(new Dimension(10, 1));
- jPanel3.setPreferredSize(new Dimension(10, 1));
+
caseSensitive.setHorizontalAlignment(SwingConstants.LEFT);
caseSensitive.setText(MessageManager.getString("label.match_case"));
actionsPanel.add(createFeatures, null);
this.add(jLabelFind, java.awt.BorderLayout.WEST);
this.add(actionsPanel, java.awt.BorderLayout.EAST);
+
+ JPanel jPanel2 = new JPanel();
+ jPanel2.setPreferredSize(new Dimension(10, 1));
+ JPanel jPanel3 = new JPanel();
+ jPanel3.setPreferredSize(new Dimension(10, 1));
+ JPanel jPanel4 = new JPanel();
+ jPanel4.setLayout(new BorderLayout());
this.add(jPanel2, java.awt.BorderLayout.SOUTH);
this.add(jPanel3, java.awt.BorderLayout.NORTH);
this.add(jPanel4, java.awt.BorderLayout.CENTER);
JPanel optionsPanel = new JPanel();
+ GridLayout optionsGridLayout = new GridLayout();
optionsGridLayout.setHgap(0);
optionsGridLayout.setRows(2);
optionsGridLayout.setVgap(2);
if (!searchBox.isPopupVisible())
{
e.consume();
- findNext_actionPerformed(null);
+ findNext_actionPerformed();
}
}
}
- protected void findNext_actionPerformed(ActionEvent e)
+ protected void findNext_actionPerformed()
{
}
- protected void findAll_actionPerformed(ActionEvent e)
+ protected void findAll_actionPerformed()
{
}
{
}
- public void textfield_caretUpdate(CaretEvent e)
+ public void textfield_caretUpdate()
{
- if (searchBox.getUserInput().indexOf(">") > -1)
+ // disabled as appears to be running a non-functional
+ if (false && searchBox.getUserInput().indexOf(">") > -1)
{
SwingUtilities.invokeLater(new Runnable()
{
str = jalview.analysis.AlignSeq.extractGaps(
jalview.util.Comparison.GapChars,
al.getSequenceAt(0).getSequenceAsString());
-
+ // todo and what? set str as searchBox text?
}
}
});
{
private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
- protected JComboBox<String> xCombobox = new JComboBox<String>();
+ protected JComboBox<String> xCombobox = new JComboBox<>();
- protected JComboBox<String> yCombobox = new JComboBox<String>();
+ protected JComboBox<String> yCombobox = new JComboBox<>();
- protected JComboBox<String> zCombobox = new JComboBox<String>();
-
- protected JMenu scoreModelMenu = new JMenu();
+ protected JComboBox<String> zCombobox = new JComboBox<>();
protected JMenu viewMenu = new JMenu();
protected JMenu associateViewsMenu = new JMenu();
- protected JMenu calcSettings = new JMenu();
-
- protected JCheckBoxMenuItem nuclSetting = new JCheckBoxMenuItem();
-
- protected JCheckBoxMenuItem protSetting = new JCheckBoxMenuItem();
-
protected JLabel statusBar = new JLabel();
protected JPanel statusPanel = new JPanel();
+ protected JMenuItem originalSeqData;
+
+ /**
+ * Constructor
+ */
public GPCAPanel()
{
try
@Override
public void actionPerformed(ActionEvent e)
{
- zCombobox_actionPerformed(e);
+ doDimensionChange();
}
});
yCombobox.setFont(VERDANA_12);
@Override
public void actionPerformed(ActionEvent e)
{
- yCombobox_actionPerformed(e);
+ doDimensionChange();
}
});
xCombobox.setFont(VERDANA_12);
@Override
public void actionPerformed(ActionEvent e)
{
- xCombobox_actionPerformed(e);
+ doDimensionChange();
}
});
JButton resetButton = new JButton();
@Override
public void actionPerformed(ActionEvent e)
{
- resetButton_actionPerformed(e);
+ resetButton_actionPerformed();
}
});
JMenu fileMenu = new JMenu();
@Override
public void actionPerformed(ActionEvent e)
{
- eps_actionPerformed(e);
+ eps_actionPerformed();
}
});
JMenuItem png = new JMenuItem("PNG");
@Override
public void actionPerformed(ActionEvent e)
{
- png_actionPerformed(e);
+ png_actionPerformed();
}
});
JMenuItem outputValues = new JMenuItem();
@Override
public void actionPerformed(ActionEvent e)
{
- outputValues_actionPerformed(e);
+ outputValues_actionPerformed();
}
});
JMenuItem outputPoints = new JMenuItem();
@Override
public void actionPerformed(ActionEvent e)
{
- outputPoints_actionPerformed(e);
+ outputPoints_actionPerformed();
}
});
JMenuItem outputProjPoints = new JMenuItem();
@Override
public void actionPerformed(ActionEvent e)
{
- outputProjPoints_actionPerformed(e);
+ outputProjPoints_actionPerformed();
}
});
JMenuItem print = new JMenuItem();
@Override
public void actionPerformed(ActionEvent e)
{
- print_actionPerformed(e);
+ print_actionPerformed();
}
});
viewMenu.setText(MessageManager.getString("action.view"));
{
}
});
- scoreModelMenu
- .setText(MessageManager.getString("label.select_score_model"));
- scoreModelMenu.addMenuListener(new MenuListener()
- {
- @Override
- public void menuSelected(MenuEvent e)
- {
- scoreModel_menuSelected();
- }
-
- @Override
- public void menuDeselected(MenuEvent e)
- {
- }
-
- @Override
- public void menuCanceled(MenuEvent e)
- {
- }
- });
showLabels.setText(MessageManager.getString("label.show_labels"));
showLabels.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- showLabels_actionPerformed(e);
+ showLabels_actionPerformed();
}
});
JMenuItem bgcolour = new JMenuItem();
@Override
public void actionPerformed(ActionEvent e)
{
- bgcolour_actionPerformed(e);
+ bgcolour_actionPerformed();
}
});
- JMenuItem originalSeqData = new JMenuItem();
+ originalSeqData = new JMenuItem();
originalSeqData.setText(MessageManager.getString("label.input_data"));
originalSeqData.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- originalSeqData_actionPerformed(e);
+ originalSeqData_actionPerformed();
}
});
associateViewsMenu.setText(
MessageManager.getString("label.associate_nodes_with"));
- calcSettings.setText(MessageManager.getString("action.change_params"));
- nuclSetting
- .setText(MessageManager.getString("label.nucleotide_matrix"));
- protSetting.setText(MessageManager.getString("label.protein_matrix"));
- nuclSetting.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- nuclSetting_actionPerfomed(arg0);
- }
- });
- protSetting.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- protSetting_actionPerfomed(arg0);
- }
- });
- calcSettings.add(nuclSetting);
- calcSettings.add(protSetting);
- calcSettings.add(scoreModelMenu);
statusPanel.setLayout(new GridLayout());
statusBar.setFont(VERDANA_12);
// statusPanel.setBackground(Color.lightGray);
JMenuBar jMenuBar1 = new JMenuBar();
jMenuBar1.add(fileMenu);
jMenuBar1.add(viewMenu);
- jMenuBar1.add(calcSettings);
setJMenuBar(jMenuBar1);
fileMenu.add(saveMenu);
fileMenu.add(outputValues);
viewMenu.add(associateViewsMenu);
}
- protected void scoreModel_menuSelected()
- {
- // TODO Auto-generated method stub
-
- }
-
- protected void resetButton_actionPerformed(ActionEvent e)
+ protected void resetButton_actionPerformed()
{
- // TODO Auto-generated method stub
-
}
- protected void protSetting_actionPerfomed(ActionEvent arg0)
+ protected void outputPoints_actionPerformed()
{
- // TODO Auto-generated method stub
-
}
- protected void nuclSetting_actionPerfomed(ActionEvent arg0)
+ protected void outputProjPoints_actionPerformed()
{
- // TODO Auto-generated method stub
-
}
- protected void outputPoints_actionPerformed(ActionEvent e)
+ protected void eps_actionPerformed()
{
- // TODO Auto-generated method stub
-
}
- protected void outputProjPoints_actionPerformed(ActionEvent e)
+ protected void png_actionPerformed()
{
- // TODO Auto-generated method stub
-
}
- protected void xCombobox_actionPerformed(ActionEvent e)
+ protected void outputValues_actionPerformed()
{
}
- protected void yCombobox_actionPerformed(ActionEvent e)
+ protected void print_actionPerformed()
{
}
- protected void zCombobox_actionPerformed(ActionEvent e)
+ protected void showLabels_actionPerformed()
{
}
- public void eps_actionPerformed(ActionEvent e)
+ protected void bgcolour_actionPerformed()
{
-
}
- public void png_actionPerformed(ActionEvent e)
+ protected void originalSeqData_actionPerformed()
{
-
}
- public void outputValues_actionPerformed(ActionEvent e)
+ protected void viewMenu_menuSelected()
{
-
}
- public void print_actionPerformed(ActionEvent e)
+ protected void doDimensionChange()
{
-
- }
-
- public void showLabels_actionPerformed(ActionEvent e)
- {
-
- }
-
- public void bgcolour_actionPerformed(ActionEvent e)
- {
-
- }
-
- public void originalSeqData_actionPerformed(ActionEvent e)
- {
-
- }
-
- public void viewMenu_menuSelected()
- {
-
}
}
*/
package jalview.jbgui;
+import jalview.bin.Cache;
import jalview.fts.core.FTSDataColumnPreferences;
import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.gui.Desktop;
+import jalview.gui.JalviewBooleanRadioButtons;
+import jalview.gui.JvOptionPane;
import jalview.gui.JvSwingUtils;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.BackupFilenameParts;
+import jalview.io.BackupFiles;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.event.ActionListener;
import java.awt.event.FocusEvent;
import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+import java.util.HashMap;
+import java.util.Map;
import javax.swing.AbstractCellEditor;
import javax.swing.BorderFactory;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
+import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
+import javax.swing.JSpinner;
import javax.swing.JTabbedPane;
import javax.swing.JTable;
+import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.ListSelectionModel;
+import javax.swing.SpinnerModel;
+import javax.swing.SpinnerNumberModel;
import javax.swing.SwingConstants;
import javax.swing.border.Border;
import javax.swing.border.EmptyBorder;
private static final Font LABEL_FONT_ITALIC = JvSwingUtils
.getLabelFont(false, true);
+ private static final Font LABEL_FONT_BOLD = JvSwingUtils
+ .getLabelFont(true, false);
+
/*
* Visual tab components
*/
protected JCheckBox sortByTree = new JCheckBox();
-
/*
* Web Services tab
*/
protected JPanel wsTab = new JPanel();
+ /*
+ * Backups tab components
+ * a lot of these are member variables instead of local variables only so that they
+ * can be enabled/disabled easily in one go
+ */
+
+ protected JCheckBox enableBackupFiles = new JCheckBox();
+
+ protected JPanel presetsPanel = new JPanel();
+
+ protected JButton revertButton = new JButton();
+
+ protected JComboBox<IntKeyStringValueEntry> backupfilesPresetsCombo = new JComboBox<>();
+
+ protected JPanel suffixPanel = new JPanel();
+
+ protected JPanel keepfilesPanel = new JPanel();
+
+ protected JPanel exampleFilesPanel = new JPanel();
+
+ protected JTextField suffixTemplate = new JTextField(null, 8);
+
+ protected JLabel suffixTemplateLabel = new JLabel();
+
+ protected JLabel suffixDigitsLabel = new JLabel();
+
+ protected JSpinner suffixDigitsSpinner = new JSpinner();
+
+ protected JalviewBooleanRadioButtons suffixReverse = new JalviewBooleanRadioButtons();
+
+ protected JalviewBooleanRadioButtons backupfilesKeepAll = new JalviewBooleanRadioButtons();
+
+ public JSpinner backupfilesRollMaxSpinner = new JSpinner();
+
+ protected JLabel oldBackupFilesLabel = new JLabel();
+
+ protected JalviewBooleanRadioButtons backupfilesConfirmDelete = new JalviewBooleanRadioButtons();
+
+ protected JTextArea backupfilesExampleLabel = new JTextArea();
+
/**
* Creates a new GPreferences object.
*/
tabbedPane.add(initConnectionsTab(),
MessageManager.getString("label.connections"));
+ tabbedPane.add(initBackupsTab(),
+ MessageManager.getString("label.backups"));
+
tabbedPane.add(initLinksTab(),
MessageManager.getString("label.urllinks"));
linkTab.setLayout(new GridBagLayout());
// Set up table for Url links
+ linkUrlTable.getTableHeader().setReorderingAllowed(false);
linkUrlTable.setFillsViewportHeight(true);
linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
linkUrlTable.setAutoCreateRowSorter(true);
hiddenColour_actionPerformed(hiddenColour);
}
});
-
+
useLegacyGap = new JCheckBox(
MessageManager.getString("label.ov_legacy_gap"));
useLegacyGap.setFont(LABEL_FONT);
useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
- gapLabel = new JLabel(
- MessageManager.getString("label.gap_colour"));
+ gapLabel = new JLabel(MessageManager.getString("label.gap_colour"));
gapLabel.setFont(LABEL_FONT);
gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
gapLabel.setVerticalTextPosition(SwingConstants.TOP);
return visualTab;
}
+ /**
+ * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
+ */
+
+ protected void loadLastSavedBackupsOptions()
+ {
+ enableBackupFiles
+ .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
+ setComboIntStringKey(backupfilesPresetsCombo,
+ Cache.getDefault(BackupFiles.NS + "_PRESET", 1));
+ suffixTemplate.setText(Cache.getDefault(BackupFiles.SUFFIX,
+ ".bak" + BackupFiles.NUM_PLACEHOLDER));
+ suffixDigitsSpinner
+ .setValue(Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3));
+ suffixReverse.setSelected(
+ Cache.getDefault(BackupFiles.REVERSE_ORDER, false));
+ backupfilesKeepAll
+ .setSelected(Cache.getDefault(BackupFiles.NO_MAX, false));
+ backupfilesRollMaxSpinner
+ .setValue(Cache.getDefault(BackupFiles.ROLL_MAX, 3));
+ backupfilesConfirmDelete.setSelected(
+ Cache.getDefault(BackupFiles.CONFIRM_DELETE_OLD, true));
+
+ backupsOptionsSetEnabled();
+ updateBackupFilesExampleLabel();
+ }
+
+ private boolean warnAboutSuffixReverseChange()
+ {
+ boolean savedSuffixReverse = Cache.getDefault(BackupFiles.REVERSE_ORDER,
+ false);
+ int savedSuffixDigits = Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3);
+ String savedSuffixTemplate = Cache.getDefault(BackupFiles.SUFFIX,
+ ".bak" + BackupFiles.NUM_PLACEHOLDER);
+
+ boolean nowSuffixReverse = suffixReverse.isSelected();
+ int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
+ String nowSuffixTemplate = suffixTemplate.getText();
+ return nowSuffixReverse != savedSuffixReverse
+ && nowSuffixDigits == savedSuffixDigits
+ && nowSuffixTemplate != null
+ && nowSuffixTemplate.equals(savedSuffixTemplate);
+ }
+
+ /**
+ * Initialises the Backups tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initBackupsTab()
+ {
+ JPanel backupsTab = new JPanel();
+ backupsTab.setBorder(new TitledBorder(
+ MessageManager.getString("label.backup_files")));
+ backupsTab.setLayout(new GridBagLayout());
+
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.weightx = 0.0;
+ gbc.weighty = 0.0;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+ gbc.fill = GridBagConstraints.NONE;
+
+ initBackupsTabPresetsPanel();
+ initBackupsTabSuffixPanel();
+ initBackupsTabKeepFilesPanel();
+ initBackupsTabFilenameExamplesPanel();
+
+ enableBackupFiles.setFont(LABEL_FONT_BOLD);
+ enableBackupFiles
+ .setText(MessageManager.getString("label.enable_backupfiles"));
+ enableBackupFiles.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // enable other options only when the first is checked
+ backupsOptionsSetEnabled();
+ }
+ });
+
+
+ // enable checkbox 1 col
+ gbc.gridwidth = 1;
+ gbc.gridheight = 1;
+ gbc.gridx = 0;
+ gbc.gridy = 0; // row 0
+ backupsTab.add(enableBackupFiles, gbc);
+
+ // summary of scheme box (over two rows)
+ gbc.gridx = 1;
+ gbc.weightx = 0.0;
+ gbc.gridheight = 2;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_END;
+ gbc.fill = GridBagConstraints.BOTH;
+ backupsTab.add(exampleFilesPanel, gbc);
+ gbc.gridheight = 1;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+ gbc.fill = GridBagConstraints.NONE;
+
+ // fill empty space on right
+ gbc.gridx++;
+ gbc.weightx = 1.0;
+ backupsTab.add(new JPanel(), gbc);
+
+ // schemes box
+ gbc.weightx = 0.0;
+ gbc.gridx = 0;
+ gbc.gridy++; // row 1
+ backupsTab.add(presetsPanel, gbc);
+
+ // gbc.anchor = GridBagConstraints.NORTHWEST;
+ // now using whole row
+ gbc.gridwidth = 2;
+ gbc.gridheight = 1;
+ // keep files box
+ gbc.gridx = 0;
+ gbc.gridy++; // row 2
+ backupsTab.add(keepfilesPanel, gbc);
+
+ // filename strategy box
+ gbc.gridy++; // row 3
+ backupsTab.add(suffixPanel, gbc);
+
+ // fill empty space
+ gbc.gridy++; // row 4
+ gbc.weighty = 1.0;
+ backupsTab.add(new JPanel(), gbc);
+
+ backupsOptionsSetEnabled();
+ return backupsTab;
+ }
+
+ protected static final int BACKUPFILESSCHEMECUSTOMISE = 0;
+
+ private static final IntKeyStringValueEntry[] backupfilesPresetEntries = {
+ new IntKeyStringValueEntry(1,
+ MessageManager.getString("label.default")),
+ new IntKeyStringValueEntry(2,
+ MessageManager.getString("label.single_file")),
+ new IntKeyStringValueEntry(3,
+ MessageManager.getString("label.keep_all_versions")),
+ new IntKeyStringValueEntry(4,
+ MessageManager.getString("label.rolled_backups")),
+ // ...
+ // IMPORTANT, keep "Custom" entry with key 0 (even though it appears last)
+ new IntKeyStringValueEntry(BACKUPFILESSCHEMECUSTOMISE,
+ MessageManager.getString("label.customise")) };
+
+ private static final Map<Integer, BackupFilesPresetEntry> backupfilesPresetEntriesValues = new HashMap<Integer, BackupFilesPresetEntry>()
+ {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 125L;
+
+ {
+ put(1, new BackupFilesPresetEntry(
+ ".bak" + BackupFiles.NUM_PLACEHOLDER, 3, false, false, 3,
+ false));
+ put(2, new BackupFilesPresetEntry("~", 1, false, false, 1, false));
+ put(3, new BackupFilesPresetEntry(".v" + BackupFiles.NUM_PLACEHOLDER,
+ 3, false, true, 10, true));
+ put(4, new BackupFilesPresetEntry(
+ "_bak." + BackupFiles.NUM_PLACEHOLDER, 1, true, false, 9,
+ false));
+ }
+ };
+
+ private JPanel initBackupsTabPresetsPanel()
+ {
+
+ String title = MessageManager.getString("label.schemes");
+ // TitledBorder tb = new TitledBorder(new EmptyBorder(0, 0, 0, 0), title);
+ // TitledBorder tb = new TitledBorder(title);
+ // tb.setTitleFont(LABEL_FONT);
+ // presetsPanel.setBorder(tb);
+
+ presetsPanel.setLayout(new GridBagLayout());
+
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.weightx = 0.0;
+ gbc.weighty = 0.0;
+ gbc.anchor = GridBagConstraints.BASELINE_LEADING;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.gridwidth = 1;
+ gbc.gridheight = 1;
+
+ // "Scheme: "
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ presetsPanel.add(new JLabel(title + ":"), gbc);
+
+ for (int i = 0; i < backupfilesPresetEntries.length; i++)
+ {
+ backupfilesPresetsCombo.addItem(backupfilesPresetEntries[i]);
+ }
+
+ // put "Previously saved scheme" item in italics (it's not really
+ // selectable, as such -- it deselects itself when selected) and
+ // "Customise" in bold
+ backupfilesPresetsCombo
+ .setRenderer(new BackupFilesPresetsComboBoxRenderer());
+ backupfilesPresetsCombo.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ backupsTabUpdatePresets();
+ }
+ });
+
+ // dropdown list of preset schemes
+ gbc.gridx = 1;
+ presetsPanel.add(backupfilesPresetsCombo, gbc);
+
+ revertButton.setText(MessageManager.getString("label.cancel_changes"));
+ revertButton.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadLastSavedBackupsOptions();
+ }
+
+ });
+ revertButton.setFont(LABEL_FONT);
+
+ // "Cancel changes" button (aligned with combo box above)
+ gbc.gridx = 1;
+ gbc.gridy++;
+ presetsPanel.add(revertButton, gbc);
+
+ return presetsPanel;
+ }
+
+ private JPanel initBackupsTabFilenameExamplesPanel()
+ {
+ String title = MessageManager
+ .getString("label.summary_of_backups_scheme");
+ TitledBorder tb = new TitledBorder(title);
+ exampleFilesPanel.setBorder(tb);
+ exampleFilesPanel.setLayout(new GridBagLayout());
+
+
+ backupfilesExampleLabel.setEditable(false);
+ backupfilesExampleLabel
+ .setBackground(exampleFilesPanel.getBackground());
+
+ updateBackupFilesExampleLabel();
+
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.weightx = 1.0;
+ gbc.weighty = 1.0;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+
+ exampleFilesPanel.add(backupfilesExampleLabel, gbc);
+ return exampleFilesPanel;
+ }
+
+ private void backupsTabUpdatePresets()
+ {
+ IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
+ .getSelectedItem();
+ int key = entry.getKey();
+ String value = entry.getValue();
+
+ // BACKUPFILESSCHEMECUSTOMISE (==0) reserved for "Custom"
+ if (key != BACKUPFILESSCHEMECUSTOMISE)
+ {
+ if (backupfilesPresetEntriesValues.containsKey(key))
+ {
+ backupsSetOptions(backupfilesPresetEntriesValues.get(key));
+ }
+ else
+ {
+ System.out.println("Preset '" + value + "' not implemented");
+ }
+ }
+
+ backupfilesCustomOptionsSetEnabled();
+ updateBackupFilesExampleLabel();
+ }
+
+ protected int getComboIntStringKey(JComboBox<IntKeyStringValueEntry> c)
+ {
+ IntKeyStringValueEntry e = (IntKeyStringValueEntry) c.getSelectedItem();
+ return e != null ? e.getKey() : 0;
+ }
+
+ protected void setComboIntStringKey(JComboBox<IntKeyStringValueEntry> c,
+ int key)
+ {
+ for (int i = 0; i < c.getItemCount(); i++)
+ {
+ IntKeyStringValueEntry e = c.getItemAt(i);
+ if (e.getKey() == key)
+ {
+ c.setSelectedIndex(i);
+ break;
+ }
+ }
+ backupsTabUpdatePresets();
+ }
+
+ private JPanel initBackupsTabSuffixPanel()
+ {
+ suffixPanel.setBorder(new TitledBorder(
+ MessageManager.getString("label.backup_filename_strategy")));
+ suffixPanel.setLayout(new GridBagLayout());
+
+ suffixTemplateLabel
+ .setText(MessageManager.getString("label.append_to_filename"));
+ suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ suffixTemplateLabel.setFont(LABEL_FONT);
+
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.append_to_filename_tooltip"));
+ suffixTemplate.setToolTipText(tooltip);
+ suffixTemplate.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ updateBackupFilesExampleLabel();
+ backupfilesCustomOptionsSetEnabled();
+ }
+
+ });
+ KeyListener kl = new KeyListener()
+ {
+ @Override
+ public void keyReleased(KeyEvent e)
+ {
+ updateBackupFilesExampleLabel();
+ backupfilesCustomOptionsSetEnabled();
+ }
+
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ }
+
+ // disable use of ':' or '/' or '\'
+ @Override
+ public void keyTyped(KeyEvent e)
+ {
+ char c = e.getKeyChar();
+ if (c == ':' || c == '/' || c == '\\')
+ {
+ // don't process ':' or '/' or '\'
+ e.consume();
+ }
+ }
+
+ };
+ suffixTemplate.addKeyListener(kl);
+
+ // digits spinner
+ suffixDigitsLabel
+ .setText(MessageManager.getString("label.index_digits"));
+ suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ suffixDigitsLabel.setFont(LABEL_FONT);
+ int defaultmin = 1;
+ int defaultmax = 6;
+ ChangeListener c = new ChangeListener()
+ {
+ @Override
+ public void stateChanged(ChangeEvent e)
+ {
+ updateBackupFilesExampleLabel();
+ }
+
+ };
+ setIntegerSpinner(suffixDigitsSpinner, defaultmin, defaultmax, 3, c);
+
+ suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
+ MessageManager.getString("label.increment_index"));
+ suffixReverse.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ boolean okay = true;
+ if (warnAboutSuffixReverseChange())
+ {
+ // Warning popup
+ okay = confirmSuffixReverseChange();
+ }
+ if (okay)
+ {
+ updateBackupFilesExampleLabel();
+ }
+ else
+ {
+ boolean savedSuffixReverse = Cache
+ .getDefault(BackupFiles.REVERSE_ORDER, false);
+ suffixReverse.setSelected(savedSuffixReverse);
+ }
+ }
+ });
+
+ GridBagConstraints sgbc = new GridBagConstraints();
+
+ // first row (template text box)
+ sgbc.anchor = GridBagConstraints.WEST;
+ sgbc.gridx = 0;
+ sgbc.gridy = 0;
+ sgbc.gridwidth = 1;
+ sgbc.gridheight = 1;
+ sgbc.weightx = 1.0;
+ sgbc.weighty = 0.0;
+ sgbc.fill = GridBagConstraints.NONE;
+ suffixPanel.add(suffixTemplateLabel, sgbc);
+
+ sgbc.gridx = 1;
+ sgbc.fill = GridBagConstraints.HORIZONTAL;
+ suffixPanel.add(suffixTemplate, sgbc);
+
+ // second row (number of digits spinner)
+ sgbc.gridy = 1;
+
+ sgbc.gridx = 0;
+ sgbc.fill = GridBagConstraints.NONE;
+ suffixPanel.add(suffixDigitsLabel, sgbc);
+
+ sgbc.gridx = 1;
+ sgbc.fill = GridBagConstraints.HORIZONTAL;
+ suffixPanel.add(suffixDigitsSpinner, sgbc);
+
+ // third row (forward order radio selection)
+ sgbc.gridx = 0;
+ sgbc.gridy = 2;
+ sgbc.gridwidth = GridBagConstraints.REMAINDER;
+ sgbc.fill = GridBagConstraints.HORIZONTAL;
+ suffixPanel.add(suffixReverse.getFalseButton(), sgbc);
+
+ // fourth row (reverse order radio selection)
+ sgbc.gridy = 3;
+ suffixPanel.add(suffixReverse.getTrueButton(), sgbc);
+ return suffixPanel;
+ }
+
+ private boolean confirmSuffixReverseChange()
+ {
+ boolean ret = false;
+ String warningMessage = MessageManager
+ .getString("label.warning_confirm_change_reverse");
+ int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
+ warningMessage,
+ MessageManager.getString("label.change_increment_decrement"),
+ JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
+
+ ret = (confirm == JvOptionPane.YES_OPTION);
+ return ret;
+ }
+
+ private JPanel initBackupsTabKeepFilesPanel()
+ {
+ keepfilesPanel.setBorder(
+ new TitledBorder(MessageManager.getString("label.keep_files")));
+ keepfilesPanel.setLayout(new GridBagLayout());
+
+ backupfilesKeepAll.setLabels(
+ MessageManager.getString("label.keep_all_backup_files"),
+ MessageManager.getString(
+ "label.keep_only_this_number_of_backup_files"));
+ backupfilesKeepAll.addTrueActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ updateBackupFilesExampleLabel();
+ }
+ });
+ backupfilesKeepAll.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ keepRollMaxOptionsEnabled();
+ updateBackupFilesExampleLabel();
+ }
+ });
+
+ ChangeListener c = new ChangeListener()
+ {
+ @Override
+ public void stateChanged(ChangeEvent e)
+ {
+ updateBackupFilesExampleLabel();
+ }
+
+ };
+ setIntegerSpinner(backupfilesRollMaxSpinner, 1, 999, 4, true, c);
+
+ backupfilesConfirmDelete.setLabels(
+ MessageManager.getString("label.always_ask"),
+ MessageManager.getString("label.auto_delete"));
+ // update the enabled section
+ keepRollMaxOptionsEnabled();
+
+ GridBagConstraints kgbc = new GridBagConstraints();
+
+ // first row (template text box)
+ kgbc.anchor = GridBagConstraints.WEST;
+ kgbc.gridx = 0;
+ kgbc.gridy = 0;
+ kgbc.gridwidth = GridBagConstraints.REMAINDER;
+ kgbc.gridheight = 1;
+ kgbc.weightx = 1.0;
+ kgbc.weighty = 0.0;
+ kgbc.fill = GridBagConstraints.HORIZONTAL;
+ keepfilesPanel.add(backupfilesKeepAll.getTrueButton(), kgbc);
+
+ // second row
+ kgbc.gridy = 1;
+
+ kgbc.gridx = 0;
+ kgbc.gridwidth = GridBagConstraints.RELATIVE;
+ keepfilesPanel.add(backupfilesKeepAll.getFalseButton(), kgbc);
+
+ kgbc.gridx = 1;
+ kgbc.gridwidth = GridBagConstraints.REMAINDER;
+ keepfilesPanel.add(backupfilesRollMaxSpinner, kgbc);
+
+ // third row (indented)
+ kgbc.gridy = 2;
+ kgbc.insets = new Insets(0, 20, 0, 0);
+
+ kgbc.gridx = 0;
+ kgbc.gridwidth = GridBagConstraints.REMAINDER;
+ kgbc.fill = GridBagConstraints.HORIZONTAL;
+ kgbc.weightx = 1.0;
+ /*
+ keepfilesPanel.add(backupfilesConfirmDelete.getTrueButton(), kgbc);
+
+ // fourth row (indented)
+ kgbc.gridy = 3;
+ keepfilesPanel.add(backupfilesConfirmDelete.getFalseButton(), kgbc);
+ */
+
+ JPanel jp = new JPanel();
+ jp.setLayout(new FlowLayout());
+ oldBackupFilesLabel
+ .setText(MessageManager
+ .getString("label.autodelete_old_backup_files"));
+ oldBackupFilesLabel.setFont(LABEL_FONT);
+ oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ jp.add(oldBackupFilesLabel);
+ jp.add(backupfilesConfirmDelete.getTrueButton());
+ jp.add(backupfilesConfirmDelete.getFalseButton());
+ keepfilesPanel.add(jp, kgbc);
+
+ return keepfilesPanel;
+ }
+
+ protected void updateBackupFilesExampleLabel()
+ {
+ int exampleindex = 12;
+ String base = MessageManager.getString("label.filename") + ".fa";
+ if (base == null || base.length() == 0)
+ {
+ base = "file_name.fa";
+ }
+
+ boolean reverse = suffixReverse.isSelected();
+ boolean keepAll = backupfilesKeepAll.isSelected();
+ int rollMax = 4;
+ String suffix = suffixTemplate.getText();
+ int digits = 3;
+
+ backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
+ if (suffix == null || suffix.length() == 0)
+ {
+ backupfilesExampleLabel
+ .setText(MessageManager.getString("label.no_backup_files"));
+ backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
+ return;
+ }
+
+ rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
+ rollMax = rollMax < 1 ? 1 : rollMax;
+
+ if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
+ {
+ rollMax = 1;
+ }
+
+ digits = getSpinnerInt(suffixDigitsSpinner, 3);
+ digits = digits < 1 ? 1 : digits;
+
+ int lowersurround = 2;
+ int uppersurround = 0;
+ StringBuilder exampleSB = new StringBuilder();
+ boolean firstLine = true;
+ if (reverse)
+ {
+
+ int min = 1;
+ int max = keepAll ? exampleindex : rollMax;
+ for (int index = min; index <= max; index++)
+ {
+ if (index == min + lowersurround && index < max - uppersurround - 1)
+ {
+ exampleSB.append("\n...");
+ }
+ else if (index > min + lowersurround && index < max - uppersurround)
+ {
+ // nothing
+ }
+ else
+ {
+ if (firstLine)
+ {
+ firstLine = false;
+ }
+ else
+ {
+ exampleSB.append("\n");
+ }
+ exampleSB.append(BackupFilenameParts.getBackupFilename(index,
+ base, suffix, digits));
+ if (min == max)
+ {
+ // no extra text needed
+ }
+ else if (index == min)
+ {
+ String newest = MessageManager.getString("label.braced_newest");
+ if (newest != null && newest.length() > 0)
+ {
+ exampleSB.append(" " + newest);
+ }
+ }
+ else if (index == max)
+ {
+ String oldest = MessageManager.getString("label.braced_oldest");
+ if (oldest != null && oldest.length() > 0)
+ {
+ exampleSB.append(" " + oldest);
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+
+ int min = (keepAll || exampleindex - rollMax < 0) ? 1
+ : exampleindex - rollMax + 1;
+ int max = exampleindex;
+
+ for (int index = min; index <= max; index++)
+ {
+
+ if (index == min + lowersurround && index < max - uppersurround - 1)
+ {
+ exampleSB.append("\n...");
+ }
+ else if (index > min + lowersurround && index < max - uppersurround)
+ {
+ // nothing
+ }
+ else
+ {
+ if (firstLine)
+ {
+ firstLine = false;
+ }
+ else
+ {
+ exampleSB.append("\n");
+ }
+ exampleSB.append(BackupFilenameParts.getBackupFilename(index,
+ base, suffix, digits));
+ if (min == max)
+ {
+ // no extra text needed
+ }
+ else if (index == min)
+ {
+ String oldest = MessageManager.getString("label.braced_oldest");
+ if (oldest != null && oldest.length() > 0)
+ {
+ exampleSB.append(" " + oldest);
+ }
+ }
+ else if (index == max)
+ {
+ String newest = MessageManager.getString("label.braced_newest");
+ if (newest != null && newest.length() > 0)
+ {
+ exampleSB.append(" " + newest);
+ }
+ }
+ }
+ }
+
+ }
+
+ backupfilesExampleLabel.setText(exampleSB.toString());
+ }
+
+ protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
+ boolean useExistingVal, ChangeListener c)
+ {
+ int i = def;
+ if (useExistingVal)
+ {
+ try
+ {
+ i = Integer.parseInt((String) s.getValue());
+ } catch (Exception e)
+ {
+ System.out.println(
+ "Exception casting the initial value of s.getValue()");
+ }
+ }
+
+ setIntegerSpinner(s, min, max, i, c);
+ }
+
+ protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
+ ChangeListener c)
+ {
+ // integer spinner for number of digits
+ if (def > max)
+ {
+ max = def;
+ }
+ SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
+ s.setModel(sModel);
+
+ s.addChangeListener(c);
+
+ }
+
+ protected static int getSpinnerInt(JSpinner s, int def)
+ {
+ int i = def;
+ try
+ {
+ s.commitEdit();
+ i = (Integer) s.getValue();
+ } catch (Exception e)
+ {
+ System.out.println("Failed casting (Integer) JSpinner s.getValue()");
+ }
+ return i;
+ }
+
+ private void keepRollMaxOptionsEnabled()
+ {
+ boolean enabled = backupfilesKeepAll.isEnabled()
+ && !backupfilesKeepAll.isSelected();
+ oldBackupFilesLabel.setEnabled(enabled);
+ backupfilesRollMaxSpinner.setEnabled(enabled);
+ backupfilesConfirmDelete.setEnabled(enabled);
+ }
+
+ private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
+ {
+ boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+ && getComboIntStringKey(backupfilesPresetsCombo) == 0
+ && suffixTemplate.getText()
+ .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
+ keepfilesPanel.setEnabled(enabled);
+ backupfilesKeepAll.setEnabled(enabled);
+ oldBackupFilesLabel.setEnabled(enabled);
+ keepRollMaxOptionsEnabled();
+ }
+
+ private void backupfilesSuffixTemplateDigitsSetEnabled()
+ {
+ boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
+ .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
+ suffixDigitsLabel.setEnabled(enabled);
+ suffixDigitsSpinner.setEnabled(enabled);
+ suffixReverse.setEnabled(enabled);
+ }
+
+ private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
+ {
+ boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+ && getComboIntStringKey(backupfilesPresetsCombo) == 0;
+ suffixPanel.setEnabled(enabled);
+ suffixTemplateLabel.setEnabled(enabled);
+ suffixTemplate.setEnabled(enabled);
+ backupfilesSuffixTemplateDigitsSetEnabled();
+ }
+
+ protected void backupfilesCustomOptionsSetEnabled()
+ {
+ int scheme = getComboIntStringKey(backupfilesPresetsCombo);
+ boolean enabled = scheme == 0 && enableBackupFiles.isSelected();
+
+ backupfilesSuffixTemplateSetEnabled(enabled);
+ backupfilesKeepAllSetEnabled(enabled);
+ }
+
+ private void backupfilesSummarySetEnabled()
+ {
+ boolean enabled = enableBackupFiles.isSelected();
+ backupfilesExampleLabel.setEnabled(enabled);
+ exampleFilesPanel.setEnabled(enabled);
+ }
+
+ private void backupfilesPresetsSetEnabled()
+ {
+ boolean enabled = enableBackupFiles.isSelected();
+ presetsPanel.setEnabled(enabled);
+ backupfilesPresetsCombo.setEnabled(enabled);
+ }
+
+ protected void backupsOptionsSetEnabled()
+ {
+ backupfilesPresetsSetEnabled();
+ backupfilesSummarySetEnabled();
+ backupfilesCustomOptionsSetEnabled();
+ }
+
+ protected void backupsSetOptions(String suffix, int digits,
+ boolean reverse, boolean keepAll, int rollMax,
+ boolean confirmDelete)
+ {
+ suffixTemplate.setText(suffix);
+ suffixDigitsSpinner.setValue(digits);
+ suffixReverse.setSelected(reverse);
+ backupfilesKeepAll.setSelected(keepAll);
+ backupfilesRollMaxSpinner.setValue(rollMax);
+ backupfilesConfirmDelete.setSelected(confirmDelete);
+ }
+
+ protected void backupsSetOptions(BackupFilesPresetEntry p)
+ {
+ backupsSetOptions(p.suffix, p.digits, p.reverse, p.keepAll, p.rollMax,
+ p.confirmDelete);
+ }
+
protected void autoIdWidth_actionPerformed()
{
// TODO Auto-generated method stub
}
}
+
+class IntKeyStringValueEntry
+{
+ int k;
+
+ String v;
+
+ public IntKeyStringValueEntry(int k, String v)
+ {
+ this.k = k;
+ this.v = v;
+ }
+
+ @Override
+ public String toString()
+ {
+ return this.getValue();
+ }
+
+ public int getKey()
+ {
+ return k;
+ }
+
+ public String getValue()
+ {
+ return v;
+ }
+}
+
+class BackupFilesPresetEntry
+{
+ String suffix;
+
+ int digits;
+
+ boolean reverse;
+
+ boolean keepAll;
+
+ int rollMax;
+
+ boolean confirmDelete;
+
+ public BackupFilesPresetEntry(String suffix, int digits, boolean reverse,
+ boolean keepAll, int rollMax, boolean confirmDelete)
+ {
+ this.suffix = suffix;
+ this.digits = digits;
+ this.reverse = reverse;
+ this.keepAll = keepAll;
+ this.rollMax = rollMax;
+ this.confirmDelete = confirmDelete;
+ }
+}
+
+class BackupFilesPresetsComboBoxRenderer extends DefaultListCellRenderer
+{
+ /**
+ *
+ */
+ private static final long serialVersionUID = 88L;
+
+ @Override
+ public Component getListCellRendererComponent(JList list, Object value,
+ int index, boolean isSelected, boolean cellHasFocus)
+ {
+ super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
+
+ try {
+ IntKeyStringValueEntry e = (IntKeyStringValueEntry) value;
+ if (e.getKey() == GPreferences.BACKUPFILESSCHEMECUSTOMISE)
+ {
+ // "Customise" item
+ this.setFont(this.getFont().deriveFont(Font.BOLD));
+ }
+ } catch (Exception e) {
+ return this;
+ }
+
+ return this;
+ }
+}
refreshWs.setText(MessageManager.getString("action.refresh_services"));
refreshWs.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
refreshWs_actionPerformed(e);
resetWs.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
resetWs_actionPerformed(e);
.getString("label.index_web_services_menu_by_host_site"));
indexByHost.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
indexByHost_actionPerformed(e);
indexByType.setText(MessageManager.getString("label.index_by_type"));
indexByType.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
indexByType_actionPerformed(e);
MessageManager.getString("label.enable_jabaws_services"));
enableJws2Services.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
enableJws2Services_actionPerformed(e);
"label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up"));
displayWsWarning.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
displayWsWarning_actionPerformed(e);
newWsUrl.setText(MessageManager.getString("label.new_service_url"));
newWsUrl.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
newWsUrl_actionPerformed(e);
editWsUrl.setText(MessageManager.getString("label.edit_service_url"));
editWsUrl.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
editWsUrl_actionPerformed(e);
.setText(MessageManager.getString("label.delete_service_url"));
deleteWsUrl.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
deleteWsUrl_actionPerformed(e);
.setToolTipText(MessageManager.getString("label.move_url_up"));
moveWsUrlUp.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
moveWsUrlUp_actionPerformed(e);
MessageManager.getString("label.move_url_down"));
moveWsUrlDown.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
moveWsUrlDown_actionPerformed(e);
.setText(MessageManager.getString("label.add_sbrs_definition"));
newSbrsUrl.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
newSbrsUrl_actionPerformed(e);
MessageManager.getString("label.edit_sbrs_definition"));
editSbrsUrl.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
editSbrsUrl_actionPerformed(e);
MessageManager.getString("label.delete_sbrs_definition"));
deleteSbrsUrl.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
deleteSbrsUrl_actionPerformed(e);
wsListUrlPanel.setBorder(BorderFactory.createEtchedBorder());
wsListUrlPanel.setLayout(new BorderLayout());
wsListPane.setBorder(BorderFactory.createEtchedBorder());
- wsListPane.getViewport().add(wsList);
wsList.setPreferredSize(new Dimension(482, 202));
+ wsList.getTableHeader().setReorderingAllowed(false);
+ wsListPane.getViewport().add(wsList);
wsListPane.setPreferredSize(new Dimension(380, 80));
wsList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
wsList.setColumnSelectionAllowed(false);
wsList.addMouseListener(new MouseListener()
{
+ @Override
public void mouseClicked(MouseEvent e)
{
if (e.getClickCount() > 1)
}
+ @Override
public void mouseEntered(MouseEvent e)
{
}
+ @Override
public void mouseExited(MouseEvent e)
{
}
+ @Override
public void mousePressed(MouseEvent e)
{
}
+ @Override
public void mouseReleased(MouseEvent e)
{
sbrsList.addMouseListener(new MouseListener()
{
+ @Override
public void mouseClicked(MouseEvent e)
{
if (e.getClickCount() > 1)
}
+ @Override
public void mouseEntered(MouseEvent e)
{
}
+ @Override
public void mouseExited(MouseEvent e)
{
}
+ @Override
public void mousePressed(MouseEvent e)
{
}
+ @Override
public void mouseReleased(MouseEvent e)
{
import jalview.util.MessageManager;
import java.io.PrintStream;
+import java.util.Arrays;
/**
* A class to model rectangular matrices of double values and operations on them
public class Matrix implements MatrixI
{
/*
- * the cell values in row-major order
+ * maximum number of iterations for tqli
*/
- private double[][] value;
+ private static final int MAX_ITER = 45;
+ // fudge - add 15 iterations, just in case
/*
* the number of rows
*/
- protected int rows;
+ final protected int rows;
/*
* the number of columns
*/
- protected int cols;
+ final protected int cols;
+
+ /*
+ * the cell values in row-major order
+ */
+ private double[][] value;
protected double[] d; // Diagonal
protected double[] e; // off diagonal
/**
- * maximum number of iterations for tqli
+ * Constructor given number of rows and columns
*
+ * @param colCount
+ * @param rowCount
*/
- private static final int maxIter = 45; // fudge - add 15 iterations, just in
- // case
-
- /**
- * Default constructor
- */
- public Matrix()
+ protected Matrix(int rowCount, int colCount)
{
-
+ rows = rowCount;
+ cols = colCount;
}
/**
}
}
- /**
- * Returns a new matrix which is the transpose of this one
- *
- * @return
- */
@Override
public MatrixI transpose()
{
}
}
- /**
- * Returns a new matrix which is the result of premultiplying this matrix by
- * the supplied argument. If this of size AxB (A rows and B columns), and the
- * argument is CxA (C rows and A columns), the result is of size CxB.
- *
- * @param in
- *
- * @return
- * @throws IllegalArgumentException
- * if the number of columns in the pre-multiplier is not equal to
- * the number of rows in the multiplicand (this)
- */
@Override
public MatrixI preMultiply(MatrixI in)
{
return out;
}
- /**
- * Returns a new matrix which is the result of postmultiplying this matrix by
- * the supplied argument. If this of size AxB (A rows and B columns), and the
- * argument is BxC (B rows and C columns), the result is of size AxC.
- * <p>
- * This method simply returns the result of in.preMultiply(this)
- *
- * @param in
- *
- * @return
- * @throws IllegalArgumentException
- * if the number of rows in the post-multiplier is not equal to the
- * number of columns in the multiplicand (this)
- * @see #preMultiply(Matrix)
- */
@Override
public MatrixI postMultiply(MatrixI in)
{
return in.preMultiply(this);
}
- /**
- * Answers a new matrix with a copy of the values in this one
- *
- * @return
- */
@Override
public MatrixI copy()
{
System.arraycopy(value[i], 0, newmat[i], 0, value[i].length);
}
- return new Matrix(newmat);
+ Matrix m = new Matrix(newmat);
+ if (this.d != null)
+ {
+ m.d = Arrays.copyOf(this.d, this.d.length);
+ }
+ if (this.e != null)
+ {
+ m.e = Arrays.copyOf(this.e, this.e.length);
+ }
+
+ return m;
}
/**
{
iter++;
- if (iter == maxIter)
+ if (iter == MAX_ITER)
{
throw new Exception(MessageManager.formatMessage(
"exception.matrix_too_many_iteration", new String[]
- { "tqli", Integer.valueOf(maxIter).toString() }));
+ { "tqli", Integer.valueOf(MAX_ITER).toString() }));
}
else
{
{
iter++;
- if (iter == maxIter)
+ if (iter == MAX_ITER)
{
throw new Exception(MessageManager.formatMessage(
"exception.matrix_too_many_iteration", new String[]
- { "tqli2", Integer.valueOf(maxIter).toString() }));
+ { "tqli2", Integer.valueOf(MAX_ITER).toString() }));
}
else
{
}
}
}
+
+ @Override
+ public void setD(double[] v)
+ {
+ d = v;
+ }
+
+ @Override
+ public void setE(double[] v)
+ {
+ e = v;
+ }
+
+ public double getTotal()
+ {
+ double d = 0d;
+ for (int i = 0; i < this.height(); i++)
+ {
+ for (int j = 0; j < this.width(); j++)
+ {
+ d += value[i][j];
+ }
+ }
+ return d;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public boolean equals(MatrixI m2, double delta)
+ {
+ if (m2 == null || this.height() != m2.height()
+ || this.width() != m2.width())
+ {
+ return false;
+ }
+ for (int i = 0; i < this.height(); i++)
+ {
+ for (int j = 0; j < this.width(); j++)
+ {
+ double diff = this.getValue(i, j) - m2.getValue(i, j);
+ if (Math.abs(diff) > delta)
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
}
import java.io.PrintStream;
+/**
+ * An interface that describes a rectangular matrix of double values and
+ * operations on it
+ */
public interface MatrixI
{
/**
*/
double[] getRow(int i);
+ /**
+ * Answers a new matrix with a copy of the values in this one
+ *
+ * @return
+ */
MatrixI copy();
+ /**
+ * Returns a new matrix which is the transpose of this one
+ *
+ * @return
+ */
MatrixI transpose();
+ /**
+ * Returns a new matrix which is the result of premultiplying this matrix by
+ * the supplied argument. If this of size AxB (A rows and B columns), and the
+ * argument is CxA (C rows and A columns), the result is of size CxB.
+ *
+ * @param in
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if the number of columns in the pre-multiplier is not equal to
+ * the number of rows in the multiplicand (this)
+ */
MatrixI preMultiply(MatrixI m);
+ /**
+ * Returns a new matrix which is the result of postmultiplying this matrix by
+ * the supplied argument. If this of size AxB (A rows and B columns), and the
+ * argument is BxC (B rows and C columns), the result is of size AxC.
+ * <p>
+ * This method simply returns the result of in.preMultiply(this)
+ *
+ * @param in
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if the number of rows in the post-multiplier is not equal to the
+ * number of columns in the multiplicand (this)
+ * @see #preMultiply(Matrix)
+ */
MatrixI postMultiply(MatrixI m);
double[] getD();
double[] getE();
+ void setD(double[] v);
+
+ void setE(double[] v);
+
void print(PrintStream ps, String format);
void printD(PrintStream ps, String format);
* @param d
*/
void multiply(double d);
+
+ /**
+ * Answers true if the two matrices have the same dimensions, and corresponding values all differ by no
+ * more than delta (which should be a positive value), else false
+ *
+ * @param m2
+ * @param delta
+ * @return
+ */
+ boolean equals(MatrixI m2, double delta);
}
*/
package jalview.math;
+import jalview.datamodel.Point;
+
+import java.util.HashMap;
+import java.util.Map;
+
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * Model for a 3x3 matrix which provides methods for rotation in 3-D space
*/
public class RotatableMatrix
{
- float[][] matrix;
+ private static final int DIMS = 3;
- float[] temp;
+ /*
+ * cache the most used rotations: +/- 1, 2, 3, 4 degrees around x or y axis
+ */
+ private static Map<Axis, Map<Float, float[][]>> cachedRotations;
- float[][] rot;
+ static
+ {
+ cachedRotations = new HashMap<>();
+ for (Axis axis : Axis.values())
+ {
+ HashMap<Float, float[][]> map = new HashMap<>();
+ cachedRotations.put(axis, map);
+ for (int deg = 1; deg < 5; deg++)
+ {
+ float[][] rotation = getRotation(deg, axis);
+ map.put(Float.valueOf(deg), rotation);
+ rotation = getRotation(-deg, axis);
+ map.put(Float.valueOf(-deg), rotation);
+ }
+ }
+ }
- /**
- * Creates a new RotatableMatrix object.
- *
- * @param rows
- * DOCUMENT ME!
- * @param cols
- * DOCUMENT ME!
- */
- public RotatableMatrix(int rows, int cols)
+ public enum Axis
{
- matrix = new float[rows][cols];
+ X, Y, Z
+ };
- temp = new float[3];
+ float[][] matrix;
- rot = new float[3][3];
+ /**
+ * Constructor creates a new identity matrix (all values zero except for 1 on
+ * the diagonal)
+ */
+ public RotatableMatrix()
+ {
+ matrix = new float[DIMS][DIMS];
+ for (int j = 0; j < DIMS; j++)
+ {
+ matrix[j][j] = 1f;
+ }
}
/**
- * DOCUMENT ME!
+ * Sets the value at position (i, j) of the matrix
*
* @param i
- * DOCUMENT ME!
* @param j
- * DOCUMENT ME!
* @param value
- * DOCUMENT ME!
*/
- public void addElement(int i, int j, float value)
+ public void setValue(int i, int j, float value)
{
matrix[i][j] = value;
}
/**
- * DOCUMENT ME!
+ * Answers the value at position (i, j) of the matrix
+ *
+ * @param i
+ * @param j
+ * @return
+ */
+ public float getValue(int i, int j)
+ {
+ return matrix[i][j];
+ }
+
+ /**
+ * Prints the matrix in rows of space-delimited values
*/
public void print()
{
}
/**
- * DOCUMENT ME!
+ * Rotates the matrix through the specified number of degrees around the
+ * specified axis
*
* @param degrees
- * DOCUMENT ME!
* @param axis
- * DOCUMENT ME!
*/
- public void rotate(float degrees, char axis)
+ public void rotate(float degrees, Axis axis)
{
- float costheta = (float) Math.cos((degrees * Math.PI) / (float) 180.0);
+ float[][] rot = getRotation(degrees, axis);
- float sintheta = (float) Math.sin((degrees * Math.PI) / (float) 180.0);
+ preMultiply(rot);
+ }
- if (axis == 'z')
+ /**
+ * Answers a matrix which, when it pre-multiplies another matrix, applies a
+ * rotation of the specified number of degrees around the specified axis
+ *
+ * @param degrees
+ * @param axis
+ * @return
+ * @see https://en.wikipedia.org/wiki/Rotation_matrix#Basic_rotations
+ */
+ protected static float[][] getRotation(float degrees, Axis axis)
+ {
+ Float floatValue = Float.valueOf(degrees);
+ if (cachedRotations.get(axis).containsKey(floatValue))
{
- rot[0][0] = (float) costheta;
-
- rot[0][1] = (float) -sintheta;
-
- rot[0][2] = (float) 0.0;
-
- rot[1][0] = (float) sintheta;
-
- rot[1][1] = (float) costheta;
-
- rot[1][2] = (float) 0.0;
-
- rot[2][0] = (float) 0.0;
-
- rot[2][1] = (float) 0.0;
-
- rot[2][2] = (float) 1.0;
-
- preMultiply(rot);
+ // System.out.println("getRotation from cache: " + (int) degrees);
+ return cachedRotations.get(axis).get(floatValue);
}
- if (axis == 'x')
- {
- rot[0][0] = (float) 1.0;
-
- rot[0][1] = (float) 0.0;
-
- rot[0][2] = (float) 0.0;
-
- rot[1][0] = (float) 0.0;
+ float costheta = (float) Math.cos(degrees * Math.PI / 180f);
- rot[1][1] = (float) costheta;
+ float sintheta = (float) Math.sin(degrees * Math.PI / 180f);
- rot[1][2] = (float) sintheta;
+ float[][] rot = new float[DIMS][DIMS];
- rot[2][0] = (float) 0.0;
-
- rot[2][1] = (float) -sintheta;
-
- rot[2][2] = (float) costheta;
-
- preMultiply(rot);
- }
-
- if (axis == 'y')
+ switch (axis)
{
- rot[0][0] = (float) costheta;
-
- rot[0][1] = (float) 0.0;
-
- rot[0][2] = (float) -sintheta;
-
- rot[1][0] = (float) 0.0;
-
- rot[1][1] = (float) 1.0;
-
- rot[1][2] = (float) 0.0;
-
- rot[2][0] = (float) sintheta;
-
- rot[2][1] = (float) 0.0;
-
- rot[2][2] = (float) costheta;
-
- preMultiply(rot);
+ case X:
+ rot[0][0] = 1f;
+ rot[1][1] = costheta;
+ rot[1][2] = sintheta;
+ rot[2][1] = -sintheta;
+ rot[2][2] = costheta;
+ break;
+ case Y:
+ rot[0][0] = costheta;
+ rot[0][2] = -sintheta;
+ rot[1][1] = 1f;
+ rot[2][0] = sintheta;
+ rot[2][2] = costheta;
+ break;
+ case Z:
+ rot[0][0] = costheta;
+ rot[0][1] = -sintheta;
+ rot[1][0] = sintheta;
+ rot[1][1] = costheta;
+ rot[2][2] = 1f;
+ break;
}
+ return rot;
}
/**
- * DOCUMENT ME!
+ * Answers a new array of float values which is the result of pre-multiplying
+ * this matrix by the given vector. Each value of the result is the dot
+ * product of the vector with one column of this matrix. The matrix and input
+ * vector are not modified.
*
* @param vect
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @return
*/
public float[] vectorMultiply(float[] vect)
{
- temp[0] = vect[0];
-
- temp[1] = vect[1];
-
- temp[2] = vect[2];
+ float[] result = new float[DIMS];
- for (int i = 0; i < 3; i++)
+ for (int i = 0; i < DIMS; i++)
{
- temp[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1])
+ result[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1])
+ (matrix[i][2] * vect[2]);
}
- vect[0] = temp[0];
-
- vect[1] = temp[1];
-
- vect[2] = temp[2];
-
- return vect;
+ return result;
}
/**
- * DOCUMENT ME!
+ * Performs pre-multiplication of this matrix by the given one. Value (i, j)
+ * of the result is the dot product of the i'th row of <code>mat</code> with
+ * the j'th column of this matrix.
*
* @param mat
- * DOCUMENT ME!
*/
public void preMultiply(float[][] mat)
{
- float[][] tmp = new float[3][3];
+ float[][] tmp = new float[DIMS][DIMS];
- for (int i = 0; i < 3; i++)
+ for (int i = 0; i < DIMS; i++)
{
- for (int j = 0; j < 3; j++)
+ for (int j = 0; j < DIMS; j++)
{
tmp[i][j] = (mat[i][0] * matrix[0][j]) + (mat[i][1] * matrix[1][j])
+ (mat[i][2] * matrix[2][j]);
}
}
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- matrix[i][j] = tmp[i][j];
- }
- }
+ matrix = tmp;
}
/**
- * DOCUMENT ME!
+ * Performs post-multiplication of this matrix by the given one. Value (i, j)
+ * of the result is the dot product of the i'th row of this matrix with the
+ * j'th column of <code>mat</code>.
*
* @param mat
- * DOCUMENT ME!
*/
public void postMultiply(float[][] mat)
{
- float[][] tmp = new float[3][3];
+ float[][] tmp = new float[DIMS][DIMS];
- for (int i = 0; i < 3; i++)
+ for (int i = 0; i < DIMS; i++)
{
- for (int j = 0; j < 3; j++)
+ for (int j = 0; j < DIMS; j++)
{
tmp[i][j] = (matrix[i][0] * mat[0][j]) + (matrix[i][1] * mat[1][j])
+ (matrix[i][2] * mat[2][j]);
}
}
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- matrix[i][j] = tmp[i][j];
- }
- }
+ matrix = tmp;
}
/**
*/
public static void main(String[] args)
{
- RotatableMatrix m = new RotatableMatrix(3, 3);
+ RotatableMatrix m = new RotatableMatrix();
- m.addElement(0, 0, 1);
+ m.setValue(0, 0, 1);
- m.addElement(0, 1, 0);
+ m.setValue(0, 1, 0);
- m.addElement(0, 2, 0);
+ m.setValue(0, 2, 0);
- m.addElement(1, 0, 0);
+ m.setValue(1, 0, 0);
- m.addElement(1, 1, 2);
+ m.setValue(1, 1, 2);
- m.addElement(1, 2, 0);
+ m.setValue(1, 2, 0);
- m.addElement(2, 0, 0);
+ m.setValue(2, 0, 0);
- m.addElement(2, 1, 0);
+ m.setValue(2, 1, 0);
- m.addElement(2, 2, 1);
+ m.setValue(2, 2, 1);
m.print();
- RotatableMatrix n = new RotatableMatrix(3, 3);
+ RotatableMatrix n = new RotatableMatrix();
- n.addElement(0, 0, 2);
+ n.setValue(0, 0, 2);
- n.addElement(0, 1, 1);
+ n.setValue(0, 1, 1);
- n.addElement(0, 2, 1);
+ n.setValue(0, 2, 1);
- n.addElement(1, 0, 2);
+ n.setValue(1, 0, 2);
- n.addElement(1, 1, 1);
+ n.setValue(1, 1, 1);
- n.addElement(1, 2, 1);
+ n.setValue(1, 2, 1);
- n.addElement(2, 0, 2);
+ n.setValue(2, 0, 2);
- n.addElement(2, 1, 1);
+ n.setValue(2, 1, 1);
- n.addElement(2, 2, 1);
+ n.setValue(2, 2, 1);
n.print();
}
/**
- * DOCUMENT ME!
+ * Performs a vector multiplication whose result is the Point representing the
+ * input point's value vector post-multiplied by this matrix.
+ *
+ * @param coord
+ * @return
*/
- public void setIdentity()
+ public Point vectorMultiply(Point coord)
{
- matrix[0][0] = (float) 1.0;
-
- matrix[1][1] = (float) 1.0;
-
- matrix[2][2] = (float) 1.0;
-
- matrix[0][1] = (float) 0.0;
-
- matrix[0][2] = (float) 0.0;
-
- matrix[1][0] = (float) 0.0;
-
- matrix[1][2] = (float) 0.0;
-
- matrix[2][0] = (float) 0.0;
-
- matrix[2][1] = (float) 0.0;
+ float[] v = vectorMultiply(new float[] { coord.x, coord.y, coord.z });
+ return new Point(v[0], v[1], v[2]);
}
}
*/
public SparseMatrix(double[][] v)
{
- rows = v.length;
- if (rows > 0)
- {
- cols = v[0].length;
- }
+ super(v.length, v.length > 0 ? v[0].length : 0);
+
sparseColumns = new SparseDoubleArray[cols];
/*
*/
package jalview.project;
+import static jalview.math.RotatableMatrix.Axis.X;
+import static jalview.math.RotatableMatrix.Axis.Y;
+import static jalview.math.RotatableMatrix.Axis.Z;
+
import jalview.analysis.Conservation;
+import jalview.analysis.PCA;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.GraphLine;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Point;
import jalview.datamodel.RnaViewerModel;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.gui.FeatureRenderer;
import jalview.gui.JvOptionPane;
import jalview.gui.OOMWarning;
+import jalview.gui.PCAPanel;
import jalview.gui.PaintRefresher;
import jalview.gui.SplitFrame;
import jalview.gui.StructureViewer;
import jalview.gui.StructureViewer.ViewerType;
import jalview.gui.StructureViewerBase;
import jalview.gui.TreePanel;
+import jalview.io.BackupFiles;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.NewickFile;
+import jalview.math.Matrix;
+import jalview.math.MatrixI;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
import jalview.util.jarInputStreamProvider;
import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.PCAModel;
import jalview.viewmodel.ViewportRanges;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import jalview.xml.binding.jalview.Annotation.ThresholdLine;
import jalview.xml.binding.jalview.AnnotationColourScheme;
import jalview.xml.binding.jalview.AnnotationElement;
+import jalview.xml.binding.jalview.DoubleMatrix;
+import jalview.xml.binding.jalview.DoubleVector;
import jalview.xml.binding.jalview.Feature;
import jalview.xml.binding.jalview.Feature.OtherData;
import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
+import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
+import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
+import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
+import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
+import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
import jalview.xml.binding.jalview.JalviewModel.Tree;
import jalview.xml.binding.jalview.JalviewModel.UserColours;
import jalview.xml.binding.jalview.JalviewModel.Viewport;
import jalview.xml.binding.jalview.Mapping;
import jalview.xml.binding.jalview.NoValueColour;
import jalview.xml.binding.jalview.ObjectFactory;
+import jalview.xml.binding.jalview.PcaDataType;
import jalview.xml.binding.jalview.Pdbentry.Property;
import jalview.xml.binding.jalview.Sequence;
import jalview.xml.binding.jalview.Sequence.DBRef;
private static final String UTF_8 = "UTF-8";
+ /**
+ * prefix for recovering datasets for alignments with multiple views where
+ * non-existent dataset IDs were written for some views
+ */
+ private static final String UNIQSEQSETID = "uniqueSeqSetId.";
+
// use this with nextCounter() to make unique names for entities
private int counter = 0;
public void saveState(File statefile)
{
FileOutputStream fos = null;
+
try
{
+
fos = new FileOutputStream(statefile);
+
JarOutputStream jout = new JarOutputStream(fos);
saveState(jout);
+ fos.close();
} catch (Exception e)
{
+ Cache.log.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)
{
- errorMessage = "Couldn't write Jalview Archive to output file '"
+ errorMessage = "Did't write Jalview Archive to output file '"
+ statefile + "' - See console error log for details";
}
else
{
- errorMessage += "(output file was '" + statefile + "')";
+ errorMessage += "(Didn't write Jalview Archive to output file '"
+ + statefile + ")";
}
e.printStackTrace();
} finally
{
try
{
- FileOutputStream fos = new FileOutputStream(jarFile);
+ // create backupfiles object and get new temp filename destination
+ BackupFiles backupfiles = new BackupFiles(jarFile);
+ FileOutputStream fos = new FileOutputStream(
+ backupfiles.getTempFilePath());
+
JarOutputStream jout = new JarOutputStream(fos);
List<AlignFrame> frames = new ArrayList<>();
}
;
jout.close();
- return true;
+ boolean success = true;
+
+ backupfiles.setWriteSuccess(success);
+ success = backupfiles.rollBackupsAndRenameTempFile();
+
+ return success;
} catch (Exception ex)
{
errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
tree.setXpos(tp.getX());
tree.setYpos(tp.getY());
tree.setId(makeHashCode(tp, null));
+ tree.setLinkToAllViews(
+ tp.getTreeCanvas().isApplyToAllViews());
+
// jms.addTree(tree);
object.getTree().add(tree);
}
}
}
+ /*
+ * save PCA viewers
+ */
+ if (!storeDS && Desktop.desktop != null)
+ {
+ for (JInternalFrame frame : Desktop.desktop.getAllFrames())
+ {
+ if (frame instanceof PCAPanel)
+ {
+ PCAPanel panel = (PCAPanel) frame;
+ if (panel.getAlignViewport().getAlignment() == jal)
+ {
+ savePCA(panel, object);
+ }
+ }
+ }
+ }
+
// SAVE ANNOTATIONS
/**
* store forward refs from an annotationRow to any groups
}
/**
+ * Writes PCA viewer attributes and computed values to an XML model object and
+ * adds it to the JalviewModel. Any exceptions are reported by logging.
+ */
+ protected void savePCA(PCAPanel panel, JalviewModel object)
+ {
+ try
+ {
+ PcaViewer viewer = new PcaViewer();
+ viewer.setHeight(panel.getHeight());
+ viewer.setWidth(panel.getWidth());
+ viewer.setXpos(panel.getX());
+ viewer.setYpos(panel.getY());
+ viewer.setTitle(panel.getTitle());
+ PCAModel pcaModel = panel.getPcaModel();
+ viewer.setScoreModelName(pcaModel.getScoreModelName());
+ viewer.setXDim(panel.getSelectedDimensionIndex(X));
+ viewer.setYDim(panel.getSelectedDimensionIndex(Y));
+ viewer.setZDim(panel.getSelectedDimensionIndex(Z));
+ viewer.setBgColour(
+ panel.getRotatableCanvas().getBackgroundColour().getRGB());
+ viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
+ float[] spMin = panel.getRotatableCanvas().getSeqMin();
+ SeqPointMin spmin = new SeqPointMin();
+ spmin.setXPos(spMin[0]);
+ spmin.setYPos(spMin[1]);
+ spmin.setZPos(spMin[2]);
+ viewer.setSeqPointMin(spmin);
+ float[] spMax = panel.getRotatableCanvas().getSeqMax();
+ SeqPointMax spmax = new SeqPointMax();
+ spmax.setXPos(spMax[0]);
+ spmax.setYPos(spMax[1]);
+ spmax.setZPos(spMax[2]);
+ viewer.setSeqPointMax(spmax);
+ viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
+ viewer.setLinkToAllViews(
+ panel.getRotatableCanvas().isApplyToAllViews());
+ SimilarityParamsI sp = pcaModel.getSimilarityParameters();
+ viewer.setIncludeGaps(sp.includeGaps());
+ viewer.setMatchGaps(sp.matchGaps());
+ viewer.setIncludeGappedColumns(sp.includeGappedColumns());
+ viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
+
+ /*
+ * sequence points on display
+ */
+ for (jalview.datamodel.SequencePoint spt : pcaModel
+ .getSequencePoints())
+ {
+ SequencePoint point = new SequencePoint();
+ point.setSequenceRef(seqHash(spt.getSequence()));
+ point.setXPos(spt.coord.x);
+ point.setYPos(spt.coord.y);
+ point.setZPos(spt.coord.z);
+ viewer.getSequencePoint().add(point);
+ }
+
+ /*
+ * (end points of) axes on display
+ */
+ for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
+ {
+
+ Axis axis = new Axis();
+ axis.setXPos(p.x);
+ axis.setYPos(p.y);
+ axis.setZPos(p.z);
+ viewer.getAxis().add(axis);
+ }
+
+ /*
+ * raw PCA data (note we are not restoring PCA inputs here -
+ * alignment view, score model, similarity parameters)
+ */
+ PcaDataType data = new PcaDataType();
+ viewer.setPcaData(data);
+ PCA pca = pcaModel.getPcaData();
+
+ DoubleMatrix pm = new DoubleMatrix();
+ saveDoubleMatrix(pca.getPairwiseScores(), pm);
+ data.setPairwiseMatrix(pm);
+
+ DoubleMatrix tm = new DoubleMatrix();
+ saveDoubleMatrix(pca.getTridiagonal(), tm);
+ data.setTridiagonalMatrix(tm);
+
+ DoubleMatrix eigenMatrix = new DoubleMatrix();
+ data.setEigenMatrix(eigenMatrix);
+ saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
+
+ object.getPcaViewer().add(viewer);
+ } catch (Throwable t)
+ {
+ Cache.log.error("Error saving PCA: " + t.getMessage());
+ }
+ }
+
+ /**
+ * Stores values from a matrix into an XML element, including (if present) the
+ * D or E vectors
+ *
+ * @param m
+ * @param xmlMatrix
+ * @see #loadDoubleMatrix(DoubleMatrix)
+ */
+ protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
+ {
+ xmlMatrix.setRows(m.height());
+ xmlMatrix.setColumns(m.width());
+ for (int i = 0; i < m.height(); i++)
+ {
+ DoubleVector row = new DoubleVector();
+ for (int j = 0; j < m.width(); j++)
+ {
+ row.getV().add(m.getValue(i, j));
+ }
+ xmlMatrix.getRow().add(row);
+ }
+ if (m.getD() != null)
+ {
+ DoubleVector dVector = new DoubleVector();
+ for (double d : m.getD())
+ {
+ dVector.getV().add(d);
+ }
+ xmlMatrix.setD(dVector);
+ }
+ if (m.getE() != null)
+ {
+ DoubleVector eVector = new DoubleVector();
+ for (double e : m.getE())
+ {
+ eVector.getV().add(e);
+ }
+ xmlMatrix.setE(eVector);
+ }
+ }
+
+ /**
+ * Loads XML matrix data into a new Matrix object, including the D and/or E
+ * vectors (if present)
+ *
+ * @param mData
+ * @return
+ * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
+ */
+ protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
+ {
+ int rows = mData.getRows();
+ double[][] vals = new double[rows][];
+
+ for (int i = 0; i < rows; i++)
+ {
+ List<Double> dVector = mData.getRow().get(i).getV();
+ vals[i] = new double[dVector.size()];
+ int dvi = 0;
+ for (Double d : dVector)
+ {
+ vals[i][dvi++] = d;
+ }
+ }
+
+ MatrixI m = new Matrix(vals);
+
+ if (mData.getD() != null)
+ {
+ List<Double> dVector = mData.getD().getV();
+ double[] vec = new double[dVector.size()];
+ int dvi = 0;
+ for (Double d : dVector)
+ {
+ vec[dvi++] = d;
+ }
+ m.setD(vec);
+ }
+ if (mData.getE() != null)
+ {
+ List<Double> dVector = mData.getE().getV();
+ double[] vec = new double[dVector.size()];
+ int dvi = 0;
+ for (Double d : dVector)
+ {
+ vec[dvi++] = d;
+ }
+ m.setE(vec);
+ }
+
+ return m;
+ }
+
+ /**
* Save any Varna viewers linked to this sequence. Writes an rnaViewer element
* for each viewer, with
* <ul>
: null;
// ////////////////////////////////
+ // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
+ //
+ //
+ // If we just load in the same jar file again, the sequenceSetId
+ // will be the same, and we end up with multiple references
+ // to the same sequenceSet. We must modify this id on load
+ // so that each load of the file gives a unique id
+
+ /**
+ * used to resolve correct alignment dataset for alignments with multiple
+ * views
+ */
+ String uniqueSeqSetId = null;
+ String viewId = null;
+ if (view != null)
+ {
+ uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
+ viewId = (view.getId() == null ? null
+ : view.getId() + uniqueSetSuffix);
+ }
+
+ // ////////////////////////////////
// LOAD SEQUENCES
List<SequenceI> hiddenSeqs = null;
// finally, verify all data in vamsasSet is actually present in al
// passing on flag indicating if it is actually a stored dataset
- recoverDatasetFor(vamsasSet, al, isdsal);
+ recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
}
if (referenceseqForView != null)
}
else
{
- cs = ColourSchemeProperty.getColourScheme(al,
+ cs = ColourSchemeProperty.getColourScheme(null, al,
jGroup.getColour());
}
}
// ///////////////////////////////
// LOAD VIEWPORT
- // If we just load in the same jar file again, the sequenceSetId
- // will be the same, and we end up with multiple references
- // to the same sequenceSet. We must modify this id on load
- // so that each load of the file gives a unique id
- String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
- String viewId = (view.getId() == null ? null
- : view.getId() + uniqueSetSuffix);
AlignFrame af = null;
AlignViewport av = null;
// now check to see if we really need to create a new viewport.
if (loadTreesAndStructures)
{
loadTrees(jalviewModel, view, af, av, ap);
+ loadPCAViewers(jalviewModel, ap);
loadPDBStructures(jprovider, jseqs, af, ap);
loadRnaViewers(jprovider, jseqs, ap);
}
// TODO: verify 'associate with all views' works still
tp.getTreeCanvas().setViewport(av); // af.viewport;
tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
-
}
+ tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
if (tp == null)
{
warn("There was a problem recovering stored Newick tree: \n"
}
else
{
- cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
+ cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
+ view.getBgColour());
}
}
+ /*
+ * turn off 'alignment colour applies to all groups'
+ * while restoring global colour scheme
+ */
+ viewport.setColourAppliesToAllGroups(false);
viewport.setGlobalColourScheme(cs);
viewport.getResidueShading().setThreshold(pidThreshold,
view.isIgnoreGapsinConsensus());
viewport.getResidueShading()
.setConsensus(viewport.getSequenceConsensusHash());
- viewport.setColourAppliesToAllGroups(false);
-
if (safeBoolean(view.isConservationSelected()) && cs != null)
{
viewport.getResidueShading()
.setConservationInc(safeInt(view.getConsThreshold()));
}
-
af.changeColour(cs);
-
viewport.setColourAppliesToAllGroups(true);
viewport
float min = safeFloat(safeFloat(setting.getMin()));
float max = setting.getMax() == null ? 1f
: setting.getMax().floatValue();
- FeatureColourI gc = new FeatureColour(minColour, maxColour,
+ FeatureColourI gc = new FeatureColour(maxColour, minColour,
+ maxColour,
noValueColour, min, max);
if (setting.getAttributeName().size() > 0)
{
else
{
cs = new AnnotationColourGradient(matchedAnnotation,
- ColourSchemeProperty.getColourScheme(al,
+ ColourSchemeProperty.getColourScheme(af.getViewport(), al,
viewAnnColour.getColourScheme()),
safeInt(viewAnnColour.getAboveThreshold()));
}
}
private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
- boolean ignoreUnrefed)
+ boolean ignoreUnrefed, String uniqueSeqSetId)
{
jalview.datamodel.AlignmentI ds = getDatasetFor(
vamsasSet.getDatasetId());
+ AlignmentI xtant_ds = ds;
+ if (xtant_ds == null)
+ {
+ // good chance we are about to create a new dataset, but check if we've
+ // seen some of the dataset sequence IDs before.
+ // TODO: skip this check if we are working with project generated by
+ // version 2.11 or later
+ xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
+ if (xtant_ds != null)
+ {
+ ds = xtant_ds;
+ addDatasetRef(vamsasSet.getDatasetId(), ds);
+ }
+ }
Vector dseqs = null;
+ if (!ignoreUnrefed)
+ {
+ // recovering an alignment View
+ AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
+ if (seqSetDS != null)
+ {
+ if (ds != null && ds != seqSetDS)
+ {
+ 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.");
+ }
+ }
+ ds = seqSetDS;
+ addDatasetRef(vamsasSet.getDatasetId(), ds);
+ }
+ }
if (ds == null)
{
+ // try even harder to restore dataset
+ AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
// create a list of new dataset sequences
dseqs = new Vector();
}
if (al.getDataset() == null && !ignoreUnrefed)
{
al.setDataset(ds);
+ // register dataset for the alignment's uniqueSeqSetId for legacy projects
+ addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
}
+ updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
}
/**
+ * XML dataset sequence ID to materialised dataset reference
+ */
+ HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
+
+ /**
+ * @return the first materialised dataset reference containing a dataset
+ * sequence referenced in the given view
+ * @param list
+ * - sequences from the view
+ */
+ AlignmentI checkIfHasDataset(List<Sequence> list)
+ {
+ for (Sequence restoredSeq : list)
+ {
+ AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
+ if (datasetFor != null)
+ {
+ return datasetFor;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Register ds as the containing dataset for the dataset sequences referenced
+ * by sequences in list
+ *
+ * @param list
+ * - sequences in a view
+ * @param ds
+ */
+ void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
+ {
+ for (Sequence restoredSeq : list)
+ {
+ AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
+ if (prevDS != null && prevDS != ds)
+ {
+ warn("Dataset sequence appears in many datasets: "
+ + restoredSeq.getDsseqid());
+ // TODO: try to merge!
+ }
+ }
+ }
+ /**
*
* @param vamsasSeq
* sequence definition to create/merge dataset sequence for
jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
fto, m.getMapFromUnit().intValue(),
m.getMapToUnit().intValue());
- // if (m.getMappingChoice() != null)
- // {
- // MappingChoice mc = m.getMappingChoice();
+
+ /*
+ * (optional) choice of dseqFor or Sequence
+ */
if (m.getDseqFor() != null)
{
String dsfor = m.getDseqFor();
if (seqRefIds.containsKey(dsfor))
{
- /**
+ /*
* recover from hash
*/
jmap.setTo(seqRefIds.get(dsfor));
frefedSequence.add(newMappingRef(dsfor, jmap));
}
}
- else
+ else if (m.getSequence() != null)
{
- /**
+ /*
* local sequence definition
*/
Sequence ms = m.getSequence();
initSeqRefs();
JalviewModel jm = saveState(ap, null, null, null);
+ addDatasetRef(
+ jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
+ ap.getAlignment().getDataset());
+
uniqueSetSuffix = "";
// jm.getJalviewModelSequence().getViewport(0).setId(null);
jm.getViewport().get(0).setId(null);
}
/**
+ * Loads any saved PCA viewers
+ *
+ * @param jms
+ * @param ap
+ */
+ protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
+ {
+ try
+ {
+ List<PcaViewer> pcaviewers = model.getPcaViewer();
+ for (PcaViewer viewer : pcaviewers)
+ {
+ String modelName = viewer.getScoreModelName();
+ SimilarityParamsI params = new SimilarityParams(
+ viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
+ viewer.isIncludeGaps(),
+ viewer.isDenominateByShortestLength());
+
+ /*
+ * create the panel (without computing the PCA)
+ */
+ PCAPanel panel = new PCAPanel(ap, modelName, params);
+
+ panel.setTitle(viewer.getTitle());
+ panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
+ viewer.getWidth(), viewer.getHeight()));
+
+ boolean showLabels = viewer.isShowLabels();
+ panel.setShowLabels(showLabels);
+ panel.getRotatableCanvas().setShowLabels(showLabels);
+ panel.getRotatableCanvas()
+ .setBgColour(new Color(viewer.getBgColour()));
+ panel.getRotatableCanvas()
+ .setApplyToAllViews(viewer.isLinkToAllViews());
+
+ /*
+ * load PCA output data
+ */
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getScoreModel(modelName, ap);
+ PCA pca = new PCA(null, scoreModel, params);
+ PcaDataType pcaData = viewer.getPcaData();
+
+ MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
+ pca.setPairwiseScores(pairwise);
+
+ MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
+ pca.setTridiagonal(triDiag);
+
+ MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
+ pca.setEigenmatrix(result);
+
+ panel.getPcaModel().setPCA(pca);
+
+ /*
+ * we haven't saved the input data! (JAL-2647 to do)
+ */
+ panel.setInputData(null);
+
+ /*
+ * add the sequence points for the PCA display
+ */
+ List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
+ for (SequencePoint sp : viewer.getSequencePoint())
+ {
+ String seqId = sp.getSequenceRef();
+ SequenceI seq = seqRefIds.get(seqId);
+ if (seq == null)
+ {
+ throw new IllegalStateException(
+ "Unmatched seqref for PCA: " + seqId);
+ }
+ Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
+ jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
+ seq, pt);
+ seqPoints.add(seqPoint);
+ }
+ panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
+
+ /*
+ * set min-max ranges and scale after setPoints (which recomputes them)
+ */
+ panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
+ SeqPointMin spMin = viewer.getSeqPointMin();
+ float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
+ spMin.getZPos() };
+ SeqPointMax spMax = viewer.getSeqPointMax();
+ float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
+ spMax.getZPos() };
+ panel.getRotatableCanvas().setSeqMinMax(min, max);
+
+ // todo: hold points list in PCAModel only
+ panel.getPcaModel().setSequencePoints(seqPoints);
+
+ panel.setSelectedDimensionIndex(viewer.getXDim(), X);
+ panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
+ panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
+
+ // is this duplication needed?
+ panel.setTop(seqPoints.size() - 1);
+ panel.getPcaModel().setTop(seqPoints.size() - 1);
+
+ /*
+ * add the axes' end points for the display
+ */
+ for (int i = 0; i < 3; i++)
+ {
+ Axis axis = viewer.getAxis().get(i);
+ panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
+ axis.getXPos(), axis.getYPos(), axis.getZPos());
+ }
+
+ Desktop.addInternalFrame(panel, MessageManager.formatMessage(
+ "label.calc_title", "PCA", modelName), 475, 450);
+ }
+ } catch (Exception ex)
+ {
+ Cache.log.error("Error loading PCA: " + ex.toString());
+ }
+ }
+
+ /**
* Populates an XML model of the feature colour scheme for one feature type
*
* @param featureType
noValueColour = maxcol;
}
- colour = new FeatureColour(mincol, maxcol, noValueColour,
+ colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
safeFloat(colourModel.getMin()),
safeFloat(colourModel.getMax()));
final List<String> attributeName = colourModel.getAttributeName();
import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
-import jalview.datamodel.Range;
+import jalview.datamodel.ContiguousI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
/*
* if columns are all gapped, or sequence has no features, nothing to do
*/
- Range visiblePositions = seq.findPositions(start+1, end+1);
+ ContiguousI visiblePositions = seq.findPositions(start + 1, end + 1);
if (visiblePositions == null || !seq.getFeatures().hasFeatures())
{
return null;
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
private IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
{
AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
getColourScheme(), aboveAnnotationThreshold);
}
else
{
- seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
+ seqannot = new IdentityHashMap<>();
}
// resolve the context containing all the annotation for the sequence
AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
if (annotationThreshold != null)
{
if ((aboveAnnotationThreshold == ABOVE_THRESHOLD
- && aj.value < annotationThreshold.value)
+ && aj.value <= annotationThreshold.value)
|| (aboveAnnotationThreshold == BELOW_THRESHOLD
- && aj.value > annotationThreshold.value))
+ && aj.value >= annotationThreshold.value))
{
return Color.white;
}
&& aboveAnnotationThreshold == ABOVE_THRESHOLD
&& value >= ann.threshold.value)
{
- range = (value - ann.threshold.value)
+ range = ann.graphMax == ann.threshold.value ? 1f
+ : (value - ann.threshold.value)
/ (ann.graphMax - ann.threshold.value);
}
else if (thresholdIsMinMax && ann.threshold != null
&& aboveAnnotationThreshold == BELOW_THRESHOLD
&& value <= ann.threshold.value)
{
- range = (value - ann.graphMin) / (ann.threshold.value - ann.graphMin);
+ range = ann.graphMin == ann.threshold.value ? 0f
+ : (value - ann.graphMin)
+ / (ann.threshold.value - ann.graphMin);
}
else
{
@Override
public String getSchemeName()
{
- return "Annotation";
+ return ANNOTATION_COLOUR;
}
@Override
package jalview.schemes;
import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.AlignViewportI;
import jalview.api.analysis.PairwiseScoreModelI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import java.awt.Color;
-import java.util.Map;
public class Blosum62ColourScheme extends ResidueColourScheme
{
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new Blosum62ColourScheme();
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
import java.awt.Color;
-import java.util.Map;
/**
* DOCUMENT ME!
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new BuriedColourScheme();
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
}
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
{
ClustalxColourScheme css = new ClustalxColourScheme(sg,
- hiddenRepSequences);
+ view == null ? null : view.getHiddenRepSequences());
css.includeGaps = includeGaps;
return css;
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
* new instance for each call to this method, as different instances may have
* differing shading by consensus or percentage identity applied.
*
+ * @param viewport
+ * - the parent viewport
* @param sg
- * @param hiddenRepSequences
+ * - the collection of sequences to be coloured
* @return copy of current scheme with any inherited settings transferred
*/
- ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+ ColourSchemeI getInstance(AlignViewportI viewport,
+ AnnotatedCollectionI sg);
/**
* Answers true if the colour scheme is suitable for the given data, else
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.util.ColorUtils;
* @param name
* @return
*/
- public static ColourSchemeI getColourScheme(AnnotatedCollectionI forData,
+ public static ColourSchemeI getColourScheme(AlignViewportI view,
+ AnnotatedCollectionI forData,
String name)
{
if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
* create a new instance of it
*/
ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
+ view,
forData, null);
if (scheme != null)
{
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
* store in an order-preserving map, so items can be added to menus
* in the order in which they are 'discovered'
*/
- schemes = new LinkedHashMap<String, ColourSchemeI>();
+ schemes = new LinkedHashMap<>();
for (JalviewColourScheme cs : JalviewColourScheme.values())
{
{
System.err.println("Error instantiating colour scheme for "
+ cs.toString() + " " + e.getMessage());
+ e.printStackTrace();
}
}
}
*
* @param name
* name of the colour scheme
+ * @param viewport
* @param forData
* the data to be coloured
* @param optional
* @return
*/
public ColourSchemeI getColourScheme(String name,
- AnnotatedCollectionI forData,
+ AlignViewportI viewport, AnnotatedCollectionI forData,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
if (name == null)
return null;
}
ColourSchemeI cs = schemes.get(name.toLowerCase());
- return cs == null ? null : cs.getInstance(forData, hiddenRepSequences);
+ return cs == null ? null
+ : cs.getInstance(viewport, forData);
}
/**
public ColourSchemeI getColourScheme(String name,
AnnotatedCollectionI forData)
{
- return getColourScheme(name, forData, null);
+ return getColourScheme(name, null, forData, null);
}
/**
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
import jalview.util.ColorUtils;
import java.awt.Color;
*/
public class CovariationColourScheme extends ResidueColourScheme
{
- public Map<String, Color> helixcolorhash = new Hashtable<String, Color>();
+ public Map<String, Color> helixcolorhash = new Hashtable<>();
- public Map<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
+ public Map<Integer, String> positionsToHelix = new Hashtable<>();
int numHelix = 0;
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new CovariationColourScheme(coll.getAlignmentAnnotation()[0]);
}
import jalview.datamodel.features.FeatureMatcher;
import jalview.util.ColorUtils;
import jalview.util.Format;
+import jalview.util.MessageManager;
import java.awt.Color;
import java.util.StringTokenizer;
*/
public class FeatureColour implements FeatureColourI
{
+ private static final String I18N_LABEL = MessageManager
+ .getString("label.label");
+
+ private static final String I18N_SCORE = MessageManager
+ .getString("label.score");
+
private static final String ABSOLUTE = "abso";
private static final String ABOVE = "above";
Color maxColour = ColorUtils.parseColourString(maxcol);
Color noColour = noValueColour.equals(NO_VALUE_MAX) ? maxColour
: (noValueColour.equals(NO_VALUE_NONE) ? null : minColour);
- featureColour = new FeatureColour(minColour, maxColour, noColour, min,
- max);
+ featureColour = new FeatureColour(maxColour, minColour, maxColour,
+ noColour, min, max);
featureColour.setColourByLabel(minColour == null);
featureColour.setAutoScaled(autoScaled);
if (byAttribute)
}
/**
- * Constructor given a simple colour
+ * Constructor given a simple colour. This also 'primes' a graduated colour
+ * range, where the maximum colour is the given simple colour, and the minimum
+ * colour a paler shade of it. This is for convenience when switching from a
+ * simple colour to a graduated colour scheme.
*
* @param c
*/
public FeatureColour(Color c)
{
- minColour = Color.WHITE;
- maxColour = Color.BLACK;
- noColour = DEFAULT_NO_COLOUR;
- minRed = 0f;
- minGreen = 0f;
- minBlue = 0f;
- deltaRed = 0f;
- deltaGreen = 0f;
- deltaBlue = 0f;
- colour = c;
- }
+ /*
+ * set max colour to the simple colour, min colour to a paler shade of it
+ */
+ this(c, c == null ? Color.white : ColorUtils.bleachColour(c, 0.9f),
+ c == null ? Color.black : c, DEFAULT_NO_COLOUR, 0, 0);
- /**
- * Constructor given a colour range and a score range, defaulting 'no value
- * colour' to be the same as minimum colour
- *
- * @param low
- * @param high
- * @param min
- * @param max
- */
- public FeatureColour(Color low, Color high, float min, float max)
- {
- this(low, high, low, min, max);
+ /*
+ * but enforce simple colour for now!
+ */
+ setGraduatedColour(false);
}
/**
}
/**
- * Copy constructor with new min/max ranges
- *
- * @param fc
- * @param min
- * @param max
- */
- public FeatureColour(FeatureColour fc, float min, float max)
- {
- this(fc);
- updateBounds(min, max);
- }
-
- /**
- * Constructor for a graduated colour
+ * Constructor that sets both simple and graduated colour values. This allows
+ * alternative colour schemes to be 'preserved' while switching between them
+ * to explore their effects on the visualisation.
+ * <p>
+ * This sets the colour scheme to 'graduated' by default. Override this if
+ * wanted by calling <code>setGraduatedColour(false)</code> for a simple
+ * colour, or <code>setColourByLabel(true)</code> for colour by label.
*
+ * @param myColour
* @param low
* @param high
* @param noValueColour
* @param min
* @param max
*/
- public FeatureColour(Color low, Color high, Color noValueColour,
- float min, float max)
+ public FeatureColour(Color myColour, Color low, Color high,
+ Color noValueColour, float min, float max)
{
if (low == null)
{
{
high = Color.black;
}
- graduatedColour = true;
- colour = null;
+ colour = myColour;
minColour = low;
maxColour = high;
+ setGraduatedColour(true);
noColour = noValueColour;
threshold = Float.NaN;
isHighToLow = min >= max;
* Sets the 'graduated colour' flag. If true, also sets 'colour by label' to
* false.
*/
- void setGraduatedColour(boolean b)
+ public void setGraduatedColour(boolean b)
{
graduatedColour = b;
if (b)
/**
* Returns the colour for the given instance of the feature. This may be a
- * simple colour, a colour generated from the feature description (if
- * isColourByLabel()), or a colour derived from the feature score (if
- * isGraduatedColour()).
+ * simple colour, a colour generated from the feature description or other
+ * attribute (if isColourByLabel()), or a colour derived from the feature
+ * score or other attribute (if isGraduatedColour()).
+ * <p>
+ * Answers null if feature score (or attribute) value lies outside a
+ * configured threshold.
*
* @param feature
* @return
sb.append(BAR).append(Format.getHexString(getMinColour()))
.append(BAR);
sb.append(Format.getHexString(getMaxColour())).append(BAR);
- String noValue = minColour.equals(noColour) ? NO_VALUE_MIN
- : (maxColour.equals(noColour) ? NO_VALUE_MAX
- : NO_VALUE_NONE);
+
+ /*
+ * 'no value' colour should be null, min or max colour;
+ * if none of these, coerce to minColour
+ */
+ String noValue = NO_VALUE_MIN;
+ if (maxColour.equals(noColour))
+ {
+ noValue = NO_VALUE_MAX;
+ }
+ if (noColour == null)
+ {
+ noValue = NO_VALUE_NONE;
+ }
sb.append(noValue).append(BAR);
if (!isAutoScaled())
{
attributeName = name;
}
+ @Override
+ public boolean isOutwithThreshold(SequenceFeature feature)
+ {
+ if (!isGraduatedColour())
+ {
+ return false;
+ }
+ float scr = feature.getScore();
+ if (attributeName != null)
+ {
+ try
+ {
+ String attVal = feature.getValueAsString(attributeName);
+ scr = Float.valueOf(attVal);
+ } catch (Throwable e)
+ {
+ scr = Float.NaN;
+ }
+ }
+ if (Float.isNaN(scr))
+ {
+ return false;
+ }
+
+ return ((isAboveThreshold() && scr <= threshold)
+ || (isBelowThreshold() && scr >= threshold));
+ }
+
+ @Override
+ public String getDescription()
+ {
+ if (isSimpleColour())
+ {
+ return "r=" + colour.getRed() + ",g=" + colour.getGreen() + ",b="
+ + colour.getBlue();
+ }
+ StringBuilder tt = new StringBuilder();
+ String by = null;
+
+ if (getAttributeName() != null)
+ {
+ by = FeatureMatcher.toAttributeDisplayName(getAttributeName());
+ }
+ else if (isColourByLabel())
+ {
+ by = I18N_LABEL;
+ }
+ else
+ {
+ by = I18N_SCORE;
+ }
+ tt.append(MessageManager.formatMessage("action.by_title_param", by));
+
+ /*
+ * add threshold if any
+ */
+ if (isAboveThreshold() || isBelowThreshold())
+ {
+ tt.append(" (");
+ if (isColourByLabel())
+ {
+ /*
+ * Jalview features file supports the combination of
+ * colour by label or attribute text with score threshold
+ */
+ tt.append(I18N_SCORE).append(" ");
+ }
+ tt.append(isAboveThreshold() ? "> " : "< ");
+ tt.append(getThreshold()).append(")");
+ }
+
+ return tt.toString();
+ }
+
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
-
-import java.util.Map;
/**
* Colourscheme that takes its colours from some other colourscheme
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new FollowerColourScheme();
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
import java.awt.Color;
-import java.util.Map;
public class HelixColourScheme extends ScoreColourScheme
{
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new HelixColourScheme();
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
import java.awt.Color;
-import java.util.Map;
/**
* DOCUMENT ME!
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new HydrophobicColourScheme();
}
--- /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.schemes;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Map;
+
+/**
+ * shade sequences using the colour shown in the ID panel. Useful to map
+ * sequence groupings onto residue data (eg tree subgroups visualised on
+ * structures or overview window)
+ *
+ * @author jprocter
+ */
+public class IdColourScheme implements ColourSchemeI
+{
+ AlignViewportI view = null;
+
+ public IdColourScheme()
+ {
+
+ }
+ public IdColourScheme(AlignViewportI view, AnnotatedCollectionI coll)
+ {
+ this.view = view;
+ }
+
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.IdColour.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
+ {
+ return new IdColourScheme(view, coll);
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ }
+
+ @Override
+ public Color findColour(char symbol, int position, SequenceI seq,
+ String consensusResidue, float pid)
+ {
+ // rather than testing if coll is a sequence group, and if so looking at
+ // ((SequenceGroup)coll).idColour
+ // we always return the sequence ID colour, in case the user has customised
+ // the displayed Id colour by right-clicking an internal node in the tree.
+ if (view == null)
+ {
+ return Color.WHITE;
+ }
+ Color col = view.getSequenceColour(seq);
+ return Color.WHITE.equals(col) ? Color.WHITE : col.darker();
+ }
+
+ @Override
+ public boolean hasGapColour()
+ {
+ return false;
+ }
+
+ @Override
+ public boolean isApplicableTo(AnnotatedCollectionI ac)
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
+}
Nucleotide("Nucleotide", NucleotideColourScheme.class),
PurinePyrimidine("Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
RNAHelices("RNA Helices", RNAHelicesColour.class),
- TCoffee("T-Coffee Scores", TCoffeeColourScheme.class);
+ TCoffee("T-Coffee Scores", TCoffeeColourScheme.class),
+ IdColour("Sequence ID", IdColourScheme.class);
// RNAInteraction("RNA Interaction type", RNAInteractionColourScheme.class)
private String name;
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
-
-import java.util.Map;
/**
* DOCUMENT ME!
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new NucleotideColourScheme();
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import java.awt.Color;
-import java.util.Map;
public class PIDColourScheme extends ResidueColourScheme
{
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new PIDColourScheme();
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
-
-import java.util.Map;
/**
* Class is based off of NucleotideColourScheme
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new PurinePyrimidineColourScheme();
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
* Maps sequence positions to the RNA helix they belong to. Key: position,
* Value: helix TODO: Revise or drop in favour of annotation position numbers
*/
- public Hashtable<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
+ public Hashtable<Integer, String> positionsToHelix = new Hashtable<>();
/**
* Number of helices in the RNA secondary structure
annotation.getRNAStruc();
lastrefresh = annotation._rnasecstr.hashCode();
numHelix = 0;
- positionsToHelix = new Hashtable<Integer, String>();
+ positionsToHelix = new Hashtable<>();
// Figure out number of helices
// Length of rnasecstr is the number of pairs of positions that base pair
}
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
{
return new RNAHelicesColour(sg);
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import java.awt.Color;
-import java.util.Map;
public class RNAInteractionColourScheme extends ResidueColourScheme
{
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new RNAInteractionColourScheme();
}
public static final String USER_DEFINED_MENU = "*User Defined*";
/*
+ * the canonical name of the annotation colour scheme
+ * (may be used to identify it in menu items)
+ */
+ public static final String ANNOTATION_COLOUR = "Annotation";
+
+ /*
* lookup up by character value e.g. 'G' to the colors array index
* e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K
*/
*/
package jalview.schemes;
+import jalview.analysis.GeneticCodes;
+
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
public static String START = "ATG";
- /**
- * Nucleotide Ambiguity Codes
- */
- public static final Map<String, String[]> ambiguityCodes = new Hashtable<>();
-
- /**
- * Codon triplets with additional symbols for unambiguous codons that include
- * ambiguity codes
- */
- public static final Hashtable<String, String> codonHash2 = new Hashtable<>();
-
- /**
- * all ambiguity codes for a given base
- */
- public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<>();
-
- static
- {
- /*
- * Ambiguity codes as per http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- */
- ambiguityCodes.put("R", new String[] { "A", "G" });
- ambiguityCodes.put("Y", new String[] { "T", "C" });
- ambiguityCodes.put("W", new String[] { "A", "T" });
- ambiguityCodes.put("S", new String[] { "G", "C" });
- ambiguityCodes.put("M", new String[] { "A", "C" });
- ambiguityCodes.put("K", new String[] { "G", "T" });
- ambiguityCodes.put("H", new String[] { "A", "T", "C" });
- ambiguityCodes.put("B", new String[] { "G", "T", "C" });
- ambiguityCodes.put("V", new String[] { "G", "A", "C" });
- ambiguityCodes.put("D", new String[] { "G", "A", "T" });
- ambiguityCodes.put("N", new String[] { "G", "A", "T", "C" });
-
- // Now build codon translation table
- codonHash2.put("AAA", "K");
- codonHash2.put("AAG", "K");
- codonHash2.put("AAC", "N");
- codonHash2.put("AAT", "N");
-
- codonHash2.put("CAA", "Q");
- codonHash2.put("CAG", "Q");
- codonHash2.put("CAC", "H");
- codonHash2.put("CAT", "H");
-
- codonHash2.put("GAA", "E");
- codonHash2.put("GAG", "E");
- codonHash2.put("GAC", "D");
- codonHash2.put("GAT", "D");
-
- codonHash2.put("TAC", "Y");
- codonHash2.put("TAT", "Y");
-
- codonHash2.put("ACA", "T");
- codonHash2.put("ACC", "T");
- codonHash2.put("ACT", "T");
- codonHash2.put("ACG", "T");
-
- codonHash2.put("CCA", "P");
- codonHash2.put("CCG", "P");
- codonHash2.put("CCC", "P");
- codonHash2.put("CCT", "P");
-
- codonHash2.put("GCA", "A");
- codonHash2.put("GCG", "A");
- codonHash2.put("GCC", "A");
- codonHash2.put("GCT", "A");
-
- codonHash2.put("TCA", "S");
- codonHash2.put("TCG", "S");
- codonHash2.put("TCC", "S");
- codonHash2.put("TCT", "S");
- codonHash2.put("AGC", "S");
- codonHash2.put("AGT", "S");
-
- codonHash2.put("AGA", "R");
- codonHash2.put("AGG", "R");
- codonHash2.put("CGA", "R");
- codonHash2.put("CGG", "R");
- codonHash2.put("CGC", "R");
- codonHash2.put("CGT", "R");
-
- codonHash2.put("GGA", "G");
- codonHash2.put("GGG", "G");
- codonHash2.put("GGC", "G");
- codonHash2.put("GGT", "G");
-
- codonHash2.put("TGA", "*");
- codonHash2.put("TAA", "*");
- codonHash2.put("TAG", "*");
-
- codonHash2.put("TGG", "W");
-
- codonHash2.put("TGC", "C");
- codonHash2.put("TGT", "C");
-
- codonHash2.put("ATA", "I");
- codonHash2.put("ATC", "I");
- codonHash2.put("ATT", "I");
-
- codonHash2.put("ATG", "M");
-
- codonHash2.put("CTA", "L");
- codonHash2.put("CTG", "L");
- codonHash2.put("CTC", "L");
- codonHash2.put("CTT", "L");
- codonHash2.put("TTA", "L");
- codonHash2.put("TTG", "L");
-
- codonHash2.put("GTA", "V");
- codonHash2.put("GTG", "V");
- codonHash2.put("GTC", "V");
- codonHash2.put("GTT", "V");
-
- codonHash2.put("TTC", "F");
- codonHash2.put("TTT", "F");
-
- buildAmbiguityCodonSet();
- }
-
- /**
- * programmatic generation of codons including ambiguity codes
- */
- public static void buildAmbiguityCodonSet()
- {
- if (_ambiguityCodes.size() > 0)
- {
- System.err
- .println("Ignoring multiple calls to buildAmbiguityCodonSet");
- return;
- }
- // Invert the ambiguity code set
- for (Map.Entry<String, String[]> acode : ambiguityCodes.entrySet())
- {
- for (String r : acode.getValue())
- {
- List<String> codesfor = _ambiguityCodes.get(r);
- if (codesfor == null)
- {
- _ambiguityCodes.put(r, codesfor = new ArrayList<>());
- }
- if (!codesfor.contains(acode.getKey()))
- {
- codesfor.add(acode.getKey());
- }
- else
- {
- System.err.println(
- "Inconsistency in the IUBMB ambiguity code nomenclature table: collision for "
- + acode.getKey() + " in residue " + r);
- }
- }
- }
- // and programmatically add in the ambiguity codes that yield the same amino
- // acid
- String[] unambcodons = codonHash2.keySet()
- .toArray(new String[codonHash2.size()]);
- for (String codon : unambcodons)
- {
- String residue = codonHash2.get(codon);
- String acodon[][] = new String[codon.length()][];
- for (int i = 0, iSize = codon.length(); i < iSize; i++)
- {
- String _ac = "" + codon.charAt(i);
- List<String> acodes = _ambiguityCodes.get(_ac);
- if (acodes != null)
- {
- acodon[i] = acodes.toArray(new String[acodes.size()]);
- }
- else
- {
- acodon[i] = new String[] {};
- }
- }
- // enumerate all combinations and test for veracity of translation
- int tpos[] = new int[codon.length()],
- cpos[] = new int[codon.length()];
- for (int i = 0; i < tpos.length; i++)
- {
- tpos[i] = -1;
- }
- tpos[acodon.length - 1] = 0;
- int ipos, j;
- while (tpos[0] < acodon[0].length)
- {
- // make all codons for this combination
- char allres[][] = new char[tpos.length][];
- String _acodon = "";
- for (ipos = 0; ipos < tpos.length; ipos++)
- {
- if (acodon[ipos].length == 0 || tpos[ipos] < 0)
- {
- _acodon += codon.charAt(ipos);
- allres[ipos] = new char[] { codon.charAt(ipos) };
- }
- else
- {
- _acodon += acodon[ipos][tpos[ipos]];
- String[] altbase = ambiguityCodes.get(acodon[ipos][tpos[ipos]]);
- allres[ipos] = new char[altbase.length];
- j = 0;
- for (String ab : altbase)
- {
- allres[ipos][j++] = ab.charAt(0);
- }
- }
- }
- // test all codons for this combination
- for (ipos = 0; ipos < cpos.length; ipos++)
- {
- cpos[ipos] = 0;
- }
- boolean valid = true;
- do
- {
- String _codon = "";
- for (j = 0; j < cpos.length; j++)
- {
- _codon += allres[j][cpos[j]];
- }
- String tr = codonHash2.get(_codon);
- if (valid = (tr != null && tr.equals(residue)))
- {
- // advance to next combination
- ipos = acodon.length - 1;
- while (++cpos[ipos] >= allres[ipos].length && ipos > 0)
- {
- cpos[ipos] = 0;
- ipos--;
- }
- }
- } while (valid && cpos[0] < allres[0].length);
- if (valid)
- {
- // Add this to the set of codons we will translate
- // System.out.println("Adding ambiguity codon: " + _acodon + " for "
- // + residue);
- codonHash2.put(_acodon, residue);
- }
- else
- {
- // System.err.println("Rejecting ambiguity codon: " + _acodon
- // + " for " + residue);
- }
- // next combination
- ipos = acodon.length - 1;
- while (++tpos[ipos] >= acodon[ipos].length && ipos > 0)
- {
- tpos[ipos] = -1;
- ipos--;
- }
- }
- }
- }
-
// Stores residue codes/names and colours and other things
public static Map<String, Map<String, Integer>> propHash = new Hashtable<>();
public static String codonTranslate(String lccodon)
{
- String cdn = codonHash2.get(lccodon.toUpperCase());
- if ("*".equals(cdn))
+ String peptide = GeneticCodes.getInstance().getStandardCodeTable()
+ .translate(lccodon);
+ if ("*".equals(peptide))
{
- return STOP;
+ return "STOP";
}
- return cdn;
+ return peptide;
}
- public static Hashtable<String, String> toDssp3State;
+ /*
+ * lookup of (A-Z) alternative secondary structure symbols'
+ * equivalents in DSSP3 notation
+ */
+ private static char[] toDssp3State;
static
{
- toDssp3State = new Hashtable<>();
- toDssp3State.put("H", "H");
- toDssp3State.put("E", "E");
- toDssp3State.put("C", " ");
- toDssp3State.put(" ", " ");
- toDssp3State.put("T", " ");
- toDssp3State.put("B", "E");
- toDssp3State.put("G", "H");
- toDssp3State.put("I", "H");
- toDssp3State.put("X", " ");
+ toDssp3State = new char[9]; // for 'A'-'I'; extend if needed
+ Arrays.fill(toDssp3State, ' ');
+ toDssp3State['B' - 'A'] = 'E';
+ toDssp3State['E' - 'A'] = 'E';
+ toDssp3State['G' - 'A'] = 'H';
+ toDssp3State['H' - 'A'] = 'H';
+ toDssp3State['I' - 'A'] = 'H';
}
/**
* translate from other dssp secondary structure alphabets to 3-state
*
- * @param ssstring
- * @return ssstring as a three-state secondary structure assignment.
+ * @param ssString
+ * @return ssstring
*/
- public static String getDssp3state(String ssstring)
+ public static String getDssp3state(String ssString)
{
- if (ssstring == null)
+ if (ssString == null)
{
return null;
}
- StringBuffer ss = new StringBuffer();
- for (int i = 0; i < ssstring.length(); i++)
+ int lookupSize = toDssp3State.length;
+ int len = ssString.length();
+ char[] trans = new char[len];
+ for (int i = 0; i < len; i++)
{
- String ssc = ssstring.substring(i, i + 1);
- if (toDssp3State.containsKey(ssc))
+ char c = ssString.charAt(i);
+ int index = c - 'A';
+ if (index < 0 || index >= lookupSize)
{
- ss.append(toDssp3State.get(ssc));
+ trans[i] = ' ';
}
else
{
- ss.append(" ");
+ trans[i] = toDssp3State[index];
}
}
- return ss.toString();
+ return new String(trans);
}
static
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import java.awt.Color;
-import java.util.Map;
/**
* DOCUMENT ME!
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new ScoreColourScheme(symbolIndex, scores, min, max);
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
import java.awt.Color;
-import java.util.Map;
/**
* DOCUMENT ME!
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new StrandColourScheme();
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
// assume only one set of TCOFFEE scores - but could have more than one
// potentially.
- List<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> annots = new ArrayList<>();
// Search alignment to get all tcoffee annotation and pick one set of
// annotation to use to colour seqs.
- seqMap = new IdentityHashMap<SequenceI, Color[]>();
+ seqMap = new IdentityHashMap<>();
AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
? alignment
: alignment.getContext();
}
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
{
return new TCoffeeColourScheme(sg);
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
-
-import java.util.Map;
public class TaylorColourScheme extends ResidueColourScheme
{
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new TaylorColourScheme();
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
import java.awt.Color;
-import java.util.Map;
/**
* DOCUMENT ME!
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new TurnColourScheme();
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
import jalview.util.ColorUtils;
import jalview.util.StringUtils;
}
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
{
return new UserColourScheme(this);
}
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
-
-import java.util.Map;
/**
* DOCUMENT ME!
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new ZappoColourScheme();
}
/*
* lookup from lower-case form of a name to its canonical (standardised) form
*/
- private static Map<String, String> canonicalSourceNameLookup = new HashMap<String, String>();
+ private static Map<String, String> canonicalSourceNameLookup = new HashMap<>();
- private static Map<String, String> dasCoordinateSystemsLookup = new HashMap<String, String>();
static
{
canonicalSourceNameLookup.get(k));
}
- dasCoordinateSystemsLookup.put("pdbresnum", DBRefSource.PDB);
- dasCoordinateSystemsLookup.put("uniprot", DBRefSource.UNIPROT);
- dasCoordinateSystemsLookup.put("embl", DBRefSource.EMBL);
- // dasCoordinateSystemsLookup.put("embl", DBRefSource.EMBLCDS);
}
/**
{
return dbrefs;
}
- HashSet<String> srcs = new HashSet<String>();
+ HashSet<String> srcs = new HashSet<>();
for (String src : sources)
{
srcs.add(src.toUpperCase());
}
- List<DBRefEntry> res = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> res = new ArrayList<>();
for (DBRefEntry dbr : dbrefs)
{
String source = getCanonicalName(dbr.getSource());
}
/**
- * isDasCoordinateSystem
- *
- * @param string
- * String
- * @param dBRefEntry
- * DBRefEntry
- * @return boolean true if Source DBRefEntry is compatible with DAS
- * CoordinateSystem name
- */
-
- public static boolean isDasCoordinateSystem(String string,
- DBRefEntry dBRefEntry)
- {
- if (string == null || dBRefEntry == null)
- {
- return false;
- }
- String coordsys = dasCoordinateSystemsLookup.get(string.toLowerCase());
- return coordsys == null ? false
- : coordsys.equals(dBRefEntry.getSource());
- }
-
- /**
* look up source in an internal list of database reference sources and return
* the canonical jalview name for the source, or the original string if it has
* no canonical form.
static List<DBRefEntry> searchRefs(DBRefEntry[] refs, DBRefEntry entry,
DbRefComp comparator)
{
- List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> rfs = new ArrayList<>();
if (refs == null || entry == null)
{
return rfs;
public static List<DBRefEntry> searchRefsForSource(DBRefEntry[] dbRefs,
String source)
{
- List<DBRefEntry> matches = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> matches = new ArrayList<>();
if (dbRefs != null && source != null)
{
for (DBRefEntry dbref : dbRefs)
// nothing to do
return;
}
- List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> selfs = new ArrayList<>();
{
DBRefEntry[] selfArray = selectDbRefs(!sequence.isProtein(),
sequence.getDBRefs());
selfs.remove(p);
}
}
- List<DBRefEntry> toPromote = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> toPromote = new ArrayList<>();
for (DBRefEntry p : pr)
{
- List<String> promType = new ArrayList<String>();
+ List<String> promType = new ArrayList<>();
if (sequence.isProtein())
{
switch (getCanonicalName(p.getSource()))
--- /dev/null
+package jalview.util;
+
+import org.json.simple.JSONArray;
+
+public class JSONUtils
+{
+
+ /**
+ * Converts a JSONArray of values to a string as a comma-separated list.
+ * Answers null if the array is null or empty.
+ *
+ * @param jsonArray
+ * @return
+ */
+ public static String arrayToList(JSONArray jsonArray)
+ {
+ if (jsonArray == null)
+ {
+ return null;
+ }
+
+ StringBuilder sb = new StringBuilder();
+ for (int i = 0; i < jsonArray.size(); i++)
+ {
+ if (i > 0)
+ {
+ sb.append(",");
+ }
+ sb.append(jsonArray.get(i).toString());
+ }
+ return sb.length() == 0 ? null : sb.toString();
+ }
+
+}
* retain any colour thresholds per group while
* changing choice of colour scheme (JAL-2386)
*/
- sg.setColourScheme(cs);
+ sg.setColourScheme(
+ cs == null ? null : cs.getInstance(this, sg));
if (cs != null)
{
sg.getGroupColourScheme().alignmentChanged(sg,
public void invertColumnSelection()
{
colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
+ isColSelChanged(true);
}
@Override
{
return currentTree;
}
+
+ /**
+ * flag set to indicate if structure views might be out of sync with sequences
+ * in the alignment
+ */
+
+ private boolean needToUpdateStructureViews = false;
+
+ @Override
+ public boolean isUpdateStructures()
+ {
+ return needToUpdateStructureViews;
+ }
+
+ @Override
+ public void setUpdateStructures(boolean update)
+ {
+ needToUpdateStructureViews = update;
+ }
+
+ @Override
+ public boolean needToUpdateStructureViews()
+ {
+ boolean update = needToUpdateStructureViews;
+ needToUpdateStructureViews = false;
+ return update;
+ }
+
+ @Override
+ public void addSequenceGroup(SequenceGroup sequenceGroup)
+ {
+ alignment.addGroup(sequenceGroup);
+
+ Color col = sequenceGroup.idColour;
+ if (col != null)
+ {
+ col = col.brighter();
+
+ for (SequenceI sq : sequenceGroup.getSequences())
+ {
+ setSequenceColour(sq, col);
+ }
+ }
+
+ if (codingComplement != null)
+ {
+ SequenceGroup mappedGroup = MappingUtils
+ .mapSequenceGroup(sequenceGroup, this, codingComplement);
+ if (mappedGroup.getSequences().size() > 0)
+ {
+ codingComplement.getAlignment().addGroup(mappedGroup);
+
+ if (col != null)
+ {
+ for (SequenceI seq : mappedGroup.getSequences())
+ {
+ codingComplement.setSequenceColour(seq, col);
+ }
+ }
+ }
+ // propagate the structure view update flag according to our own setting
+ codingComplement.setUpdateStructures(needToUpdateStructureViews);
+ }
+ }
}
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.AlignmentView;
+import jalview.datamodel.Point;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
+import java.util.List;
import java.util.Vector;
public class PCAModel
{
- private volatile PCA pca;
-
- int top;
+ /*
+ * inputs
+ */
+ private AlignmentView inputData;
- AlignmentView seqstrings;
+ private final SequenceI[] seqs;
- SequenceI[] seqs;
+ private final SimilarityParamsI similarityParams;
/*
- * Name of score model used to calculate PCA
+ * options - score model, nucleotide / protein
*/
- ScoreModelI scoreModel;
+ private ScoreModelI scoreModel;
private boolean nucleotide = false;
- private Vector<SequencePoint> points;
+ /*
+ * outputs
+ */
+ private PCA pca;
- private SimilarityParamsI similarityParams;
+ int top;
+
+ private List<SequencePoint> points;
/**
* Constructor given sequence data, score model and score calculation
public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
ScoreModelI modelName, SimilarityParamsI params)
{
- seqstrings = seqData;
+ inputData = seqData;
seqs = sqs;
nucleotide = nuc;
scoreModel = modelName;
similarityParams = params;
}
- public void run()
+ /**
+ * Performs the PCA calculation (in the same thread) and extracts result data
+ * needed for visualisation by PCAPanel
+ */
+ public void calculate()
{
- pca = new PCA(seqstrings, scoreModel, similarityParams);
- pca.run();
+ pca = new PCA(inputData, scoreModel, similarityParams);
+ pca.run(); // executes in same thread, wait for completion
// Now find the component coordinates
int ii = 0;
// top = pca.getM().height() - 1;
top = height - 1;
- points = new Vector<SequencePoint>();
- float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
+ points = new Vector<>();
+ Point[] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
for (int i = 0; i < height; i++)
{
SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
- points.addElement(sp);
+ points.add(sp);
}
}
}
/**
+ * Answers the index of the principal dimension of the PCA
*
- *
- * @return index of principle dimension of PCA
+ * @return
*/
public int getTop()
{
return top;
}
+ public void setTop(int t)
+ {
+ top = t;
+ }
+
/**
- * update the 2d coordinates for the list of points to the given dimensions
+ * Updates the 3D coordinates for the list of points to the given dimensions.
* Principal dimension is getTop(). Next greatest eigenvector is getTop()-1.
* Note - pca.getComponents starts counting the spectrum from rank-2 to zero,
* rather than rank-1, so getComponents(dimN ...) == updateRcView(dimN+1 ..)
public void updateRcView(int dim1, int dim2, int dim3)
{
// note: actual indices for components are dim1-1, etc (patch for JAL-1123)
- float[][] scores = pca.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
+ Point[] scores = pca.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
for (int i = 0; i < pca.getHeight(); i++)
{
- points.elementAt(i).coord = scores[i];
+ points.get(i).coord = scores[i];
}
}
return pca.getDetails();
}
- public AlignmentView getSeqtrings()
+ public AlignmentView getInputData()
+ {
+ return inputData;
+ }
+
+ public void setInputData(AlignmentView data)
{
- return seqstrings;
+ inputData = data;
}
public String getPointsasCsv(boolean transformed, int xdim, int ydim,
}
else
{
- // output current x,y,z coords for points
- fl = getPointPosition(s);
- for (int d = 0; d < fl.length; d++)
- {
- csv.append(",");
- csv.append(fl[d]);
- }
+ Point p = points.get(s).coord;
+ csv.append(",").append(p.x);
+ csv.append(",").append(p.y);
+ csv.append(",").append(p.z);
}
csv.append("\n");
}
return csv.toString();
}
+ public String getScoreModelName()
+ {
+ return scoreModel == null ? "" : scoreModel.getName();
+ }
+
+ public void setScoreModel(ScoreModelI sm)
+ {
+ this.scoreModel = sm;
+ }
+
/**
+ * Answers the parameters configured for pairwise similarity calculations
*
- * @return x,y,z positions of point s (index into points) under current
- * transform.
+ * @return
*/
- public double[] getPointPosition(int s)
+ public SimilarityParamsI getSimilarityParameters()
{
- double pts[] = new double[3];
- float[] p = points.elementAt(s).coord;
- pts[0] = p[0];
- pts[1] = p[1];
- pts[2] = p[2];
- return pts;
+ return similarityParams;
}
- public String getScoreModelName()
+ public List<SequencePoint> getSequencePoints()
{
- return scoreModel == null ? "" : scoreModel.getName();
+ return points;
}
- public void setScoreModel(ScoreModelI sm)
+ public void setSequencePoints(List<SequencePoint> sp)
{
- this.scoreModel = sm;
+ points = sp;
+ }
+
+ /**
+ * Answers the object holding the values of the computed PCA
+ *
+ * @return
+ */
+ public PCA getPcaData()
+ {
+ return pca;
}
+ public void setPCA(PCA data)
+ {
+ pca = data;
+ }
}
*/
public int getVisibleAlignmentWidth()
{
- return al.getWidth() - al.getHiddenColumns().getSize();
+ return al.getVisibleWidth();
}
/**
}
/**
- * Removes from the list of features any that duplicate the location of a
- * feature of the same type. Should be used only for features of the same,
- * simple, feature colour (which normally implies the same feature type). Does
- * not check visibility settings for feature type or feature group. No
- * filtering is done if transparency, or any feature filters, are in force.
+ * Removes from the list of features any whose group is not shown, or that are
+ * visible and duplicate the location of a visible feature of the same type.
+ * Should be used only for features of the same, simple, feature colour (which
+ * normally implies the same feature type). No filtering is done if
+ * transparency, or any feature filters, are in force.
*
* @param features
*/
while (it.hasNext())
{
SequenceFeature sf = it.next();
+ if (featureGroupNotShown(sf))
+ {
+ it.remove();
+ continue;
+ }
/*
* a feature is redundant for rendering purposes if it has the
* (checking type and isContactFeature as a fail-safe here, although
* currently they are guaranteed to match in this context)
*/
- if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
+ if (lastFeature != null
+ && sf.getBegin() == lastFeature.getBegin()
&& sf.getEnd() == lastFeature.getEnd()
&& sf.isContactFeature() == lastFeature.isContactFeature()
&& sf.getType().equals(lastFeature.getType()))
return filter == null ? true : filter.matches(sf);
}
+ @Override
+ public boolean isVisible(SequenceFeature feature)
+ {
+ if (feature == null)
+ {
+ return false;
+ }
+ if (getFeaturesDisplayed() == null
+ || !getFeaturesDisplayed().isVisible(feature.getType()))
+ {
+ return false;
+ }
+ if (featureGroupNotShown(feature))
+ {
+ return false;
+ }
+ FeatureColourI fc = featureColours.get(feature.getType());
+ if (fc != null && fc.isOutwithThreshold(feature))
+ {
+ return false;
+ }
+ if (!featureMatchesFilters(feature))
+ {
+ return false;
+ }
+ return true;
+ }
+
}
protected void eraseConsensus(int aWidth)
{
AlignmentAnnotation consensus = getConsensusAnnotation();
- consensus.annotations = new Annotation[aWidth];
+ if (consensus != null)
+ {
+ consensus.annotations = new Annotation[aWidth];
+ }
AlignmentAnnotation gap = getGapAnnotation();
if (gap != null)
{
int startShift = absStart - sequenceStart + 1;
if (startShift != 0)
{
- modified |= sequence.getFeatures().shiftFeatures(startShift);
+ modified |= sequence.getFeatures().shiftFeatures(1,
+ startShift);
}
}
}
// and remove it from the rest
// TODO: decide if we should remove annotated sequence from set
sdataset.remove(sequence);
- // TODO: should we make a note of sequences that have received new DB
- // ids, so we can query all enabled DAS servers for them ?
}
}
return modified;
SequenceI uniprotEntryToSequence(Entry entry)
{
String id = getUniprotEntryId(entry);
- String seqString = entry.getSequence().getValue();
-
/*
- * for backwards compatibility with Castor processing,
- * remove any internal spaces
+ * Sequence should not include any whitespace, but JAXB leaves these in
*/
- if (seqString.indexOf(' ') > -1)
- {
- seqString = seqString.replace(" ", "");
- }
+ String seqString = entry.getSequence().getValue().replaceAll("\\s*",
+ "");
+
SequenceI sequence = new Sequence(id,
seqString);
sequence.setDescription(getUniprotEntryDescription(entry));
{
// set graduated color as fading to white for minimum, and
// autoscaling to values on alignment
- FeatureColourI ggc = new FeatureColour(Color.white,
- gc.getColour(), Float.MIN_VALUE, Float.MAX_VALUE);
+ FeatureColourI ggc = new FeatureColour(gc.getColour(),
+ Color.white, gc.getColour(), Color.white,
+ Float.MIN_VALUE, Float.MAX_VALUE);
ggc.setAutoScaled(true);
fr.setColour(ft, ggc);
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for DoubleMatrix complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="DoubleMatrix">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="row" type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="D" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
+ * <element name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="rows" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="columns" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "DoubleMatrix", namespace = "www.jalview.org", propOrder = {
+ "row",
+ "d",
+ "e"
+})
+public class DoubleMatrix {
+
+ protected List<DoubleVector> row;
+ @XmlElement(name = "D")
+ protected DoubleVector d;
+ @XmlElement(name = "E")
+ protected DoubleVector e;
+ @XmlAttribute(name = "rows")
+ protected Integer rows;
+ @XmlAttribute(name = "columns")
+ protected Integer columns;
+
+ /**
+ * Gets the value of the row property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the row property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getRow().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DoubleVector }
+ *
+ *
+ */
+ public List<DoubleVector> getRow() {
+ if (row == null) {
+ row = new ArrayList<DoubleVector>();
+ }
+ return this.row;
+ }
+
+ /**
+ * Gets the value of the d property.
+ *
+ * @return
+ * possible object is
+ * {@link DoubleVector }
+ *
+ */
+ public DoubleVector getD() {
+ return d;
+ }
+
+ /**
+ * Sets the value of the d property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DoubleVector }
+ *
+ */
+ public void setD(DoubleVector value) {
+ this.d = value;
+ }
+
+ /**
+ * Gets the value of the e property.
+ *
+ * @return
+ * possible object is
+ * {@link DoubleVector }
+ *
+ */
+ public DoubleVector getE() {
+ return e;
+ }
+
+ /**
+ * Sets the value of the e property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DoubleVector }
+ *
+ */
+ public void setE(DoubleVector value) {
+ this.e = value;
+ }
+
+ /**
+ * Gets the value of the rows property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getRows() {
+ return rows;
+ }
+
+ /**
+ * Sets the value of the rows property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setRows(Integer value) {
+ this.rows = value;
+ }
+
+ /**
+ * Gets the value of the columns property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getColumns() {
+ return columns;
+ }
+
+ /**
+ * Sets the value of the columns property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setColumns(Integer value) {
+ this.columns = value;
+ }
+
+}
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for DoubleVector complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="DoubleVector">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="v" type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "DoubleVector", namespace = "www.jalview.org", propOrder = {
+ "v"
+})
+public class DoubleVector {
+
+ @XmlElement(type = Double.class)
+ protected List<Double> v;
+
+ /**
+ * Gets the value of the v property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the v property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getV().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Double }
+ *
+ *
+ */
+ public List<Double> getV() {
+ if (v == null) {
+ v = new ArrayList<Double>();
+ }
+ return this.v;
+ }
+
+}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
* <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
* <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
* <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="sequencePoint" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="axis" maxOccurs="3" minOccurs="3">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMin">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMax">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attGroup ref="{www.jalview.org}SimilarityParams"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
* </restriction>
* </complexContent>
* </complexType>
"viewport",
"userColours",
"tree",
+ "pcaViewer",
"featureSettings"
})
public class JalviewModel {
@XmlElement(name = "UserColours")
protected List<JalviewModel.UserColours> userColours;
protected List<JalviewModel.Tree> tree;
+ @XmlElement(name = "PcaViewer")
+ protected List<JalviewModel.PcaViewer> pcaViewer;
@XmlElement(name = "FeatureSettings")
protected JalviewModel.FeatureSettings featureSettings;
}
/**
+ * Gets the value of the pcaViewer property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getPcaViewer().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer }
+ *
+ *
+ */
+ public List<JalviewModel.PcaViewer> getPcaViewer() {
+ if (pcaViewer == null) {
+ pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
+ }
+ return this.pcaViewer;
+ }
+
+ /**
* Gets the value of the featureSettings property.
*
* @return
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence minOccurs="0">
- * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <sequence>
+ * <element name="sequencePoint" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="axis" maxOccurs="3" minOccurs="3">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMin">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMax">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
* </sequence>
* <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attGroup ref="{www.jalview.org}SimilarityParams"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
* </restriction>
* </complexContent>
* </complexType>
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
- "title",
- "newick"
+ "sequencePoint",
+ "axis",
+ "seqPointMin",
+ "seqPointMax",
+ "pcaData"
})
- public static class Tree {
+ public static class PcaViewer {
- @XmlElement(namespace = "www.jalview.org")
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.PcaViewer.Axis> axis;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected PcaDataType pcaData;
+ @XmlAttribute(name = "title")
protected String title;
- @XmlElement(namespace = "www.jalview.org")
- protected String newick;
- @XmlAttribute(name = "fontName")
- protected String fontName;
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "showBootstrap")
- protected Boolean showBootstrap;
- @XmlAttribute(name = "showDistances")
- protected Boolean showDistances;
- @XmlAttribute(name = "markUnlinked")
- protected Boolean markUnlinked;
- @XmlAttribute(name = "fitToWindow")
- protected Boolean fitToWindow;
- @XmlAttribute(name = "currentTree")
- protected Boolean currentTree;
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
+ @XmlAttribute(name = "scoreModelName")
+ protected String scoreModelName;
+ @XmlAttribute(name = "xDim")
+ protected Integer xDim;
+ @XmlAttribute(name = "yDim")
+ protected Integer yDim;
+ @XmlAttribute(name = "zDim")
+ protected Integer zDim;
+ @XmlAttribute(name = "bgColour")
+ protected Integer bgColour;
+ @XmlAttribute(name = "scaleFactor")
+ protected Float scaleFactor;
+ @XmlAttribute(name = "showLabels")
+ protected Boolean showLabels;
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
@XmlAttribute(name = "width")
protected Integer width;
@XmlAttribute(name = "height")
protected Integer xpos;
@XmlAttribute(name = "ypos")
protected Integer ypos;
+ @XmlAttribute(name = "includeGaps")
+ protected Boolean includeGaps;
+ @XmlAttribute(name = "matchGaps")
+ protected Boolean matchGaps;
+ @XmlAttribute(name = "includeGappedColumns")
+ protected Boolean includeGappedColumns;
+ @XmlAttribute(name = "denominateByShortestLength")
+ protected Boolean denominateByShortestLength;
/**
- * Gets the value of the title property.
+ * Gets the value of the sequencePoint property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSequencePoint().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.SequencePoint }
+ *
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getTitle() {
- return title;
+ public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
+ if (sequencePoint == null) {
+ sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
+ }
+ return this.sequencePoint;
}
/**
- * Sets the value of the title property.
+ * Gets the value of the axis property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the axis property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAxis().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.Axis }
+ *
*
- * @param value
- * allowed object is
- * {@link String }
- *
*/
- public void setTitle(String value) {
- this.title = value;
+ public List<JalviewModel.PcaViewer.Axis> getAxis() {
+ if (axis == null) {
+ axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
+ }
+ return this.axis;
}
/**
- * Gets the value of the newick property.
+ * Gets the value of the seqPointMin property.
*
* @return
* possible object is
- * {@link String }
+ * {@link JalviewModel.PcaViewer.SeqPointMin }
*
*/
- public String getNewick() {
- return newick;
+ public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
+ return seqPointMin;
}
/**
- * Sets the value of the newick property.
+ * Sets the value of the seqPointMin property.
*
* @param value
* allowed object is
- * {@link String }
+ * {@link JalviewModel.PcaViewer.SeqPointMin }
*
*/
- public void setNewick(String value) {
- this.newick = value;
+ public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
+ this.seqPointMin = value;
}
/**
- * Gets the value of the fontName property.
+ * Gets the value of the seqPointMax property.
*
* @return
* possible object is
- * {@link String }
+ * {@link JalviewModel.PcaViewer.SeqPointMax }
*
*/
- public String getFontName() {
- return fontName;
+ public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
+ return seqPointMax;
}
/**
- * Sets the value of the fontName property.
+ * Sets the value of the seqPointMax property.
*
* @param value
* allowed object is
- * {@link String }
+ * {@link JalviewModel.PcaViewer.SeqPointMax }
*
*/
- public void setFontName(String value) {
- this.fontName = value;
+ public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
+ this.seqPointMax = value;
}
/**
- * Gets the value of the fontSize property.
+ * Gets the value of the pcaData property.
*
* @return
* possible object is
- * {@link Integer }
+ * {@link PcaDataType }
*
*/
- public Integer getFontSize() {
- return fontSize;
+ public PcaDataType getPcaData() {
+ return pcaData;
}
/**
- * Sets the value of the fontSize property.
+ * Sets the value of the pcaData property.
*
* @param value
* allowed object is
- * {@link Integer }
+ * {@link PcaDataType }
*
*/
- public void setFontSize(Integer value) {
- this.fontSize = value;
+ public void setPcaData(PcaDataType value) {
+ this.pcaData = value;
}
/**
- * Gets the value of the fontStyle property.
+ * Gets the value of the title property.
*
* @return
* possible object is
- * {@link Integer }
+ * {@link String }
*
*/
- public Integer getFontStyle() {
- return fontStyle;
+ public String getTitle() {
+ return title;
}
/**
- * Sets the value of the fontStyle property.
+ * Sets the value of the title property.
*
* @param value
* allowed object is
- * {@link Integer }
+ * {@link String }
*
*/
- public void setFontStyle(Integer value) {
- this.fontStyle = value;
+ public void setTitle(String value) {
+ this.title = value;
}
/**
- * Gets the value of the threshold property.
+ * Gets the value of the scoreModelName property.
*
* @return
* possible object is
- * {@link Float }
+ * {@link String }
*
*/
- public Float getThreshold() {
- return threshold;
+ public String getScoreModelName() {
+ return scoreModelName;
}
/**
- * Sets the value of the threshold property.
+ * Sets the value of the scoreModelName property.
*
* @param value
* allowed object is
- * {@link Float }
+ * {@link String }
*
*/
- public void setThreshold(Float value) {
- this.threshold = value;
+ public void setScoreModelName(String value) {
+ this.scoreModelName = value;
}
/**
- * Gets the value of the showBootstrap property.
+ * Gets the value of the xDim property.
*
* @return
* possible object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public Boolean isShowBootstrap() {
- return showBootstrap;
+ public Integer getXDim() {
+ return xDim;
}
/**
- * Sets the value of the showBootstrap property.
+ * Sets the value of the xDim property.
*
* @param value
* allowed object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public void setShowBootstrap(Boolean value) {
- this.showBootstrap = value;
+ public void setXDim(Integer value) {
+ this.xDim = value;
}
/**
- * Gets the value of the showDistances property.
+ * Gets the value of the yDim property.
*
* @return
* possible object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public Boolean isShowDistances() {
- return showDistances;
+ public Integer getYDim() {
+ return yDim;
}
/**
- * Sets the value of the showDistances property.
+ * Sets the value of the yDim property.
*
* @param value
* allowed object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public void setShowDistances(Boolean value) {
- this.showDistances = value;
+ public void setYDim(Integer value) {
+ this.yDim = value;
}
/**
- * Gets the value of the markUnlinked property.
+ * Gets the value of the zDim property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getZDim() {
+ return zDim;
+ }
+
+ /**
+ * Sets the value of the zDim property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setZDim(Integer value) {
+ this.zDim = value;
+ }
+
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getBgColour() {
+ return bgColour;
+ }
+
+ /**
+ * Sets the value of the bgColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setBgColour(Integer value) {
+ this.bgColour = value;
+ }
+
+ /**
+ * Gets the value of the scaleFactor property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getScaleFactor() {
+ return scaleFactor;
+ }
+
+ /**
+ * Sets the value of the scaleFactor property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setScaleFactor(Float value) {
+ this.scaleFactor = value;
+ }
+
+ /**
+ * Gets the value of the showLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowLabels() {
+ return showLabels;
+ }
+
+ /**
+ * Sets the value of the showLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowLabels(Boolean value) {
+ this.showLabels = value;
+ }
+
+ /**
+ * Gets the value of the linkToAllViews property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isLinkToAllViews() {
+ return linkToAllViews;
+ }
+
+ /**
+ * Sets the value of the linkToAllViews property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setLinkToAllViews(Boolean value) {
+ this.linkToAllViews = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+ /**
+ * Gets the value of the includeGaps property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isIncludeGaps() {
+ return includeGaps;
+ }
+
+ /**
+ * Sets the value of the includeGaps property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setIncludeGaps(Boolean value) {
+ this.includeGaps = value;
+ }
+
+ /**
+ * Gets the value of the matchGaps property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isMatchGaps() {
+ return matchGaps;
+ }
+
+ /**
+ * Sets the value of the matchGaps property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setMatchGaps(Boolean value) {
+ this.matchGaps = value;
+ }
+
+ /**
+ * Gets the value of the includeGappedColumns property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isIncludeGappedColumns() {
+ return includeGappedColumns;
+ }
+
+ /**
+ * Sets the value of the includeGappedColumns property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setIncludeGappedColumns(Boolean value) {
+ this.includeGappedColumns = value;
+ }
+
+ /**
+ * Gets the value of the denominateByShortestLength property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isDenominateByShortestLength() {
+ return denominateByShortestLength;
+ }
+
+ /**
+ * Sets the value of the denominateByShortestLength property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setDenominateByShortestLength(Boolean value) {
+ this.denominateByShortestLength = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Axis {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMax {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMin {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SequencePoint {
+
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the sequenceRef property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequenceRef() {
+ return sequenceRef;
+ }
+
+ /**
+ * Sets the value of the sequenceRef property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequenceRef(String value) {
+ this.sequenceRef = value;
+ }
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "title",
+ "newick"
+ })
+ public static class Tree {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String title;
+ @XmlElement(namespace = "www.jalview.org")
+ protected String newick;
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "showBootstrap")
+ protected Boolean showBootstrap;
+ @XmlAttribute(name = "showDistances")
+ protected Boolean showDistances;
+ @XmlAttribute(name = "markUnlinked")
+ protected Boolean markUnlinked;
+ @XmlAttribute(name = "fitToWindow")
+ protected Boolean fitToWindow;
+ @XmlAttribute(name = "currentTree")
+ protected Boolean currentTree;
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the newick property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getNewick() {
+ return newick;
+ }
+
+ /**
+ * Sets the value of the newick property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setNewick(String value) {
+ this.newick = value;
+ }
+
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFontName() {
+ return fontName;
+ }
+
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFontName(String value) {
+ this.fontName = value;
+ }
+
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontSize() {
+ return fontSize;
+ }
+
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value) {
+ this.fontSize = value;
+ }
+
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontStyle() {
+ return fontStyle;
+ }
+
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value) {
+ this.fontStyle = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the showBootstrap property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowBootstrap() {
+ return showBootstrap;
+ }
+
+ /**
+ * Sets the value of the showBootstrap property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowBootstrap(Boolean value) {
+ this.showBootstrap = value;
+ }
+
+ /**
+ * Gets the value of the showDistances property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowDistances() {
+ return showDistances;
+ }
+
+ /**
+ * Sets the value of the showDistances property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowDistances(Boolean value) {
+ this.showDistances = value;
+ }
+
+ /**
+ * Gets the value of the markUnlinked property.
*
* @return
* possible object is
}
/**
+ * Gets the value of the linkToAllViews property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isLinkToAllViews() {
+ if (linkToAllViews == null) {
+ return false;
+ } else {
+ return linkToAllViews;
+ }
+ }
+
+ /**
+ * Sets the value of the linkToAllViews property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setLinkToAllViews(Boolean value) {
+ this.linkToAllViews = value;
+ }
+
+ /**
* Gets the value of the width property.
*
* @return
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
}
/**
+ * Create an instance of {@link JalviewModel.PcaViewer }
+ *
+ */
+ public JalviewModel.PcaViewer createJalviewModelPcaViewer() {
+ return new JalviewModel.PcaViewer();
+ }
+
+ /**
* Create an instance of {@link JalviewModel.Viewport }
*
*/
}
/**
+ * Create an instance of {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix createDoubleMatrix() {
+ return new DoubleMatrix();
+ }
+
+ /**
* Create an instance of {@link AnnotationColourScheme }
*
*/
}
/**
+ * Create an instance of {@link PcaDataType }
+ *
+ */
+ public PcaDataType createPcaDataType() {
+ return new PcaDataType();
+ }
+
+ /**
+ * Create an instance of {@link DoubleVector }
+ *
+ */
+ public DoubleVector createDoubleVector() {
+ return new DoubleVector();
+ }
+
+ /**
* Create an instance of {@link AlcodonFrame.Alcodon }
*
*/
}
/**
+ * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
+ *
+ */
+ public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint() {
+ return new JalviewModel.PcaViewer.SequencePoint();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.Axis }
+ *
+ */
+ public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis() {
+ return new JalviewModel.PcaViewer.Axis();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin() {
+ return new JalviewModel.PcaViewer.SeqPointMin();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax() {
+ return new JalviewModel.PcaViewer.SeqPointMax();
+ }
+
+ /**
* Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
*
*/
--- /dev/null
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ *
+ * The results of a PCA calculation
+ *
+ *
+ * <p>Java class for PcaDataType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType name="PcaDataType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="pairwiseMatrix" type="{www.jalview.org}DoubleMatrix"/>
+ * <element name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/>
+ * <element name="eigenMatrix" type="{www.jalview.org}DoubleMatrix"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "PcaDataType", namespace = "www.jalview.org", propOrder = {
+ "pairwiseMatrix",
+ "tridiagonalMatrix",
+ "eigenMatrix"
+})
+public class PcaDataType {
+
+ @XmlElement(required = true)
+ protected DoubleMatrix pairwiseMatrix;
+ @XmlElement(required = true)
+ protected DoubleMatrix tridiagonalMatrix;
+ @XmlElement(required = true)
+ protected DoubleMatrix eigenMatrix;
+
+ /**
+ * Gets the value of the pairwiseMatrix property.
+ *
+ * @return
+ * possible object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix getPairwiseMatrix() {
+ return pairwiseMatrix;
+ }
+
+ /**
+ * Sets the value of the pairwiseMatrix property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public void setPairwiseMatrix(DoubleMatrix value) {
+ this.pairwiseMatrix = value;
+ }
+
+ /**
+ * Gets the value of the tridiagonalMatrix property.
+ *
+ * @return
+ * possible object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix getTridiagonalMatrix() {
+ return tridiagonalMatrix;
+ }
+
+ /**
+ * Sets the value of the tridiagonalMatrix property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public void setTridiagonalMatrix(DoubleMatrix value) {
+ this.tridiagonalMatrix = value;
+ }
+
+ /**
+ * Gets the value of the eigenMatrix property.
+ *
+ * @return
+ * possible object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix getEigenMatrix() {
+ return eigenMatrix;
+ }
+
+ /**
+ * Sets the value of the eigenMatrix property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public void setEigenMatrix(DoubleMatrix value) {
+ this.eigenMatrix = value;
+ }
+
+}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2018.12.20 at 11:47:26 AM GMT
//
@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
assertEquals(AlignSeq.extractGaps(" -", " AC-G.T"), "ACG.T");
assertEquals(AlignSeq.extractGaps(" -.", " AC-G.T ."), "ACGT");
assertEquals(AlignSeq.extractGaps("-", " AC-G.T"), " ACG.T");
+ assertEquals(AlignSeq.extractGaps("-. ", " -. .-"), "");
}
@Test(groups = { "Functional" })
String dbSnp = "dbSNP";
String cosmic = "COSMIC";
+ /*
+ * NB setting "id" (as returned by Ensembl for features in JSON format);
+ * previously "ID" (as returned for GFF3 format)
+ */
SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1,
0f, ensembl);
sf1.setValue("alleles", "A,G"); // AAA -> GAA -> K/E
- sf1.setValue("ID", "var1.125A>G");
+ sf1.setValue("id", "var1.125A>G");
SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1,
0f, dbSnp);
sf2.setValue("alleles", "A,C"); // AAA -> CAA -> K/Q
- sf2.setValue("ID", "var2");
+ sf2.setValue("id", "var2");
sf2.setValue("clinical_significance", "Dodgy");
SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 1, 1,
0f, dbSnp);
sf3.setValue("alleles", "A,T"); // AAA -> TAA -> stop codon
- sf3.setValue("ID", "var3");
+ sf3.setValue("id", "var3");
sf3.setValue("clinical_significance", "Bad");
SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3,
0f, cosmic);
sf4.setValue("alleles", "A,G"); // AAA -> AAG synonymous
- sf4.setValue("ID", "var4");
+ sf4.setValue("id", "var4");
sf4.setValue("clinical_significance", "None");
SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 3, 3,
0f, ensembl);
sf5.setValue("alleles", "A,T"); // AAA -> AAT -> K/N
- sf5.setValue("ID", "sequence_variant:var5"); // prefix gets stripped off
+ sf5.setValue("id", "sequence_variant:var5"); // prefix gets stripped off
sf5.setValue("clinical_significance", "Benign");
SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 6, 6,
0f, dbSnp);
sf6.setValue("alleles", "T,C"); // TTT -> TTC synonymous
- sf6.setValue("ID", "var6");
+ sf6.setValue("id", "var6");
SequenceFeature sf7 = new SequenceFeature("sequence_variant", "", 8, 8,
0f, cosmic);
sf7.setValue("alleles", "C,A,G"); // CCC -> CAC,CGC -> P/H/R
- sf7.setValue("ID", "var7");
+ sf7.setValue("id", "var7");
sf7.setValue("clinical_significance", "Good");
List<DnaVariant> codon1Variants = new ArrayList<>();
assertEquals(1, sf.getEnd());
assertEquals("nonsynonymous_variant", sf.getType());
assertEquals("p.Lys1Asn", sf.getDescription());
- assertEquals("var5", sf.getValue("ID"));
+ assertEquals("var5", sf.getValue("id"));
assertEquals("Benign", sf.getValue("clinical_significance"));
- assertEquals("ID=var5;clinical_significance=Benign",
+ assertEquals("id=var5;clinical_significance=Benign",
sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
assertEquals(1, sf.getEnd());
assertEquals("nonsynonymous_variant", sf.getType());
assertEquals("p.Lys1Gln", sf.getDescription());
- assertEquals("var2", sf.getValue("ID"));
+ assertEquals("var2", sf.getValue("id"));
assertEquals("Dodgy", sf.getValue("clinical_significance"));
- assertEquals("ID=var2;clinical_significance=Dodgy", sf.getAttributes());
+ assertEquals("id=var2;clinical_significance=Dodgy", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
"p.Lys1Gln var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
assertEquals(1, sf.getEnd());
assertEquals("nonsynonymous_variant", sf.getType());
assertEquals("p.Lys1Glu", sf.getDescription());
- assertEquals("var1.125A>G", sf.getValue("ID"));
+ assertEquals("var1.125A>G", sf.getValue("id"));
assertNull(sf.getValue("clinical_significance"));
- assertEquals("ID=var1.125A>G", sf.getAttributes());
+ assertEquals("id=var1.125A>G", sf.getAttributes());
assertEquals(1, sf.links.size());
// link to variation is urlencoded
assertEquals(
assertEquals(1, sf.getEnd());
assertEquals("stop_gained", sf.getType());
assertEquals("Aaa/Taa", sf.getDescription());
- assertEquals("var3", sf.getValue("ID"));
+ assertEquals("var3", sf.getValue("id"));
assertEquals("Bad", sf.getValue("clinical_significance"));
- assertEquals("ID=var3;clinical_significance=Bad", sf.getAttributes());
+ assertEquals("id=var3;clinical_significance=Bad", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
"Aaa/Taa var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3",
assertEquals(1, sf.getEnd());
assertEquals("synonymous_variant", sf.getType());
assertEquals("aaA/aaG", sf.getDescription());
- assertEquals("var4", sf.getValue("ID"));
+ assertEquals("var4", sf.getValue("id"));
assertEquals("None", sf.getValue("clinical_significance"));
- assertEquals("ID=var4;clinical_significance=None", sf.getAttributes());
+ assertEquals("id=var4;clinical_significance=None", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
"aaA/aaG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
assertEquals(2, sf.getEnd());
assertEquals("synonymous_variant", sf.getType());
assertEquals("ttT/ttC", sf.getDescription());
- assertEquals("var6", sf.getValue("ID"));
+ assertEquals("var6", sf.getValue("id"));
assertNull(sf.getValue("clinical_significance"));
- assertEquals("ID=var6", sf.getAttributes());
+ assertEquals("id=var6", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
"ttT/ttC var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
assertEquals(3, sf.getEnd());
assertEquals("nonsynonymous_variant", sf.getType());
assertEquals("p.Pro3Arg", sf.getDescription());
- assertEquals("var7", sf.getValue("ID"));
+ assertEquals("var7", sf.getValue("id"));
assertEquals("Good", sf.getValue("clinical_significance"));
- assertEquals("ID=var7;clinical_significance=Good", sf.getAttributes());
+ assertEquals("id=var7;clinical_significance=Good", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
"p.Pro3Arg var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7",
assertEquals(3, sf.getEnd());
assertEquals("nonsynonymous_variant", sf.getType());
assertEquals("p.Pro3His", sf.getDescription());
- assertEquals("var7", sf.getValue("ID"));
+ assertEquals("var7", sf.getValue("id"));
assertEquals("Good", sf.getValue("clinical_significance"));
- assertEquals("ID=var7;clinical_significance=Good", sf.getAttributes());
+ assertEquals("id=var7;clinical_significance=Good", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
"p.Pro3His var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7",
assertSame(pep2, xrefs.getSequenceAt(1));
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public void tearDown()
{
SequenceFetcherFactory.setSequenceFetcher(null);
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
assertNotNull("Couldn't do a full width translation of test data.",
translated);
}
alf.getWidth(), false);
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, vcontigs);
- AlignmentI transAlf = dna.translateCdna();
+ AlignmentI transAlf = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
assertTrue("Translation failed (ipos=" + ipos
+ ") No alignment data.", transAlf != null);
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals(
"AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
}
Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
/*
* Jumble the cDNA sequences and translate.
av = new AlignViewport(cdnaReordered, cs);
contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
dna = new Dna(av, contigs);
- AlignmentI translated2 = dna.translateCdna();
+ AlignmentI translated2 = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
/*
* Check translated sequences are the same in both alignments.
import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
+import jalview.api.AlignViewportI;
+import jalview.api.FinderI;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import java.util.List;
+import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class FinderTest
{
@BeforeClass(alwaysRun = true)
private AlignmentI al;
+ private AlignViewportI av;
+
@BeforeClass(groups = "Functional")
public void setUp()
{
- String seqData = "seq1 ABCD--EF-GHI\n" + "seq2 A--BCDefHI\n"
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.applicationProperties.setProperty("PAD_GAPS",
+ Boolean.FALSE.toString());
+
+ String seqData = "seq1seq1/8-18 ABCD--EF-GHIJI\n" + "seq2 A--BCDefHI\n"
+ "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n";
af = new FileLoader().LoadFileWaitTillLoaded(seqData,
DataSourceType.PASTE);
- al = af.getViewport().getAlignment();
+ av = af.getViewport();
+ al = av.getAlignment();
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void tearDownAfterTest()
+ {
+ av.setSelectionGroup(null);
}
/**
- * Test for find all matches of a regular expression
+ * Test for find matches of a regular expression
*/
@Test(groups = "Functional")
- public void testFindAll_regex()
+ public void testFind_regex()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
- f.find("E.H"); // 'E, any character, H'
+ /*
+ * find next match only
+ */
+ Finder f = new Finder(av);
+ f.findNext("E.H", false, false); // 'E, any character, H'
+ // should match seq2 efH only
+ SearchResultsI sr = f.getSearchResults();
+ assertEquals(sr.getSize(), 1);
+ List<SearchResultMatchI> matches = sr.getResults();
+ assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
+ assertEquals(matches.get(0).getStart(), 5);
+ assertEquals(matches.get(0).getEnd(), 7);
+ f = new Finder(av);
+ f.findAll("E.H", false, false); // 'E, any character, H'
// should match seq2 efH and seq3 EFH
- SearchResultsI sr = f.getSearchResults();
+ sr = f.getSearchResults();
assertEquals(sr.getSize(), 2);
- List<SearchResultMatchI> matches = sr.getResults();
- assertSame(al.getSequenceAt(1), matches.get(0).getSequence());
- assertSame(al.getSequenceAt(2), matches.get(1).getSequence());
+ matches = sr.getResults();
+ assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
+ assertSame(matches.get(1).getSequence(), al.getSequenceAt(2));
assertEquals(matches.get(0).getStart(), 5);
assertEquals(matches.get(0).getEnd(), 7);
assertEquals(matches.get(1).getStart(), 4);
@Test(groups = "Functional")
public void testFind_residueNumber()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
- f.find("9");
+ Finder f = new Finder(av);
- // seq1 and seq4 have 9 residues; no match in other sequences
+ /*
+ * find first match should return seq1 residue 9
+ */
+ f.findNext("9", false, false);
SearchResultsI sr = f.getSearchResults();
- assertEquals(sr.getSize(), 2);
+ assertEquals(sr.getSize(), 1);
List<SearchResultMatchI> matches = sr.getResults();
- assertSame(al.getSequenceAt(0), matches.get(0).getSequence());
- assertSame(al.getSequenceAt(3), matches.get(1).getSequence());
+ assertSame(matches.get(0).getSequence(), al.getSequenceAt(0));
+ assertEquals(matches.get(0).getStart(), 9);
+ assertEquals(matches.get(0).getEnd(), 9);
+
+ /*
+ * find all matches should return seq1 and seq4 (others are too short)
+ */
+ f = new Finder(av);
+ f.findAll("9", false, false);
+ sr = f.getSearchResults();
+ assertEquals(sr.getSize(), 2);
+ matches = sr.getResults();
+ assertSame(matches.get(0).getSequence(), al.getSequenceAt(0));
+ assertSame(matches.get(1).getSequence(), al.getSequenceAt(3));
assertEquals(matches.get(0).getStart(), 9);
assertEquals(matches.get(0).getEnd(), 9);
assertEquals(matches.get(1).getStart(), 9);
assertEquals(matches.get(1).getEnd(), 9);
+
+ /*
+ * parsing of search string as integer is strict
+ */
+ f = new Finder(av);
+ f.findNext(" 9", false, false);
+ assertTrue(f.getSearchResults().isEmpty());
}
/**
public void testFindNext()
{
/*
- * start at second sequence; resIndex of -1
+ * start at second sequence; colIndex of -1
* means sequence id / description is searched
*/
- Finder f = new Finder(al, null, 1, -1);
- f.find("e"); // matches id
+ Finder f = new Finder(av);
+ PA.setValue(f, "sequenceIndex", 1);
+ PA.setValue(f, "columnIndex", -1);
+ f.findNext("e", false, false); // matches id
assertTrue(f.getSearchResults().isEmpty());
- assertEquals(f.getIdMatch().size(), 1);
- assertSame(f.getIdMatch().get(0), al.getSequenceAt(1));
-
- // resIndex is now 0 - for use in next find next
- assertEquals(f.getResIndex(), 0);
- f = new Finder(al, null, 1, 0);
- f.find("e"); // matches in sequence
- assertTrue(f.getIdMatch().isEmpty());
+ assertEquals(f.getIdMatches().size(), 1);
+ assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
+
+ // colIndex is now 0 - for use in next find next
+ // searching A--BCDefHI
+ assertEquals(PA.getValue(f, "columnIndex"), 0);
+ f = new Finder(av);
+ PA.setValue(f, "sequenceIndex", 1);
+ PA.setValue(f, "columnIndex", 0);
+ f.findNext("e", false, false); // matches in sequence
+ assertTrue(f.getIdMatches().isEmpty());
assertEquals(f.getSearchResults().getSize(), 1);
List<SearchResultMatchI> matches = f.getSearchResults().getResults();
assertEquals(matches.get(0).getStart(), 5);
assertEquals(matches.get(0).getEnd(), 5);
assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
// still in the second sequence
- assertEquals(f.getSeqIndex(), 1);
- // next residue position to search from is 5
- // (used as base 0 by RegEx so the same as 6 if base 1)
- assertEquals(f.getResIndex(), 5);
+ assertEquals(PA.getValue(f, "sequenceIndex"), 1);
+ // next column position to search from is 7
+ assertEquals(PA.getValue(f, "columnIndex"), 7);
// find next from end of sequence - finds next sequence id
- f = new Finder(al, null, 1, 5);
- f.find("e");
- assertEquals(f.getIdMatch().size(), 1);
- assertSame(f.getIdMatch().get(0), al.getSequenceAt(2));
+ f = new Finder(av);
+ PA.setValue(f, "sequenceIndex", 1);
+ PA.setValue(f, "columnIndex", 7);
+ f.findNext("e", false, false);
+ assertEquals(f.getIdMatches().size(), 1);
+ assertSame(f.getIdMatches().get(0), al.getSequenceAt(2));
+ assertTrue(f.getSearchResults().isEmpty());
}
/**
* Test for matching within sequence descriptions
*/
@Test(groups = "Functional")
- public void testFindAll_inDescription()
+ public void testFind_inDescription()
{
AlignmentI al2 = new Alignment(al);
al2.getSequenceAt(0).setDescription("BRAF");
al2.getSequenceAt(1).setDescription("braf");
- Finder f = new Finder(al2, null);
- f.setFindAll(true);
- f.setIncludeDescription(true);
-
- f.find("rAF");
- assertEquals(f.getIdMatch().size(), 2);
- assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
- assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1));
+
+ AlignViewportI av2 = new AlignViewport(al2);
+
+ /*
+ * find first match only
+ */
+ Finder f = new Finder(av2);
+ f.findNext("rAF", false, true);
+ assertEquals(f.getIdMatches().size(), 1);
+ assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
assertTrue(f.getSearchResults().isEmpty());
/*
- * case sensitive
+ * find all matches
*/
- f = new Finder(al2, null);
- f.setFindAll(true);
- f.setCaseSensitive(true);
- f.setIncludeDescription(true);
+ f = new Finder(av2);
+ f.findAll("rAF", false, true);
+ assertEquals(f.getIdMatches().size(), 2);
+ assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
+ assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
+ assertTrue(f.getSearchResults().isEmpty());
- f.find("RAF");
- assertEquals(f.getIdMatch().size(), 1);
- assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
+ /*
+ * case sensitive
+ */
+ f = new Finder(av2);
+ f.findAll("RAF", true, true);
+ assertEquals(f.getIdMatches().size(), 1);
+ assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
assertTrue(f.getSearchResults().isEmpty());
/*
al2.getSequenceAt(0).setDescription("the efh sequence");
al2.getSequenceAt(0).setName("mouseEFHkinase");
al2.getSequenceAt(1).setName("humanEFHkinase");
- f = new Finder(al2, null);
- f.setFindAll(true);
- f.setIncludeDescription(true);
+ f = new Finder(av2);
/*
* sequence matches should have no duplicates
*/
- f.find("EFH");
- assertEquals(f.getIdMatch().size(), 2);
- assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
- assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1));
+ f.findAll("EFH", false, true);
+ assertEquals(f.getIdMatches().size(), 2);
+ assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
+ assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
assertEquals(f.getSearchResults().getSize(), 2);
SearchResultMatchI match = f.getSearchResults().getResults().get(0);
- assertSame(al2.getSequenceAt(1), match.getSequence());
- assertEquals(5, match.getStart());
- assertEquals(7, match.getEnd());
+ assertSame(match.getSequence(), al2.getSequenceAt(1));
+ assertEquals(match.getStart(), 5);
+ assertEquals(match.getEnd(), 7);
match = f.getSearchResults().getResults().get(1);
- assertSame(al2.getSequenceAt(2), match.getSequence());
- assertEquals(4, match.getStart());
- assertEquals(6, match.getEnd());
+ assertSame(match.getSequence(), al2.getSequenceAt(2));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 6);
}
/**
@Test(groups = "Functional")
public void testFindAll_sequenceIds()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
+ Finder f = new Finder(av);
/*
- * case insensitive
+ * case insensitive; seq1 occurs twice in sequence id but
+ * only one match should be returned
*/
- f.find("SEQ1");
- assertEquals(f.getIdMatch().size(), 1);
- assertSame(f.getIdMatch().get(0), al.getSequenceAt(0));
- assertTrue(f.getSearchResults().isEmpty());
+ f.findAll("SEQ1", false, false);
+ assertEquals(f.getIdMatches().size(), 1);
+ assertSame(f.getIdMatches().get(0), al.getSequenceAt(0));
+ SearchResultsI searchResults = f.getSearchResults();
+ assertTrue(searchResults.isEmpty());
/*
* case sensitive
*/
- f = new Finder(al, null);
- f.setFindAll(true);
- f.setCaseSensitive(true);
- f.find("SEQ1");
- assertTrue(f.getSearchResults().isEmpty());
+ f = new Finder(av);
+ f.findAll("SEQ1", true, false);
+ searchResults = f.getSearchResults();
+ assertTrue(searchResults.isEmpty());
/*
* match both sequence id and sequence
*/
AlignmentI al2 = new Alignment(al);
+ AlignViewportI av2 = new AlignViewport(al2);
al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ"));
- f = new Finder(al2, null);
- f.setFindAll(true);
- f.find("ABZ");
- assertEquals(f.getIdMatch().size(), 1);
- assertSame(f.getIdMatch().get(0), al2.getSequenceAt(4));
- assertEquals(f.getSearchResults().getSize(), 2);
- SearchResultMatchI match = f.getSearchResults().getResults().get(0);
- assertSame(al2.getSequenceAt(4), match.getSequence());
- assertEquals(4, match.getStart());
- assertEquals(6, match.getEnd());
- match = f.getSearchResults().getResults().get(1);
- assertSame(al2.getSequenceAt(4), match.getSequence());
- assertEquals(10, match.getStart());
- assertEquals(12, match.getEnd());
+ f = new Finder(av2);
+ f.findAll("ABZ", false, false);
+ assertEquals(f.getIdMatches().size(), 1);
+ assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4));
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 2);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al2.getSequenceAt(4));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 6);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al2.getSequenceAt(4));
+ assertEquals(match.getStart(), 10);
+ assertEquals(match.getEnd(), 12);
}
/**
- * Test finding all matches of a sequence pattern in an alignment
+ * Test finding next match of a sequence pattern in an alignment
*/
@Test(groups = "Functional")
- public void testFindAll_simpleMatch()
+ public void testFind_findNext()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
+ /*
+ * efh should be matched in seq2 only
+ */
+ FinderI f = new Finder(av);
+ f.findNext("EfH", false, false);
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 5);
+ assertEquals(match.getEnd(), 7);
/*
- * case insensitive first
+ * I should be found in seq1 (twice) and seq2 (once)
*/
- f.find("EfH");
+ f = new Finder(av);
+ f.findNext("I", false, false); // find next: seq1/16
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 16);
+ assertEquals(match.getEnd(), 16);
+
+ f.findNext("I", false, false); // find next: seq1/18
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 18);
+ assertEquals(match.getEnd(), 18);
+
+ f.findNext("I", false, false); // find next: seq2/8
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 8);
+ assertEquals(match.getEnd(), 8);
+
+ f.findNext("I", false, false);
+ assertTrue(f.getSearchResults().isEmpty());
+
+ /*
+ * find should reset to start of alignment after a failed search
+ */
+ f.findNext("I", false, false); // find next: seq1/16
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 16);
+ assertEquals(match.getEnd(), 16);
+ }
+
+ /**
+ * Test for JAL-2302 to verify that sub-matches are not included in a find all
+ * result
+ */
+ @Test(groups = "Functional")
+ public void testFind_maximalResultOnly()
+ {
+ Finder f = new Finder(av);
+ f.findAll("M+", false, false);
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(3));
+ assertEquals(match.getStart(), 4); // dataset sequence positions
+ assertEquals(match.getEnd(), 8); // base 1
+ }
+
+ /**
+ * Test finding all matches of a sequence pattern in an alignment
+ */
+ @Test(groups = "Functional")
+ public void testFind_findAll()
+ {
+ Finder f = new Finder(av);
+ f.findAll("EfH", false, false);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getSize(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
- assertSame(al.getSequenceAt(1), match.getSequence());
- assertEquals(5, match.getStart());
- assertEquals(7, match.getEnd());
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 5);
+ assertEquals(match.getEnd(), 7);
match = searchResults.getResults().get(1);
- assertSame(al.getSequenceAt(2), match.getSequence());
- assertEquals(4, match.getStart());
- assertEquals(6, match.getEnd());
+ assertSame(match.getSequence(), al.getSequenceAt(2));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 6);
/*
- * case sensitive
+ * find all I should find 2 positions in seq1, 1 in seq2
*/
- f = new Finder(al, null);
- f.setFindAll(true);
- f.setCaseSensitive(true);
- f.find("BC");
+ f.findAll("I", false, false);
searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 3);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 16);
+ assertEquals(match.getEnd(), 16);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 18);
+ assertEquals(match.getEnd(), 18);
+ match = searchResults.getResults().get(2);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 8);
+ assertEquals(match.getEnd(), 8);
+ }
+
+ /**
+ * Test finding all matches, case-sensitive
+ */
+ @Test(groups = "Functional")
+ public void testFind_findAllCaseSensitive()
+ {
+ Finder f = new Finder(av);
+
+ /*
+ * BC should match seq1/9-10 and seq2/2-3
+ */
+ f.findAll("BC", true, false);
+ SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getSize(), 2);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 9);
+ assertEquals(match.getEnd(), 10);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 2);
+ assertEquals(match.getEnd(), 3);
+
+ /*
+ * bc should match seq3/1-2
+ */
+ f = new Finder(av);
+ f.findAll("bc", true, false);
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(2));
+ assertEquals(match.getStart(), 1);
+ assertEquals(match.getEnd(), 2);
+
+ f.findAll("bC", true, false);
+ assertTrue(f.getSearchResults().isEmpty());
+ }
+
+ /**
+ * Test finding next match of a sequence pattern in a selection group
+ */
+ @Test(groups = "Functional")
+ public void testFind_inSelection()
+ {
+ /*
+ * select sequences 2 and 3, columns 4-6 which contains
+ * BCD
+ * cdE
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(3);
+ sg.setEndRes(5);
+ sg.addSequence(al.getSequenceAt(1), false);
+ sg.addSequence(al.getSequenceAt(2), false);
+ av.setSelectionGroup(sg);
+
+ FinderI f = new Finder(av);
+ f.findNext("b", false, false);
+ assertTrue(f.getIdMatches().isEmpty());
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 2);
+ assertEquals(match.getEnd(), 2);
+
+ /*
+ * a second Find should not return the 'b' in seq3 as outside the selection
+ */
+ f.findNext("b", false, false);
+ assertTrue(f.getSearchResults().isEmpty());
+ assertTrue(f.getIdMatches().isEmpty());
+
+ f = new Finder(av);
+ f.findNext("d", false, false);
+ assertTrue(f.getIdMatches().isEmpty());
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
match = searchResults.getResults().get(0);
- assertSame(al.getSequenceAt(0), match.getSequence());
- assertEquals(2, match.getStart());
- assertEquals(3, match.getEnd());
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 4);
+ f.findNext("d", false, false);
+ assertTrue(f.getIdMatches().isEmpty());
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(2));
+ assertEquals(match.getStart(), 3);
+ assertEquals(match.getEnd(), 3);
+ }
+
+ /**
+ * Test finding all matches of a search pattern in a selection group
+ */
+ @Test(groups = "Functional")
+ public void testFind_findAllInSelection()
+ {
+ /*
+ * select sequences 2 and 3, columns 4-6 which contains
+ * BCD
+ * cdE
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(3);
+ sg.setEndRes(5);
+ sg.addSequence(al.getSequenceAt(1), false);
+ sg.addSequence(al.getSequenceAt(2), false);
+ av.setSelectionGroup(sg);
+
+ /*
+ * search for 'e' should match two sequence ids and one residue
+ */
+ Finder f = new Finder(av);
+ f.findAll("e", false, false);
+ assertEquals(f.getIdMatches().size(), 2);
+ assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
+ assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(2));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 4);
+
+ /*
+ * search for 'Q' should match two sequence ids only
+ */
+ f = new Finder(av);
+ f.findAll("Q", false, false);
+ assertEquals(f.getIdMatches().size(), 2);
+ assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
+ assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
+ assertTrue(f.getSearchResults().isEmpty());
+ }
+
+ /**
+ * Test finding in selection with a sequence too short to reach it
+ */
+ @Test(groups = "Functional")
+ public void testFind_findAllInSelectionWithShortSequence()
+ {
+ /*
+ * select all sequences, columns 10-12
+ * BCD
+ * cdE
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(9);
+ sg.setEndRes(11);
+ sg.addSequence(al.getSequenceAt(0), false);
+ sg.addSequence(al.getSequenceAt(1), false);
+ sg.addSequence(al.getSequenceAt(2), false);
+ sg.addSequence(al.getSequenceAt(3), false);
+ av.setSelectionGroup(sg);
+
+ /*
+ * search for 'I' should match two sequence positions
+ */
+ Finder f = new Finder(av);
+ f.findAll("I", false, false);
+ assertTrue(f.getIdMatches().isEmpty());
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 2);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 16);
+ assertEquals(match.getEnd(), 16);
match = searchResults.getResults().get(1);
- assertSame(al.getSequenceAt(1), match.getSequence());
- assertEquals(2, match.getStart());
- assertEquals(3, match.getEnd());
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 8);
+ assertEquals(match.getEnd(), 8);
}
/**
- * Test for JAL-2302 to verify that sub-matches are not included in a find all
- * result
+ * Test that find does not report hidden positions
*/
@Test(groups = "Functional")
- public void testFind_maximalResultOnly()
+ public void testFind_withHiddenColumns()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
- f.find("M+");
+ /*
+ * 0 5 9
+ * ABCD--EF-GHI
+ * A--BCDefHI
+ * --bcdEFH
+ * aa---aMMMMMaaa
+ */
+
+ /*
+ * hide 2-4 (CD- -BC bcd ---)
+ */
+ HiddenColumns hc = new HiddenColumns();
+ hc.hideColumns(2, 4);
+ al.setHiddenColumns(hc);
+
+ /*
+ * find all search for D should ignore hidden positions in seq1 and seq3,
+ * find the visible D in seq2
+ */
+ Finder f = new Finder(av);
+ f.findAll("D", false, false);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getSize(), 1);
SearchResultMatchI match = searchResults.getResults().get(0);
- assertSame(al.getSequenceAt(3), match.getSequence());
- assertEquals(4, match.getStart()); // dataset sequence positions
- assertEquals(8, match.getEnd()); // base 1
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 4);
+
+ /*
+ * hide columns 2-5:
+ * find all 'aaa' should find end of seq4 only
+ */
+ hc.hideColumns(2, 5);
+ f = new Finder(av);
+ f.findAll("aaa", false, false);
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(3));
+ assertEquals(match.getStart(), 9);
+ assertEquals(match.getEnd(), 11);
+
+ /*
+ * find all 'BE' should not match across hidden columns in seq1
+ */
+ f.findAll("BE", false, false);
+ assertTrue(f.getSearchResults().isEmpty());
+
+ /*
+ * boundary case: hide columns at end of alignment
+ * search for H should match seq3/6 only
+ */
+ hc.revealAllHiddenColumns(new ColumnSelection());
+ hc.hideColumns(8, 13);
+ f = new Finder(av);
+ f.findNext("H", false, false);
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(2));
+ assertEquals(match.getStart(), 6);
+ assertEquals(match.getEnd(), 6);
+ }
+
+ @Test(groups = "Functional")
+ public void testFind_withHiddenColumnsAndSelection()
+ {
+ /*
+ * 0 5 9
+ * ABCD--EF-GHI
+ * A--BCDefHI
+ * --bcdEFH
+ * aa---aMMMMMaaa
+ */
+
+ /*
+ * hide columns 2-4 and 6-7
+ */
+ HiddenColumns hc = new HiddenColumns();
+ hc.hideColumns(2, 4);
+ hc.hideColumns(6, 7);
+ al.setHiddenColumns(hc);
+
+ /*
+ * select rows 2-3
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(al.getSequenceAt(1), false);
+ sg.addSequence(al.getSequenceAt(2), false);
+ sg.setStartRes(0);
+ sg.setEndRes(13);
+ av.setSelectionGroup(sg);
+
+ /*
+ * find all search for A or H
+ * should match seq2/1, seq2/7, not seq3/6
+ */
+ Finder f = new Finder(av);
+ f.findAll("[AH]", false, false);
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 2);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 1);
+ assertEquals(match.getEnd(), 1);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 7);
+ assertEquals(match.getEnd(), 7);
}
}
--- /dev/null
+package jalview.analysis;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertSame;
+
+import java.util.Iterator;
+
+import org.testng.annotations.Test;
+
+public class GeneticCodesTest
+{
+ @Test(groups = "Functional")
+ public void testGetCodeTable()
+ {
+ GeneticCodes codes = GeneticCodes.getInstance();
+ assertEquals(codes.getStandardCodeTable().getName(), "Standard");
+ assertEquals(codes.getStandardCodeTable().getId(), "1");
+ assertSame(codes.getStandardCodeTable(), codes.getCodeTable("1"));
+ assertEquals(codes.getCodeTable("2").getName(),
+ "Vertebrate Mitochondrial");
+ assertEquals(codes.getCodeTable("11").getName(),
+ "Bacterial, Archaeal and Plant Plastid");
+ assertEquals(codes.getCodeTable("31").getName(),
+ "Blastocrithidia Nuclear");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetCodeTables()
+ {
+ GeneticCodes codes = GeneticCodes.getInstance();
+ Iterator<GeneticCodeI> tableIterator = codes.getCodeTables().iterator();
+ String[] ids = new String[] { "1", "2", "3", "4", "5", "6", "9", "10",
+ "11", "12", "13", "14", "15", "16", "21", "22", "23", "24", "25",
+ "26", "27", "28", "29", "30", "31" };
+ for (int i = 0; i < ids.length; i++)
+ {
+ assertEquals(tableIterator.next().getId(), ids[i]);
+ }
+ assertFalse(tableIterator.hasNext());
+ }
+
+ @Test(groups = "Functional")
+ public void testTranslate()
+ {
+ GeneticCodes codes = GeneticCodes.getInstance();
+
+ GeneticCodeI gc = codes.getCodeTable("1");
+ assertNull(gc.translate("XYZ"));
+ assertEquals(gc.translate("AGA"), "R");
+
+ gc = codes.getCodeTable("2");
+ assertEquals(gc.translate("AGA"), "*"); // variant
+ assertEquals(gc.translate("ttc"), "F"); // non-variant
+
+ // table 11 has no variant translations - should serve the standard values
+ gc = codes.getCodeTable("11");
+ assertEquals(gc.translate("ttc"), "F");
+
+ gc = codes.getCodeTable("31");
+ assertEquals(gc.translate("TGA"), "W"); // variant
+ assertEquals(gc.translate("tag"), "E"); // variant
+ assertEquals(gc.translate("AGC"), "S"); // non-variant
+ }
+
+ /**
+ * Test 'standard' codon translations (no ambiguity codes)
+ */
+ @Test(groups = { "Functional" })
+ public void testTranslate_standardTable()
+ {
+ GeneticCodeI st = GeneticCodes.getInstance().getStandardCodeTable();
+ assertEquals("F", st.translate("TTT"));
+ assertEquals("F", st.translate("TTC"));
+ assertEquals("L", st.translate("TTA"));
+ assertEquals("L", st.translate("TTG"));
+ assertEquals("L", st.translate("CTT"));
+ assertEquals("L", st.translate("CTC"));
+ assertEquals("L", st.translate("CTA"));
+ assertEquals("L", st.translate("CTG"));
+ assertEquals("I", st.translate("ATT"));
+ assertEquals("I", st.translate("ATC"));
+ assertEquals("I", st.translate("ATA"));
+ assertEquals("M", st.translate("ATG"));
+ assertEquals("V", st.translate("GTT"));
+ assertEquals("V", st.translate("GTC"));
+ assertEquals("V", st.translate("GTA"));
+ assertEquals("V", st.translate("GTG"));
+ assertEquals("S", st.translate("TCT"));
+ assertEquals("S", st.translate("TCC"));
+ assertEquals("S", st.translate("TCA"));
+ assertEquals("S", st.translate("TCG"));
+ assertEquals("P", st.translate("CCT"));
+ assertEquals("P", st.translate("CCC"));
+ assertEquals("P", st.translate("CCA"));
+ assertEquals("P", st.translate("CCG"));
+ assertEquals("T", st.translate("ACT"));
+ assertEquals("T", st.translate("ACC"));
+ assertEquals("T", st.translate("ACA"));
+ assertEquals("T", st.translate("ACG"));
+ assertEquals("A", st.translate("GCT"));
+ assertEquals("A", st.translate("GCC"));
+ assertEquals("A", st.translate("GCA"));
+ assertEquals("A", st.translate("GCG"));
+ assertEquals("Y", st.translate("TAT"));
+ assertEquals("Y", st.translate("TAC"));
+ assertEquals("*", st.translate("TAA"));
+ assertEquals("*", st.translate("TAG"));
+ assertEquals("H", st.translate("CAT"));
+ assertEquals("H", st.translate("CAC"));
+ assertEquals("Q", st.translate("CAA"));
+ assertEquals("Q", st.translate("CAG"));
+ assertEquals("N", st.translate("AAT"));
+ assertEquals("N", st.translate("AAC"));
+ assertEquals("K", st.translate("AAA"));
+ assertEquals("K", st.translate("AAG"));
+ assertEquals("D", st.translate("GAT"));
+ assertEquals("D", st.translate("GAC"));
+ assertEquals("E", st.translate("GAA"));
+ assertEquals("E", st.translate("GAG"));
+ assertEquals("C", st.translate("TGT"));
+ assertEquals("C", st.translate("TGC"));
+ assertEquals("*", st.translate("TGA"));
+ assertEquals("W", st.translate("TGG"));
+ assertEquals("R", st.translate("CGT"));
+ assertEquals("R", st.translate("CGC"));
+ assertEquals("R", st.translate("CGA"));
+ assertEquals("R", st.translate("CGG"));
+ assertEquals("S", st.translate("AGT"));
+ assertEquals("S", st.translate("AGC"));
+ assertEquals("R", st.translate("AGA"));
+ assertEquals("R", st.translate("AGG"));
+ assertEquals("G", st.translate("GGT"));
+ assertEquals("G", st.translate("GGC"));
+ assertEquals("G", st.translate("GGA"));
+ assertEquals("G", st.translate("GGG"));
+ }
+
+ /**
+ * Test a sample of codon translations involving ambiguity codes. Should
+ * return a protein value where the ambiguity does not affect the translation.
+ */
+ @Test(groups = { "Functional" })
+ public void testTranslate_standardTableAmbiguityCodes()
+ {
+ GeneticCodeI st = GeneticCodes.getInstance().getStandardCodeTable();
+ // Y is C or T
+ assertEquals("C", st.translate("TGY"));
+ // Phenylalanine first base variation
+ assertEquals("L", st.translate("YTA"));
+
+ // W is A or T
+ assertEquals("L", st.translate("CTW"));
+ assertNull(st.translate("TTW"));
+
+ // S is G or C
+ assertEquals("G", st.translate("GGS"));
+ assertNull(st.translate("ATS"));
+
+ // K is T or G
+ assertEquals("S", st.translate("TCK"));
+ assertNull(st.translate("ATK"));
+
+ // M is C or A
+ assertEquals("T", st.translate("ACM"));
+ // Arginine first base variation
+ assertEquals("R", st.translate("MGA"));
+ assertEquals("R", st.translate("MGG"));
+ assertNull(st.translate("TAM"));
+
+ // D is A, G or T
+ assertEquals("P", st.translate("CCD"));
+ assertNull(st.translate("AAD"));
+
+ // V is A, C or G
+ assertEquals("V", st.translate("GTV"));
+ assertNull(st.translate("TTV"));
+
+ // H is A, C or T
+ assertEquals("A", st.translate("GCH"));
+ assertEquals("I", st.translate("ATH"));
+ assertNull(st.translate("AGH"));
+
+ // B is C, G or T
+ assertEquals("P", st.translate("CCB"));
+ assertNull(st.translate("TAB"));
+
+ // R is A or G
+ // additional tests for JAL-1685 (resolved)
+ assertEquals("L", st.translate("CTR"));
+ assertEquals("V", st.translate("GTR"));
+ assertEquals("S", st.translate("TCR"));
+ assertEquals("P", st.translate("CCR"));
+ assertEquals("T", st.translate("ACR"));
+ assertEquals("A", st.translate("GCR"));
+ assertEquals("R", st.translate("CGR"));
+ assertEquals("G", st.translate("GGR"));
+ assertEquals("R", st.translate("AGR"));
+ assertEquals("E", st.translate("GAR"));
+ assertEquals("K", st.translate("AAR"));
+ assertEquals("L", st.translate("TTR"));
+ assertEquals("Q", st.translate("CAR"));
+ assertEquals("*", st.translate("TAR"));
+ assertEquals("*", st.translate("TRA"));
+ // Arginine first and third base ambiguity
+ assertEquals("R", st.translate("MGR"));
+ assertNull(st.translate("ATR"));
+
+ // N is any base; 8 proteins accept any base in 3rd position
+ assertEquals("L", st.translate("CTN"));
+ assertEquals("V", st.translate("GTN"));
+ assertEquals("S", st.translate("TCN"));
+ assertEquals("P", st.translate("CCN"));
+ assertEquals("T", st.translate("ACN"));
+ assertEquals("A", st.translate("GCN"));
+ assertEquals("R", st.translate("CGN"));
+ assertEquals("G", st.translate("GGN"));
+ assertNull(st.translate("ATN"));
+ assertNull(st.translate("ANT"));
+ assertNull(st.translate("NAT"));
+ assertNull(st.translate("ANN"));
+ assertNull(st.translate("NNA"));
+ assertNull(st.translate("NNN"));
+
+ // some random stuff
+ assertNull(st.translate("YWB"));
+ assertNull(st.translate("VHD"));
+ assertNull(st.translate("WSK"));
+ }
+
+ /**
+ * Test a sample of codon translations involving ambiguity codes. Should
+ * return a protein value where the ambiguity does not affect the translation.
+ */
+ @Test(groups = { "Functional" })
+ public void testTranslate_nonStandardTableAmbiguityCodes()
+ {
+ GeneticCodeI standard = GeneticCodes.getInstance()
+ .getStandardCodeTable();
+
+ /*
+ * Vertebrate Mitochondrial (Table 2)
+ */
+ GeneticCodeI gc = GeneticCodes.getInstance().getCodeTable("2");
+ // AGR is AGA or AGG - R in standard code, * in table 2
+ assertEquals(gc.translate("AGR"), "*");
+ assertEquals(standard.translate("AGR"), "R");
+ // TGR is TGA or TGG - ambiguous in standard code, W in table 2
+ assertEquals(gc.translate("TGR"), "W");
+ assertNull(standard.translate("TGR"));
+
+ /*
+ * Yeast Mitochondrial (Table 3)
+ */
+ gc = GeneticCodes.getInstance().getCodeTable("3");
+ // CTN is L in standard code, T in table 3
+ assertEquals(gc.translate("ctn"), "T");
+ assertEquals(standard.translate("CTN"), "L");
+
+ /*
+ * Alternative Yeast Nuclear (Table 12)
+ */
+ gc = GeneticCodes.getInstance().getCodeTable("12");
+ // CTG is S; in the standard code CTN is L
+ assertEquals(gc.translate("CTG"), "S");
+ assertNull(gc.translate("CTK")); // K is G or T -> S or L
+ assertEquals(standard.translate("CTK"), "L");
+ assertEquals(gc.translate("CTH"), "L"); // H is anything other than G
+ assertEquals(standard.translate("CTH"), "L");
+ assertEquals(standard.translate("CTN"), "L");
+
+ /*
+ * Trematode Mitochondrial (Table 21)
+ */
+ gc = GeneticCodes.getInstance().getCodeTable("21");
+ // AAR is K in standard code, ambiguous in table 21 as AAA=N not K
+ assertNull(gc.translate("AAR"));
+ assertEquals(standard.translate("AAR"), "K");
+ }
+
+ @Test(groups = "Functional")
+ public void testTranslateCanonical()
+ {
+ GeneticCodes codes = GeneticCodes.getInstance();
+
+ GeneticCodeI gc = codes.getCodeTable("1");
+ assertNull(gc.translateCanonical("XYZ"));
+ assertEquals(gc.translateCanonical("AGA"), "R");
+ // translateCanonical should not resolve ambiguity codes
+ assertNull(gc.translateCanonical("TGY"));
+
+ gc = codes.getCodeTable("2");
+ assertNull(gc.translateCanonical("AGR"));
+ assertEquals(gc.translateCanonical("AGA"), "*"); // variant
+ assertEquals(gc.translateCanonical("ttc"), "F"); // non-variant
+ }
+}
double newScore = PIDModel.computePID(s1, s2, params);
double oldScore = Comparison.PID(s1, s2);
assertEquals(newScore, oldScore, DELTA);
+ // and verify PIDModel calculation is symmetric
+ assertEquals(newScore, PIDModel.computePID(s2, s1, params));
/*
* same length, with gaps
newScore = PIDModel.computePID(s1, s2, params);
oldScore = Comparison.PID(s1, s2);
assertEquals(newScore, oldScore, DELTA);
+ assertEquals(newScore, PIDModel.computePID(s2, s1, params));
/*
* s2 longer than s1, with gaps
newScore = PIDModel.computePID(s1, s2, params);
oldScore = Comparison.PID(s1, s2);
assertEquals(newScore, oldScore, DELTA);
+ assertEquals(newScore, PIDModel.computePID(s2, s1, params));
/*
* s1 longer than s2, with gaps
newScore = PIDModel.computePID(s1, s2, params);
oldScore = Comparison.PID(s1, s2);
assertEquals(newScore, oldScore, DELTA);
+ assertEquals(newScore, PIDModel.computePID(s2, s1, params));
/*
* same but now also with gapped columns
newScore = PIDModel.computePID(s1, s2, params);
oldScore = Comparison.PID(s1, s2);
assertEquals(newScore, oldScore, DELTA);
+ assertEquals(newScore, PIDModel.computePID(s2, s1, params));
}
/**
*/
SimilarityParamsI params = new SimilarityParams(true, true, true, true);
assertEquals(PIDModel.computePID(s1, s2, params), 80d);
+ assertEquals(PIDModel.computePID(s2, s1, params), 80d);
/*
* match gap-char but not gap-gap
*/
params = new SimilarityParams(false, true, true, true);
assertEquals(PIDModel.computePID(s1, s2, params), 75d);
+ assertEquals(PIDModel.computePID(s2, s1, params), 75d);
/*
* include gaps but don't match them
*/
params = new SimilarityParams(true, false, true, true);
assertEquals(PIDModel.computePID(s1, s2, params), 40d);
+ assertEquals(PIDModel.computePID(s2, s1, params), 40d);
/*
* include gaps but don't match them
*/
params = new SimilarityParams(false, false, true, true);
assertEquals(PIDModel.computePID(s1, s2, params), 25d);
+ assertEquals(PIDModel.computePID(s2, s1, params), 25d);
}
/**
*/
SimilarityParamsI params = new SimilarityParams(true, true, true, false);
assertEquals(PIDModel.computePID(s1, s2, params), 500d / 6);
+ assertEquals(PIDModel.computePID(s2, s1, params), 500d / 6);
/*
* match gap-char but not gap-gap
*/
params = new SimilarityParams(false, true, true, false);
assertEquals(PIDModel.computePID(s1, s2, params), 80d);
+ assertEquals(PIDModel.computePID(s2, s1, params), 80d);
/*
* include gaps but don't match them
*/
params = new SimilarityParams(true, false, true, false);
assertEquals(PIDModel.computePID(s1, s2, params), 100d / 3);
+ assertEquals(PIDModel.computePID(s2, s1, params), 100d / 3);
/*
* include gaps but don't match them
*/
params = new SimilarityParams(false, false, true, false);
assertEquals(PIDModel.computePID(s1, s2, params), 20d);
+ assertEquals(PIDModel.computePID(s2, s1, params), 20d);
/*
* no tests for matchGaps=true, includeGaps=false
import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.ScoreMatrixFile;
+import jalview.math.Matrix;
import jalview.math.MatrixI;
import jalview.schemes.ResidueProperties;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class ScoreMatrixTest
{
@Test(groups = "Functional")
scores[1] = new float[] { -4f, 5f, 6f };
scores[2] = new float[] { 7f, 8f, 9f };
ScoreMatrix sm = new ScoreMatrix("Test", "ABC".toCharArray(), scores);
+ assertFalse(sm.isSymmetric());
assertEquals(sm.getSize(), 3);
assertArrayEquals(scores, sm.getMatrix());
assertEquals(sm.getPairwiseScore('A', 'a'), 1f);
@Test(
groups = "Functional",
- expectedExceptions = { IllegalArgumentException.class })
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testConstructor_matrixTooSmall()
{
float[][] scores = new float[2][];
@Test(
groups = "Functional",
- expectedExceptions = { IllegalArgumentException.class })
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testConstructor_matrixTooBig()
{
float[][] scores = new float[2][];
@Test(
groups = "Functional",
- expectedExceptions = { IllegalArgumentException.class })
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testConstructor_matrixNotSquare()
{
float[][] scores = new float[2][];
* @throws MalformedURLException
*/
@Test(groups = "Functional")
- public void testOutputMatrix_roundTrip() throws MalformedURLException,
- IOException
+ public void testOutputMatrix_roundTrip()
+ throws MalformedURLException, IOException
{
ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
String output = sm.outputMatrix(false);
public void testEqualsAndHashCode()
{
ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
- ScoreMatrix sm2 = new ScoreMatrix(sm.getName(), sm.getSymbols()
- .toCharArray(), sm.getMatrix());
+ ScoreMatrix sm2 = new ScoreMatrix(sm.getName(),
+ sm.getSymbols().toCharArray(), sm.getMatrix());
assertTrue(sm.equals(sm2));
assertEquals(sm.hashCode(), sm2.hashCode());
String s1 = "FR-K-S";
String s2 = "FS--L";
ScoreMatrix blosum = ScoreModels.getInstance().getBlosum62();
-
+
/*
* score gap-gap and gap-char
* shorter sequence treated as if with trailing gaps
* score = F^F + R^S + -^- + K^- + -^L + S^-
* = 6 + -1 + 1 + -4 + -4 + -4 = -6
*/
- SimilarityParamsI params = new SimilarityParams(true, true, true, false);
+ SimilarityParamsI params = new SimilarityParams(true, true, true,
+ false);
assertEquals(blosum.computeSimilarity(s1, s2, params), -6d);
// matchGap (arg2) is ignored:
params = new SimilarityParams(true, false, true, false);
assertEquals(blosum.computeSimilarity(s1, s2, params), -6d);
-
+
/*
* score gap-char but not gap-gap
* score = F^F + R^S + 0 + K^- + -^L + S^-
// matchGap (arg2) is ignored:
params = new SimilarityParams(false, false, true, false);
assertEquals(blosum.computeSimilarity(s1, s2, params), -7d);
-
+
/*
* score gap-gap but not gap-char
* score = F^F + R^S + -^- + 0 + 0 + 0
// matchGap (arg2) is ignored:
params = new SimilarityParams(true, true, false, false);
assertEquals(blosum.computeSimilarity(s1, s2, params), 6d);
-
+
/*
* score neither gap-gap nor gap-char
* score = F^F + R^S + 0 + 0 + 0 + 0
// matchGap (arg2) is ignored:
params = new SimilarityParams(true, false, true, true);
assertEquals(blosum.computeSimilarity(s1, s2, params), -2d);
-
+
/*
* score gap-char but not gap-gap
* score = F^F + R^S + 0 + K^- + -^L
// matchGap (arg2) is ignored:
params = new SimilarityParams(false, false, true, true);
assertEquals(blosum.computeSimilarity(s1, s2, params), -3d);
-
+
/*
* score gap-gap but not gap-char
* score = F^F + R^S + -^- + 0 + 0
// matchGap (arg2) is ignored:
params = new SimilarityParams(true, true, false, true);
assertEquals(blosum.computeSimilarity(s1, s2, params), 6d);
-
+
/*
* score neither gap-gap nor gap-char
* score = F^F + R^S + 0 + 0 + 0
verifySymmetric(ScoreModels.getInstance().getDefaultModel(false)); // dna
}
+ /**
+ * A helper method that inspects a loaded matrix and reports any asymmetry as
+ * a test failure
+ *
+ * @param sm
+ */
private void verifySymmetric(ScoreMatrix sm)
{
float[][] m = sm.getMatrix();
assertEquals(m[row].length, rows);
for (int col = 0; col < rows; col++)
{
- assertEquals(m[row][col], m[col][row], String.format("%s [%s, %s]",
- sm.getName(), ResidueProperties.aa[row],
- ResidueProperties.aa[col]));
+ assertEquals(m[row][col], m[col][row],
+ String.format("%s [%s, %s]", sm.getName(),
+ ResidueProperties.aa[row],
+ ResidueProperties.aa[col]));
}
}
}
* verify expected scores against ARNDCQEGHILKMFPSTWYVBZX
* scraped from https://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt
*/
- verifyValues(sm, 'A', new float[] { 4, -1, -2, -2, 0, -1, -1, 0, -2,
- -1,
- -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0 });
- verifyValues(sm, 'R', new float[] { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3,
- -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1 });
- verifyValues(sm, 'N', new float[] { -2, 0, 6, 1, -3, 0, 0, 0, 1, -3,
- -3,
- 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1 });
- verifyValues(sm, 'D', new float[] { -2, -2, 1, 6, -3, 0, 2, -1, -1, -3,
- -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1 });
- verifyValues(sm, 'C', new float[] { 0, -3, -3, -3, 9, -3, -4, -3, -3,
- -1,
- -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2 });
- verifyValues(sm, 'Q', new float[] { -1, 1, 0, 0, -3, 5, 2, -2, 0, -3,
- -2,
- 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1 });
- verifyValues(sm, 'E', new float[] { -1, 0, 0, 2, -4, 2, 5, -2, 0, -3,
- -3,
- 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1 });
- verifyValues(sm, 'G', new float[] { 0, -2, 0, -1, -3, -2, -2, 6, -2,
- -4,
- -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1 });
- verifyValues(sm, 'H', new float[] { -2, 0, 1, -1, -3, 0, 0, -2, 8, -3,
- -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1 });
- verifyValues(sm, 'I', new float[] { -1, -3, -3, -3, -1, -3, -3, -4, -3,
- 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1 });
- verifyValues(sm, 'L', new float[] { -1, -2, -3, -4, -1, -2, -3, -4, -3,
- 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1 });
- verifyValues(sm, 'K', new float[] { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3,
- -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1 });
- verifyValues(sm, 'M', new float[] { -1, -1, -2, -3, -1, 0, -2, -3, -2,
- 1,
- 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1 });
- verifyValues(sm, 'F', new float[] { -2, -3, -3, -3, -2, -3, -3, -3, -1,
- 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1 });
- verifyValues(sm, 'P', new float[] { -1, -2, -2, -1, -3, -1, -1, -2, -2,
- -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2 });
- verifyValues(sm, 'S', new float[] { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2,
- -2,
- 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0 });
- verifyValues(sm, 'T', new float[] { 0, -1, 0, -1, -1, -1, -1, -2, -2,
- -1,
- -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0 });
- verifyValues(sm, 'W', new float[] { -3, -3, -4, -4, -2, -2, -3, -2, -2,
- -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2 });
- verifyValues(sm, 'Y', new float[] { -2, -2, -2, -3, -2, -1, -2, -3, 2,
- -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1 });
- verifyValues(sm, 'V', new float[] { 0, -3, -3, -3, -1, -2, -2, -3, -3,
- 3,
- 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1 });
- verifyValues(sm, 'B', new float[] { -2, -1, 3, 4, -3, 0, 1, -1, 0, -3,
- -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1 });
- verifyValues(sm, 'Z', new float[] { -1, 0, 0, 1, -3, 3, 4, -2, 0, -3,
- -3,
- 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1 });
- verifyValues(sm, 'X', new float[] { 0, -1, -1, -1, -2, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1 });
+ verifyValues(sm, 'A',
+ new float[]
+ { 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0,
+ -3, -2, 0, -2, -1, 0 });
+ verifyValues(sm, 'R',
+ new float[]
+ { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1,
+ -3, -2, -3, -1, 0, -1 });
+ verifyValues(sm, 'N',
+ new float[]
+ { -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4,
+ -2, -3, 3, 0, -1 });
+ verifyValues(sm, 'D',
+ new float[]
+ { -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1,
+ -4, -3, -3, 4, 1, -1 });
+ verifyValues(sm, 'C',
+ new float[]
+ { 0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1,
+ -1, -2, -2, -1, -3, -3, -2 });
+ verifyValues(sm, 'Q',
+ new float[]
+ { -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2,
+ -1, -2, 0, 3, -1 });
+ verifyValues(sm, 'E',
+ new float[]
+ { -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1,
+ -3, -2, -2, 1, 4, -1 });
+ verifyValues(sm, 'G',
+ new float[]
+ { 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0,
+ -2, -2, -3, -3, -1, -2, -1 });
+ verifyValues(sm, 'H',
+ new float[]
+ { -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2,
+ -2, 2, -3, 0, 0, -1 });
+ verifyValues(sm, 'I',
+ new float[]
+ { -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2,
+ -1, -3, -1, 3, -3, -3, -1 });
+ verifyValues(sm, 'L',
+ new float[]
+ { -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2,
+ -1, -2, -1, 1, -4, -3, -1 });
+ verifyValues(sm, 'K',
+ new float[]
+ { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1,
+ -3, -2, -2, 0, 1, -1 });
+ verifyValues(sm, 'M',
+ new float[]
+ { -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1,
+ -1, -1, 1, -3, -1, -1 });
+ verifyValues(sm, 'F',
+ new float[]
+ { -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2,
+ -2, 1, 3, -1, -3, -3, -1 });
+ verifyValues(sm, 'P',
+ new float[]
+ { -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1,
+ -1, -4, -3, -2, -2, -1, -2 });
+ verifyValues(sm, 'S',
+ new float[]
+ { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3,
+ -2, -2, 0, 0, 0 });
+ verifyValues(sm, 'T',
+ new float[]
+ { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1,
+ 5, -2, -2, 0, -1, -1, 0 });
+ verifyValues(sm, 'W',
+ new float[]
+ { -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3,
+ -2, 11, 2, -3, -4, -3, -2 });
+ verifyValues(sm, 'Y',
+ new float[]
+ { -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2,
+ -2, 2, 7, -1, -3, -2, -1 });
+ verifyValues(sm, 'V',
+ new float[]
+ { 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0,
+ -3, -1, 4, -3, -2, -1 });
+ verifyValues(sm, 'B',
+ new float[]
+ { -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1,
+ -4, -3, -3, 4, 1, -1 });
+ verifyValues(sm, 'Z',
+ new float[]
+ { -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1,
+ -3, -2, -2, 1, 4, -1 });
+ verifyValues(sm, 'X',
+ new float[]
+ { 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0,
+ 0, -2, -1, -1, -1, -1, -1 });
}
/**
+ "</table>";
assertEquals(html, expected);
}
+
+ @Test(groups = "Functional")
+ public void testIsSymmetric()
+ {
+ double delta = 0.0001d;
+ float[][] scores = new float[][] { { 1f, -2f }, { -2f, 3f } };
+ ScoreMatrix sm = new ScoreMatrix("Test", "AB".toCharArray(), scores);
+ assertTrue(sm.isSymmetric());
+
+ /*
+ * verify that with a symmetric score matrix,
+ * pairwise similarity matrix is also symmetric
+ * seq1.seq1 = 5*A.A + 3*B.B = 5+9 = 14
+ * seq1.seq2 = 3*A.A + 2*A.B + B.A + 2*B.B = 3 + -4 + -2 + 6 = 3
+ * seq2.seq1 = 3*A.A + A.B + 2*B.A + 2*B.B = 3 + -2 + -4 + 6 = 3
+ * seq2.seq2 = 4*A.A + 4*B.B = 4 + 12 = 16
+ */
+ SimilarityParamsI params = new SimilarityParams(true, true, true,
+ false);
+ String seq1 = "AAABBBAA";
+ String seq2 = "AABBABBA";
+ String[] seqs1 = new String[] { seq1, seq2 };
+ MatrixI res1 = sm.findSimilarities(seqs1, params);
+ assertTrue(
+ res1.equals(new Matrix(new double[][]
+ { { 14d, 3d }, { 3d, 16d } }), delta));
+
+ /*
+ * order of sequences affects diagonal, but not off-diagonal values
+ * [0, 0] is now seq2.seq2, [1, 1] is seq1.seq1
+ * [0, 1] is now seq2.seq1 = seq1.seq2 by symmetry
+ */
+ String[] seqs2 = new String[] { seq2, seq1 };
+ MatrixI res2 = sm.findSimilarities(seqs2, params);
+ assertFalse(res1.equals(res2));
+ assertTrue(res2.equals(new Matrix(new double[][]
+ { { 16d, 3d }, { 3d, 14d } }), delta));
+
+ /*
+ * now make the score matrix asymmetric
+ * seq1.seq1 = 5*A.A + 3*B.B = 5+9 = 14
+ * seq1.seq2 = 3*A.A + 2*A.B + B.A + 2*B.B = 3 + -4 + 2 + 6 = 7
+ * seq2.seq1 = 3*A.A + A.B + 2*B.A + 2*B.B = 3 + -2 + 4 + 6 = 11
+ * seq2.seq2 = 4*A.A + 4*B.B = 4 + 12 = 16
+ */
+ scores = new float[][] { { 1f, -2f }, { 2f, 3f } };
+ sm = new ScoreMatrix("Test", "AB".toCharArray(), scores);
+ assertFalse(sm.isSymmetric()); // [0, 1] != [1, 0]
+ res1 = sm.findSimilarities(seqs1, params);
+ assertTrue(res1.equals(new Matrix(new double[][]
+ { { 14d, 7d }, { 11d, 16d } }), delta));
+
+ /*
+ * reverse order of sequences
+ * - reverses order of main diagonal
+ * - reflects off-diagonal values
+ */
+ res2 = sm.findSimilarities(seqs2, params);
+ assertFalse(res1.equals(res2));
+ assertTrue(
+ res2.equals(new Matrix(new double[][]
+ { { 16d, 11d }, { 7d, 14d } }), delta));
+
+ /*
+ * verify that forcing an asymmetric matrix to use
+ * symmetric calculation gives a different (wrong) result
+ */
+ PA.setValue(sm, "symmetric", true);
+ assertTrue(sm.isSymmetric()); // it's not true!
+ res2 = sm.findSimilarities(seqs1, params);
+ assertFalse(res1.equals(res2, delta));
+ }
}
assertTrue(sm instanceof SimilarityScoreModel);
assertTrue(sm instanceof PairwiseScoreModelI);
assertFalse(sm instanceof DistanceScoreModel);
- assertEquals(sm.getName(), "PID");
- assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), 0f);
- assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'r'), 1f);
+ assertEquals(sm.getName(), "DNA");
+ assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('c', 'x'), 1f);
sm = models.next();
assertTrue(sm instanceof SimilarityScoreModel);
assertTrue(sm instanceof PairwiseScoreModelI);
assertFalse(sm instanceof DistanceScoreModel);
- assertEquals(sm.getName(), "DNA");
- assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('c', 'x'), 1f);
+ assertEquals(sm.getName(), "PID");
+ assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), 0f);
+ assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'r'), 1f);
sm = models.next();
assertFalse(sm instanceof SimilarityScoreModel);
"Failed command : -open examples/uniref50.fa" },
{ "CMD [-nosortbytree] executed successfully!",
"Failed command : -nosortbytree" },
- { "CMD [-dasserver nickname=www.test.com] executed successfully!",
- "Failed command : -dasserver nickname=www.test.com" },
- { "CMD [-features examples/testdata/plantfdx.features] executed successfully!",
+ {
+ "CMD [-features examples/testdata/plantfdx.features] executed successfully!",
"Failed command : -features examples/testdata/plantfdx.features" },
{ "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
"Failed command : -annotations examples/testdata/plantfdx.annotations" },
{ "CMD [-nousagestats] executed successfully!",
"Failed command : -nousagestats" },
{ "CMD [-noquestionnaire] executed successfully!",
- "Failed command : -noquestionnaire nickname=www.test.com" } };
+ "Failed command : -noquestionnaire" } };
}
package jalview.commands;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
import jalview.datamodel.features.SequenceFeatures;
import jalview.gui.JvOptionPane;
+import java.util.Collections;
+import java.util.Comparator;
import java.util.List;
import java.util.Map;
*/
public class EditCommandTest
{
+ private static Comparator<SequenceFeature> BY_DESCRIPTION = new Comparator<SequenceFeature>()
+ {
+
+ @Override
+ public int compare(SequenceFeature o1, SequenceFeature o2)
+ {
+ return o1.getDescription().compareTo(o2.getDescription());
+ }
+ };
+
+ private EditCommand testee;
+
+ private SequenceI[] seqs;
+
+ private Alignment al;
+
/*
* compute n(n+1)/2 e.g.
* func(5) = 5 + 4 + 3 + 2 + 1 = 15
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- private EditCommand testee;
-
- private SequenceI[] seqs;
-
- private Alignment al;
-
@BeforeMethod(alwaysRun = true)
public void setUp()
{
}
/**
- * Test a Paste action, where this adds sequences to an alignment.
+ * Test a Paste action, followed by Undo and Redo
*/
@Test(groups = { "Functional" }, enabled = false)
- // TODO fix so it works
- public void testPaste_addToAlignment()
+ public void testPaste_undo_redo()
{
+ // TODO code this test properly, bearing in mind that:
+ // Paste action requires something on the clipboard (Cut/Copy)
+ // - EditCommand.paste doesn't add sequences to the alignment
+ // ... that is done in AlignFrame.paste()
+ // ... unless as a Redo
+ // ...
+
SequenceI[] newSeqs = new SequenceI[2];
newSeqs[0] = new Sequence("newseq0", "ACEFKL");
newSeqs[1] = new Sequence("newseq1", "JWMPDH");
- Edit ec = testee.new Edit(Action.PASTE, newSeqs, 0, al.getWidth(), al);
- EditCommand.paste(ec, new AlignmentI[] { al });
+ new EditCommand("Paste", Action.PASTE, newSeqs, 0, al.getWidth(), al);
assertEquals(6, al.getSequences().size());
assertEquals("1234567890", seqs[3].getSequenceAsString());
assertEquals("ACEFKL", seqs[4].getSequenceAsString());
{
// seem to need a dataset sequence on the edited sequence here
seqs[1].createDatasetSequence();
- new EditCommand("", Action.REPLACE, "ZXY", new SequenceI[] { seqs[1] },
+ assertEquals("fghjklmnopq", seqs[1].getSequenceAsString());
+ // NB command.number holds end position for a Replace command
+ new EditCommand("", Action.REPLACE, "Z-xY", new SequenceI[] { seqs[1] },
4, 8, al);
assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
+ assertEquals("fghjZ-xYopq", seqs[1].getSequenceAsString());
+ assertEquals("fghjZxYopq",
+ seqs[1].getDatasetSequence().getSequenceAsString());
assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString());
assertEquals("1234567890", seqs[3].getSequenceAsString());
- seqs[1] = new Sequence("seq1", "fghjZXYnopq");
+ }
+
+ /**
+ * Test the replace command (used to manually edit a sequence)
+ */
+ @Test(groups = { "Functional" })
+ public void testReplace_withGaps()
+ {
+ SequenceI seq = new Sequence("seq", "ABC--DEF");
+ seq.createDatasetSequence();
+ assertEquals("ABCDEF", seq.getDatasetSequence().getSequenceAsString());
+ assertEquals(1, seq.getStart());
+ assertEquals(6, seq.getEnd());
+
+ /*
+ * replace C- with XYZ
+ * NB arg4 = start column of selection for edit (base 0)
+ * arg5 = column after end of selection for edit
+ */
+ EditCommand edit = new EditCommand("", Action.REPLACE, "xyZ",
+ new SequenceI[]
+ { seq }, 2,
+ 4, al);
+ assertEquals("ABxyZ-DEF", seq.getSequenceAsString());
+ assertEquals(1, seq.getStart());
+ assertEquals(8, seq.getEnd());
+ assertEquals("ABxyZDEF",
+ seq.getDatasetSequence().getSequenceAsString());
+ assertEquals(8, seq.getDatasetSequence().getEnd());
+
+ /*
+ * undo the edit
+ */
+ AlignmentI[] views = new AlignmentI[]
+ { new Alignment(new SequenceI[] { seq }) };
+ edit.undoCommand(views);
+
+ assertEquals("ABC--DEF", seq.getSequenceAsString());
+ assertEquals("ABCDEF", seq.getDatasetSequence().getSequenceAsString());
+ assertEquals(1, seq.getStart());
+ assertEquals(6, seq.getEnd());
+ assertEquals(6, seq.getDatasetSequence().getEnd());
+
+ /*
+ * redo the edit
+ */
+ edit.doCommand(views);
+
+ assertEquals("ABxyZ-DEF", seq.getSequenceAsString());
+ assertEquals(1, seq.getStart());
+ assertEquals(8, seq.getEnd());
+ assertEquals("ABxyZDEF",
+ seq.getDatasetSequence().getSequenceAsString());
+ assertEquals(8, seq.getDatasetSequence().getEnd());
+
+ }
+
+ /**
+ * Test replace command when it doesn't cause a sequence edit (see comment in
+ */
+ @Test(groups = { "Functional" })
+ public void testReplaceFirstResiduesWithGaps()
+ {
+ // test replace when gaps are inserted at start. Start/end should change
+ // w.r.t. original edited sequence.
+ SequenceI dsseq = seqs[1].getDatasetSequence();
+ EditCommand edit = new EditCommand("", Action.REPLACE, "----",
+ new SequenceI[]
+ { seqs[1] }, 0, 4, al);
+
+ // trimmed start
+ assertEquals("----klmnopq", seqs[1].getSequenceAsString());
+ // and ds is preserved
+ assertTrue(dsseq == seqs[1].getDatasetSequence());
+ // and it is unchanged
+ assertEquals("fghjklmnopq", dsseq.getSequenceAsString());
+ // and that alignment sequence start has been adjusted
+ assertEquals(5, seqs[1].getStart());
+ assertEquals(11, seqs[1].getEnd());
+
+ AlignmentI[] views = new AlignmentI[] { new Alignment(seqs) };
+ // and undo
+ edit.undoCommand(views);
+
+ // dataset sequence unchanged
+ assertTrue(dsseq == seqs[1].getDatasetSequence());
+ // restore sequence
+ assertEquals("fghjklmnopq", seqs[1].getSequenceAsString());
+ // and start/end numbering also restored
+ assertEquals(1, seqs[1].getStart());
+ assertEquals(11, seqs[1].getEnd());
+
+ // now redo
+ edit.undoCommand(views);
+
+ // and repeat asserts for the original edit
+
+ // trimmed start
+ assertEquals("----klmnopq", seqs[1].getSequenceAsString());
+ // and ds is preserved
+ assertTrue(dsseq == seqs[1].getDatasetSequence());
+ // and it is unchanged
+ assertEquals("fghjklmnopq", dsseq.getSequenceAsString());
+ // and that alignment sequence start has been adjusted
+ assertEquals(5, seqs[1].getStart());
+ assertEquals(11, seqs[1].getEnd());
+
}
/**
* create sequence features before, after and overlapping
* a cut of columns/residues 4-7
*/
- SequenceI seq0 = seqs[0];
+ SequenceI seq0 = seqs[0]; // abcdefghjk/1-10
seq0.addSequenceFeature(new SequenceFeature("before", "", 1, 3, 0f,
null));
seq0.addSequenceFeature(new SequenceFeature("overlap left", "", 2, 6,
seq0.addSequenceFeature(new SequenceFeature("after", "", 8, 10, 0f,
null));
+ /*
+ * add some contact features
+ */
+ SequenceFeature internalContact = new SequenceFeature("disulphide bond", "", 5,
+ 6, 0f, null);
+ seq0.addSequenceFeature(internalContact); // should get deleted
+ SequenceFeature overlapLeftContact = new SequenceFeature(
+ "disulphide bond", "", 2, 6, 0f, null);
+ seq0.addSequenceFeature(overlapLeftContact); // should get deleted
+ SequenceFeature overlapRightContact = new SequenceFeature(
+ "disulphide bond", "", 5, 8, 0f, null);
+ seq0.addSequenceFeature(overlapRightContact); // should get deleted
+ SequenceFeature spanningContact = new SequenceFeature(
+ "disulphide bond", "", 2, 9, 0f, null);
+ seq0.addSequenceFeature(spanningContact); // should get shortened 3'
+
+ /*
+ * cut columns 3-6 (base 0), residues d-g 4-7
+ */
Edit ec = testee.new Edit(Action.CUT, seqs, 3, 4, al); // cols 3-6 base 0
EditCommand.cut(ec, new AlignmentI[] { al });
List<SequenceFeature> sfs = seq0.getSequenceFeatures();
SequenceFeatures.sortFeatures(sfs, true);
- assertEquals(4, sfs.size()); // feature internal to cut has been deleted
+ assertEquals(5, sfs.size()); // features internal to cut were deleted
SequenceFeature sf = sfs.get(0);
assertEquals("before", sf.getType());
assertEquals(1, sf.getBegin());
assertEquals(3, sf.getEnd());
sf = sfs.get(1);
+ assertEquals("disulphide bond", sf.getType());
+ assertEquals(2, sf.getBegin());
+ assertEquals(5, sf.getEnd()); // truncated by cut
+ sf = sfs.get(2);
assertEquals("overlap left", sf.getType());
assertEquals(2, sf.getBegin());
assertEquals(3, sf.getEnd()); // truncated by cut
- sf = sfs.get(2);
- assertEquals("overlap right", sf.getType());
- assertEquals(4, sf.getBegin()); // shifted left by cut
- assertEquals(5, sf.getEnd()); // truncated by cut
sf = sfs.get(3);
assertEquals("after", sf.getType());
assertEquals(4, sf.getBegin()); // shifted left by cut
assertEquals(6, sf.getEnd()); // shifted left by cut
+ sf = sfs.get(4);
+ assertEquals("overlap right", sf.getType());
+ assertEquals(4, sf.getBegin()); // shifted left by cut
+ assertEquals(4, sf.getEnd()); // truncated by cut
}
/**
* create a sequence features on each subrange of 1-5
*/
SequenceI seq0 = new Sequence("seq", "ABCDE");
+ int start = 8;
+ int end = 12;
+ seq0.setStart(start);
+ seq0.setEnd(end);
AlignmentI alignment = new Alignment(new SequenceI[] { seq0 });
alignment.setDataset(null);
- for (int from = 1; from <= seq0.getLength(); from++)
+
+ /*
+ * create a new alignment with shared dataset sequence
+ */
+ AlignmentI copy = new Alignment(
+ new SequenceI[]
+ { alignment.getDataset().getSequenceAt(0).deriveSequence() });
+ SequenceI copySeq0 = copy.getSequenceAt(0);
+
+ for (int from = start; from <= end; from++)
{
- for (int to = from; to <= seq0.getLength(); to++)
+ for (int to = from; to <= end; to++)
{
String desc = String.format("%d-%d", from, to);
SequenceFeature sf = new SequenceFeature("test", desc, from, to,
- 0f,
- null);
+ 0f, null);
sf.setValue("from", Integer.valueOf(from));
sf.setValue("to", Integer.valueOf(to));
seq0.addSequenceFeature(sf);
// sanity check
List<SequenceFeature> sfs = seq0.getSequenceFeatures();
assertEquals(func(5), sfs.size());
+ assertEquals(sfs, copySeq0.getSequenceFeatures());
+ String copySequenceFeatures = copySeq0.getSequenceFeatures().toString();
/*
- * now perform all possible cuts of subranges of 1-5 (followed by Undo)
+ * now perform all possible cuts of subranges of columns 1-5
* and validate the resulting remaining sequence features!
*/
SequenceI[] sqs = new SequenceI[] { seq0 };
- // goal is to have this passing for all from/to values!!
- // for (int from = 0; from < seq0.getLength(); from++)
- // {
- // for (int to = from; to < seq0.getLength(); to++)
- for (int from = 1; from < 3; from++)
+ for (int from = 0; from < seq0.getLength(); from++)
{
- for (int to = 2; to < 3; to++)
+ for (int to = from; to < seq0.getLength(); to++)
{
- testee.appendEdit(Action.CUT, sqs, from, (to - from + 1),
- alignment, true);
+ EditCommand ec = new EditCommand("Cut", Action.CUT, sqs, from, (to
+ - from + 1), alignment);
+ final String msg = String.format("Cut %d-%d ", from + 1, to + 1);
+ boolean newDatasetSequence = copySeq0.getDatasetSequence() != seq0
+ .getDatasetSequence();
+
+ verifyCut(seq0, from, to, msg, start);
+
+ /*
+ * verify copy alignment dataset sequence unaffected
+ */
+ assertEquals("Original dataset sequence was modified",
+ copySequenceFeatures,
+ copySeq0.getSequenceFeatures().toString());
+ /*
+ * verify any new dataset sequence was added to the
+ * alignment dataset
+ */
+ assertEquals("Wrong Dataset size after " + msg,
+ newDatasetSequence ? 2 : 1,
+ alignment.getDataset().getHeight());
+
+ /*
+ * undo and verify all restored
+ */
+ AlignmentI[] views = new AlignmentI[] { alignment };
+ ec.undoCommand(views);
sfs = seq0.getSequenceFeatures();
+ assertEquals("After undo of " + msg, func(5), sfs.size());
+ verifyUndo(from, to, sfs);
+
+ /*
+ * verify copy alignment dataset sequence still unaffected
+ * and alignment dataset has shrunk (if it was added to)
+ */
+ assertEquals("Original dataset sequence was modified",
+ copySequenceFeatures,
+ copySeq0.getSequenceFeatures().toString());
+ assertEquals("Wrong Dataset size after Undo of " + msg, 1,
+ alignment.getDataset().getHeight());
/*
- * confirm the number of features has reduced by the
- * number of features within the cut region i.e. by
- * func(length of cut)
+ * redo and verify
*/
- String msg = String.format("Cut %d-%d ", from, to);
- if (to - from == 4)
- {
- // all columns cut
- assertNull(sfs);
- }
- else
- {
- assertEquals(msg + "wrong number of features left", func(5)
- - func(to - from + 1), sfs.size());
- }
+ ec.doCommand(views);
+ verifyCut(seq0, from, to, msg, start);
/*
- * inspect individual features
+ * verify copy alignment dataset sequence unaffected
+ * and any new dataset sequence readded to alignment dataset
*/
- if (sfs != null)
- {
- for (SequenceFeature sf : sfs)
- {
- checkFeatureRelocation(sf, from + 1, to + 1);
- }
- }
+ assertEquals("Original dataset sequence was modified",
+ copySequenceFeatures,
+ copySeq0.getSequenceFeatures().toString());
+ assertEquals("Wrong Dataset size after Redo of " + msg,
+ newDatasetSequence ? 2 : 1,
+ alignment.getDataset().getHeight());
+
/*
* undo ready for next cut
*/
- testee.undoCommand(new AlignmentI[] { alignment });
- assertEquals(func(5), seq0.getSequenceFeatures().size());
+ ec.undoCommand(views);
+
+ /*
+ * final verify that copy alignment dataset sequence is still unaffected
+ * and that alignment dataset has shrunk
+ */
+ assertEquals("Original dataset sequence was modified",
+ copySequenceFeatures,
+ copySeq0.getSequenceFeatures().toString());
+ assertEquals("Wrong Dataset size after final Undo of " + msg, 1,
+ alignment.getDataset().getHeight());
}
}
}
/**
+ * Verify by inspection that the sequence features left on the sequence after
+ * a cut match the expected results. The trick to this is that we can parse
+ * each feature's original start-end positions from its description.
+ *
+ * @param seq0
+ * @param from
+ * @param to
+ * @param msg
+ * @param seqStart
+ */
+ protected void verifyCut(SequenceI seq0, int from, int to,
+ final String msg, int seqStart)
+ {
+ List<SequenceFeature> sfs;
+ sfs = seq0.getSequenceFeatures();
+
+ Collections.sort(sfs, BY_DESCRIPTION);
+
+ /*
+ * confirm the number of features has reduced by the
+ * number of features within the cut region i.e. by
+ * func(length of cut); exception is a cut at start or end of sequence,
+ * which retains the original coordinates, dataset sequence
+ * and all its features
+ */
+ boolean datasetRetained = from == 0 || to == 4;
+ if (datasetRetained)
+ {
+ // dataset and all features retained
+ assertEquals(msg, func(5), sfs.size());
+ }
+ else if (to - from == 4)
+ {
+ // all columns were cut
+ assertTrue(sfs.isEmpty());
+ }
+ else
+ {
+ // failure in checkFeatureRelocation is more informative!
+ assertEquals(msg + "wrong number of features left", func(5)
+ - func(to - from + 1), sfs.size());
+ }
+
+ /*
+ * inspect individual features
+ */
+ for (SequenceFeature sf : sfs)
+ {
+ verifyFeatureRelocation(sf, from + 1, to + 1, !datasetRetained,
+ seqStart);
+ }
+ }
+
+ /**
+ * Check that after Undo, every feature has start/end that match its original
+ * "start" and "end" properties
+ *
+ * @param from
+ * @param to
+ * @param sfs
+ */
+ protected void verifyUndo(int from, int to, List<SequenceFeature> sfs)
+ {
+ for (SequenceFeature sf : sfs)
+ {
+ final int oldFrom = ((Integer) sf.getValue("from")).intValue();
+ final int oldTo = ((Integer) sf.getValue("to")).intValue();
+ String msg = String.format(
+ "Undo cut of [%d-%d], feature at [%d-%d] ", from + 1, to + 1,
+ oldFrom, oldTo);
+ assertEquals(msg + "start", oldFrom, sf.getBegin());
+ assertEquals(msg + "end", oldTo, sf.getEnd());
+ }
+ }
+
+ /**
* Helper method to check a feature has been correctly relocated after a cut
*
* @param sf
* @param from
- * start of cut (first residue cut)
+ * start of cut (first residue cut 1..)
* @param to
- * end of cut (last residue cut)
+ * end of cut (last residue cut 1..)
+ * @param newDataset
+ * @param seqStart
*/
- private void checkFeatureRelocation(SequenceFeature sf, int from, int to)
+ private void verifyFeatureRelocation(SequenceFeature sf, int from, int to,
+ boolean newDataset, int seqStart)
{
// TODO handle the gapped sequence case as well
int cutSize = to - from + 1;
- int oldFrom = ((Integer) sf.getValue("from")).intValue();
- int oldTo = ((Integer) sf.getValue("to")).intValue();
+ final int oldFrom = ((Integer) sf.getValue("from")).intValue();
+ final int oldTo = ((Integer) sf.getValue("to")).intValue();
+ final int oldFromPosition = oldFrom - seqStart + 1; // 1..
+ final int oldToPosition = oldTo - seqStart + 1; // 1..
String msg = String.format(
"Feature %s relocated to %d-%d after cut of %d-%d",
sf.getDescription(), sf.getBegin(), sf.getEnd(), from, to);
- if (oldTo < from)
+ if (!newDataset)
+ {
+ // dataset retained with all features unchanged
+ assertEquals("0: " + msg, oldFrom, sf.getBegin());
+ assertEquals("0: " + msg, oldTo, sf.getEnd());
+ }
+ else if (oldToPosition < from)
{
// before cut region so unchanged
assertEquals("1: " + msg, oldFrom, sf.getBegin());
assertEquals("2: " + msg, oldTo, sf.getEnd());
}
- else if (oldFrom > to)
+ else if (oldFromPosition > to)
{
// follows cut region - shift by size of cut
- assertEquals("3: " + msg, oldFrom - cutSize, sf.getBegin());
- assertEquals("4: " + msg, oldTo - cutSize, sf.getEnd());
+ assertEquals("3: " + msg, newDataset ? oldFrom - cutSize : oldFrom,
+ sf.getBegin());
+ assertEquals("4: " + msg, newDataset ? oldTo - cutSize : oldTo,
+ sf.getEnd());
}
- else if (oldFrom < from && oldTo > to)
+ else if (oldFromPosition < from && oldToPosition > to)
{
// feature encloses cut region - shrink it right
assertEquals("5: " + msg, oldFrom, sf.getBegin());
assertEquals("6: " + msg, oldTo - cutSize, sf.getEnd());
}
- else if (oldFrom < from)
+ else if (oldFromPosition < from)
{
// feature overlaps left side of cut region - truncated right
- assertEquals("7: " + msg, from - 1, sf.getEnd());
+ assertEquals("7: " + msg, from - 1 + seqStart - 1, sf.getEnd());
}
- else if (oldTo > to)
+ else if (oldToPosition > to)
{
// feature overlaps right side of cut region - truncated left
- assertEquals("8: " + msg, from, sf.getBegin());
- assertEquals("9: " + msg, from + oldTo - to - 1, sf.getEnd());
+ assertEquals("8: " + msg, newDataset ? from + seqStart - 1 : to + 1,
+ sf.getBegin());
+ assertEquals("9: " + msg, newDataset ? from + oldTo - to - 1 : oldTo,
+ sf.getEnd());
}
else
{
* Test a cut action's relocation of sequence features
*/
@Test(groups = { "Functional" })
- public void testCut_gappedWithFeatures()
+ public void testCut_withFeatures5prime()
{
+ SequenceI seq0 = new Sequence("seq/8-11", "A-BCC");
+ seq0.createDatasetSequence();
+ assertEquals(8, seq0.getStart());
+ seq0.addSequenceFeature(new SequenceFeature("", "", 10, 11, 0f,
+ null));
+ SequenceI[] seqsArray = new SequenceI[] { seq0 };
+ AlignmentI alignment = new Alignment(seqsArray);
+
/*
- * create sequence features before, after and overlapping
- * a cut of columns/residues 4-7
+ * cut columns of A-B; same dataset sequence is retained, aligned sequence
+ * start becomes 10
*/
- SequenceI seq0 = new Sequence("seq", "A-BCC");
- seq0.addSequenceFeature(new SequenceFeature("", "", 3, 4, 0f,
- null));
- AlignmentI alignment = new Alignment(new SequenceI[] { seq0 });
- // cut columns of A-B
- Edit ec = testee.new Edit(Action.CUT, seqs, 0, 3, alignment); // cols 0-3
- // base 0
+ Edit ec = testee.new Edit(Action.CUT, seqsArray, 0, 3, alignment);
EditCommand.cut(ec, new AlignmentI[] { alignment });
/*
- * feature on CC(3-4) should now be on CC(1-2)
+ * feature on CC(10-11) should still be on CC(10-11)
*/
+ assertSame(seq0, alignment.getSequenceAt(0));
+ assertEquals(10, seq0.getStart());
List<SequenceFeature> sfs = seq0.getSequenceFeatures();
assertEquals(1, sfs.size());
SequenceFeature sf = sfs.get(0);
- assertEquals(1, sf.getBegin());
- assertEquals(2, sf.getEnd());
-
- // TODO add further cases including Undo - see JAL-2541
+ assertEquals(10, sf.getBegin());
+ assertEquals(11, sf.getEnd());
}
}
import jalview.analysis.Finder;
import jalview.api.AlignViewControllerI;
import jalview.api.FeatureColourI;
+import jalview.api.FinderI;
import jalview.datamodel.Alignment;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
* seq1 feature in columns 4-6 is hidden
* seq2 feature in columns 6-7 is shown
*/
- FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f);
+ FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
+ 0f, 10f);
fc.setAboveThreshold(true);
fc.setThreshold(5f);
af.getFeatureRenderer().setColour("Metal", fc);
/*
* test Match/Find works first
*/
- Finder f = new Finder(af.getViewport().getAlignment(), null);
- f.setFindAll(true);
- f.setCaseSensitive(true);
- f.find("M+");
+ FinderI f = new Finder(af.getViewport());
+ f.findAll("M+", true, false);
assertEquals(
"Finder found different set of results to manually created SearchResults",
sr, f.getSearchResults());
assertEquals(".JKLMNO", seq2.getSequenceAsString());
assertEquals(".PQR...", seq3.getSequenceAsString());
}
+
+ /**
+ * Test for setHiddenColumns, to check it returns true if the hidden columns
+ * have changed, else false
+ */
+ @Test(groups = { "Functional" })
+ public void testSetHiddenColumns()
+ {
+ AlignmentI al = new Alignment(new SequenceI[] {});
+ assertFalse(al.getHiddenColumns().hasHiddenColumns());
+
+ HiddenColumns hc = new HiddenColumns();
+ assertFalse(al.setHiddenColumns(hc)); // no change
+ assertSame(hc, al.getHiddenColumns());
+
+ hc.hideColumns(2, 4);
+ assertTrue(al.getHiddenColumns().hasHiddenColumns());
+
+ /*
+ * set a different object but with the same columns hidden
+ */
+ HiddenColumns hc2 = new HiddenColumns();
+ hc2.hideColumns(2, 4);
+ assertFalse(al.setHiddenColumns(hc2)); // no change
+ assertSame(hc2, al.getHiddenColumns());
+
+ assertTrue(al.setHiddenColumns(null));
+ assertNull(al.getHiddenColumns());
+ assertTrue(al.setHiddenColumns(hc));
+ assertSame(hc, al.getHiddenColumns());
+
+ al.getHiddenColumns().hideColumns(10, 12);
+ hc2.hideColumns(10, 12);
+ assertFalse(al.setHiddenColumns(hc2)); // no change
+
+ /*
+ * hide columns 15-16 then 17-18 in hc
+ * hide columns 15-18 in hc2
+ * these are not now 'equal' objects even though they
+ * represent the same set of columns
+ */
+ assertSame(hc2, al.getHiddenColumns());
+ hc.hideColumns(15, 16);
+ hc.hideColumns(17, 18);
+ hc2.hideColumns(15, 18);
+ assertFalse(hc.equals(hc2));
+ assertTrue(al.setHiddenColumns(hc)); // 'changed'
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetWidth()
+ {
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+ SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+ SequenceI seq3 = new Sequence("seq2", "-PQR");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+ assertEquals(9, a.getWidth());
+
+ // width includes hidden columns
+ a.getHiddenColumns().hideColumns(2, 5);
+ assertEquals(9, a.getWidth());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetVisibleWidth()
+ {
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+ SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+ SequenceI seq3 = new Sequence("seq2", "-PQR");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+ assertEquals(9, a.getVisibleWidth());
+
+ // width excludes hidden columns
+ a.getHiddenColumns().hideColumns(2, 5);
+ assertEquals(5, a.getVisibleWidth());
+ }
}
{
HiddenColumns hiddenCols;
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public void setup()
{
hiddenCols = new HiddenColumns();
- hiddenCols.hideColumns(2,4);
+ hiddenCols.hideColumns(2, 4);
}
Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<>();
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public void setup()
{
// create random alignment
import jalview.analysis.AlignmentGenerator;
import jalview.gui.JvOptionPane;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType;
import java.util.Arrays;
import java.util.BitSet;
assertEquals(sg.getStartRes(), 10);
assertEquals(sg.getEndRes(), 19);
}
+
+ @Test(groups = { "Functional" })
+ public void testFilterAnnotations()
+ {
+ ColumnSelection cs = new ColumnSelection();
+
+ /*
+ * filter with no conditions clears the selection
+ */
+ Annotation[] anns = new Annotation[] { null };
+ AnnotationFilterParameter filter = new AnnotationFilterParameter();
+ cs.addElement(3);
+ int added = cs.filterAnnotations(anns, filter);
+ assertEquals(0, added);
+ assertTrue(cs.isEmpty());
+
+ /*
+ * select on description (regex)
+ */
+ filter.setRegexString("w.rld");
+ filter.addRegexSearchField(SearchableAnnotationField.DESCRIPTION);
+ Annotation helix = new Annotation("(", "hello", '<', 2f);
+ Annotation sheet = new Annotation("(", "world", '<', 2f);
+ added = cs.filterAnnotations(new Annotation[] { null, helix, sheet },
+ filter);
+ assertEquals(1, added);
+ assertTrue(cs.contains(2));
+
+ /*
+ * select on label (invalid regex, exact match)
+ */
+ filter = new AnnotationFilterParameter();
+ filter.setRegexString("(");
+ filter.addRegexSearchField(SearchableAnnotationField.DISPLAY_STRING);
+ added = cs.filterAnnotations(new Annotation[] { null, helix, sheet },
+ filter);
+ assertEquals(2, added);
+ assertTrue(cs.contains(1));
+ assertTrue(cs.contains(2));
+
+ /*
+ * select Helix (secondary structure symbol H)
+ */
+ filter = new AnnotationFilterParameter();
+ filter.setFilterAlphaHelix(true);
+ helix = new Annotation("x", "desc", 'H', 0f);
+ sheet = new Annotation("x", "desc", 'E', 1f);
+ Annotation turn = new Annotation("x", "desc", 'S', 2f);
+ Annotation ann4 = new Annotation("x", "desc", 'Y', 3f);
+ added = cs
+ .filterAnnotations(new Annotation[]
+ { null, helix, sheet, turn, ann4 },
+ filter);
+ assertEquals(1, added);
+ assertTrue(cs.contains(1));
+
+ /*
+ * select Helix and Sheet (E)
+ */
+ filter.setFilterBetaSheet(true);
+ added = cs
+ .filterAnnotations(new Annotation[]
+ { null, helix, sheet, turn, ann4 }, filter);
+ assertEquals(2, added);
+ assertTrue(cs.contains(1));
+ assertTrue(cs.contains(2));
+
+ /*
+ * select Sheet and Turn (S)
+ */
+ filter.setFilterAlphaHelix(false);
+ filter.setFilterTurn(true);
+ added = cs
+ .filterAnnotations(new Annotation[]
+ { null, helix, sheet, turn, ann4 }, filter);
+ assertEquals(2, added);
+ assertTrue(cs.contains(2));
+ assertTrue(cs.contains(3));
+
+ /*
+ * select value < 2f (ann1, ann2)
+ */
+ filter = new AnnotationFilterParameter();
+ filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
+ filter.setThresholdValue(2f);
+ added = cs
+ .filterAnnotations(new Annotation[]
+ { null, helix, sheet, turn, ann4 }, filter);
+ assertEquals(2, added);
+ assertTrue(cs.contains(1));
+ assertTrue(cs.contains(2));
+
+ /*
+ * select value > 2f (ann4 only)
+ */
+ filter.setThresholdType(ThresholdType.ABOVE_THRESHOLD);
+ added = cs
+ .filterAnnotations(new Annotation[]
+ { null, helix, sheet, turn, ann4 }, filter);
+ assertEquals(1, added);
+ assertTrue(cs.contains(4));
+
+ /*
+ * select >2f or Helix
+ */
+ filter.setFilterAlphaHelix(true);
+ added = cs
+ .filterAnnotations(new Annotation[]
+ { null, helix, sheet, turn, ann4 }, filter);
+ assertEquals(2, added);
+ assertTrue(cs.contains(1));
+ assertTrue(cs.contains(4));
+
+ /*
+ * select < 1f or Helix; one annotation matches both
+ * return value should only count it once
+ */
+ filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
+ filter.setThresholdValue(1f);
+ added = cs
+ .filterAnnotations(new Annotation[]
+ { null, helix, sheet, turn, ann4 }, filter);
+ assertEquals(1, added);
+ assertTrue(cs.contains(1));
+ }
}
assertEquals(5, m.getEnd());
}
+ @Test(groups = { "Functional" })
+ public void testMatchContains()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SequenceI seq2 = new Sequence("", "abcdefghijklm");
+ SearchResultMatchI m = new SearchResults().new Match(seq1, 2, 5);
+
+ assertTrue(m.contains(seq1, 2, 5));
+ assertTrue(m.contains(seq1, 3, 5));
+ assertTrue(m.contains(seq1, 2, 4));
+ assertTrue(m.contains(seq1, 3, 3));
+
+ assertFalse(m.contains(seq1, 2, 6));
+ assertFalse(m.contains(seq1, 1, 5));
+ assertFalse(m.contains(seq1, 1, 8));
+ assertFalse(m.contains(seq2, 3, 3));
+ assertFalse(m.contains(null, 3, 3));
+ }
+
/**
* test markColumns for creating column selections
*/
"Didn't set expected number of columns in total for two successive marks",
2, tbs.cardinality());
}
+
+ /**
+ * Test to verify adding doesn't create duplicate results
+ */
+ @Test(groups = { "Functional" })
+ public void testAddResult()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SearchResultsI sr = new SearchResults();
+ sr.addResult(seq1, 3, 5);
+ assertEquals(1, sr.getSize());
+ sr.addResult(seq1, 3, 5);
+ assertEquals(1, sr.getSize());
+ sr.addResult(seq1, 3, 6);
+ assertEquals(2, sr.getSize());
+ }
}
import jalview.schemes.PIDColourScheme;
import java.awt.Color;
+import java.util.ArrayList;
import java.util.Collections;
-
-import junit.extensions.PA;
+import java.util.List;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class SequenceGroupTest
{
@Test(groups={"Functional"})
*/
assertNull(sg2.getContext());
}
+
+ @Test(groups = { "Functional" })
+ public void testConstructor_list()
+ {
+ SequenceI s1 = new Sequence("abcde", "fg");
+ SequenceI s2 = new Sequence("foo", "bar");
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
+ seqs.add(s1);
+ seqs.add(s2);
+ SequenceGroup sg = new SequenceGroup(seqs);
+
+ /*
+ * verify sg has a copy of the original list
+ */
+ List<SequenceI> sgList = sg.getSequences();
+ assertNotSame(sgList, seqs);
+ assertEquals(sgList, seqs);
+
+ /*
+ * add to sgList, original is unchanged
+ */
+ sg.addSequence(new Sequence("bar", "foo"), false);
+ assertEquals(sgList.size(), 3);
+ assertEquals(seqs.size(), 2);
+
+ /*
+ * delete from original, sgList is unchanged
+ */
+ seqs.remove(s1);
+ assertEquals(sgList.size(), 3);
+ assertEquals(seqs.size(), 1);
+ }
}
public class SequenceTest
{
-
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
assertEquals(0, sq.findIndex(2));
}
+ @Test(groups = { "Functional" })
+ public void testFindPositions()
+ {
+ SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
+
+ /*
+ * invalid inputs
+ */
+ assertNull(sq.findPositions(6, 5));
+ assertNull(sq.findPositions(0, 5));
+ assertNull(sq.findPositions(-1, 5));
+
+ /*
+ * all gapped ranges
+ */
+ assertNull(sq.findPositions(1, 1)); // 1-based columns
+ assertNull(sq.findPositions(5, 5));
+ assertNull(sq.findPositions(5, 6));
+ assertNull(sq.findPositions(5, 7));
+
+ /*
+ * all ungapped ranges
+ */
+ assertEquals(new Range(8, 8), sq.findPositions(2, 2)); // A
+ assertEquals(new Range(8, 9), sq.findPositions(2, 3)); // AB
+ assertEquals(new Range(8, 10), sq.findPositions(2, 4)); // ABC
+ assertEquals(new Range(9, 10), sq.findPositions(3, 4)); // BC
+
+ /*
+ * gap to ungapped range
+ */
+ assertEquals(new Range(8, 10), sq.findPositions(1, 4)); // ABC
+ assertEquals(new Range(11, 12), sq.findPositions(6, 9)); // DE
+
+ /*
+ * ungapped to gapped range
+ */
+ assertEquals(new Range(10, 10), sq.findPositions(4, 5)); // C
+ assertEquals(new Range(9, 13), sq.findPositions(3, 11)); // BCDEF
+
+ /*
+ * ungapped to ungapped enclosing gaps
+ */
+ assertEquals(new Range(10, 11), sq.findPositions(4, 8)); // CD
+ assertEquals(new Range(8, 13), sq.findPositions(2, 11)); // ABCDEF
+
+ /*
+ * gapped to gapped enclosing ungapped
+ */
+ assertEquals(new Range(8, 10), sq.findPositions(1, 5)); // ABC
+ assertEquals(new Range(11, 12), sq.findPositions(5, 10)); // DE
+ assertEquals(new Range(8, 13), sq.findPositions(1, 13)); // the lot
+ assertEquals(new Range(8, 13), sq.findPositions(1, 99));
+ }
+
/**
* Tests for the method that returns a dataset sequence position (start..) for
* an aligned column position (base 0).
assertEquals("test:Pos13:Col10:startCol3:endCol10:tok0",
PA.getValue(sq, "cursor").toString());
sq.sequenceChanged();
- assertEquals(12, sq.findPosition(8));
- cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(12, sq.findPosition(8)); // E12
// sequenceChanged() invalidates cursor.lastResidueColumn
cursor = (SequenceCursor) PA.getValue(sq, "cursor");
assertEquals("test:Pos12:Col9:startCol3:endCol0:tok1",
assertEquals(6, sq.getEnd());
assertNull(PA.getValue(sq, "datasetSequence"));
+ sq = new Sequence("test", "ABCDE");
+ sq.deleteChars(0, 3);
+ assertEquals("DE", sq.getSequenceAsString());
+ assertEquals(4, sq.getStart());
+ assertEquals(5, sq.getEnd());
+ assertNull(PA.getValue(sq, "datasetSequence"));
+
/*
* delete at end
*/
assertEquals(1, sq.getStart());
assertEquals(4, sq.getEnd());
assertNull(PA.getValue(sq, "datasetSequence"));
+
+ /*
+ * delete more positions than there are
+ */
+ sq = new Sequence("test/8-11", "ABCD");
+ sq.deleteChars(0, 99);
+ assertEquals("", sq.getSequenceAsString());
+ assertEquals(12, sq.getStart()); // = findPosition(99) ?!?
+ assertEquals(11, sq.getEnd());
+
+ sq = new Sequence("test/8-11", "----");
+ sq.deleteChars(0, 99); // ArrayIndexOutOfBoundsException <= 2.10.2
+ assertEquals("", sq.getSequenceAsString());
+ assertEquals(8, sq.getStart());
+ assertEquals(11, sq.getEnd());
}
@Test(groups = { "Functional" })
// cursor should now be at [D 6]
cursor = (SequenceCursor) PA.getValue(sq, "cursor");
assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor);
+ assertEquals(0, cursor.lastColumnPosition); // not yet found
+ assertEquals(13, sq.findPosition(8)); // E13
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(9, cursor.lastColumnPosition); // found
/*
* deleteChars should invalidate the cached cursor
}
@Test(groups = { "Functional" })
- public void testFindPositions()
- {
- SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
-
- /*
- * invalid inputs
- */
- assertNull(sq.findPositions(6, 5));
- assertNull(sq.findPositions(0, 5));
- assertNull(sq.findPositions(-1, 5));
-
- /*
- * all gapped ranges
- */
- assertNull(sq.findPositions(1, 1)); // 1-based columns
- assertNull(sq.findPositions(5, 5));
- assertNull(sq.findPositions(5, 6));
- assertNull(sq.findPositions(5, 7));
-
- /*
- * all ungapped ranges
- */
- assertEquals(new Range(8, 8), sq.findPositions(2, 2)); // A
- assertEquals(new Range(8, 9), sq.findPositions(2, 3)); // AB
- assertEquals(new Range(8, 10), sq.findPositions(2, 4)); // ABC
- assertEquals(new Range(9, 10), sq.findPositions(3, 4)); // BC
-
- /*
- * gap to ungapped range
- */
- assertEquals(new Range(8, 10), sq.findPositions(1, 4)); // ABC
- assertEquals(new Range(11, 12), sq.findPositions(6, 9)); // DE
-
- /*
- * ungapped to gapped range
- */
- assertEquals(new Range(10, 10), sq.findPositions(4, 5)); // C
- assertEquals(new Range(9, 13), sq.findPositions(3, 11)); // BCDEF
-
- /*
- * ungapped to ungapped enclosing gaps
- */
- assertEquals(new Range(10, 11), sq.findPositions(4, 8)); // CD
- assertEquals(new Range(8, 13), sq.findPositions(2, 11)); // ABCDEF
-
- /*
- * gapped to gapped enclosing ungapped
- */
- assertEquals(new Range(8, 10), sq.findPositions(1, 5)); // ABC
- assertEquals(new Range(11, 12), sq.findPositions(5, 10)); // DE
- assertEquals(new Range(8, 13), sq.findPositions(1, 13)); // the lot
- assertEquals(new Range(8, 13), sq.findPositions(1, 99));
- }
-
- @Test(groups = { "Functional" })
public void testGapBitset()
{
SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
import jalview.datamodel.SequenceFeature;
assertTrue(overlaps.contains(sf));
}
- /**
- * Tests for the method that returns false for an attempt to add a feature
- * that would enclose, or be enclosed by, another feature
- */
- @Test(groups = "Functional")
- public void testAddNonNestedFeature()
- {
- FeatureStore fs = new FeatureStore();
-
- String type = "Domain";
- SequenceFeature sf1 = new SequenceFeature(type, type, 10, 20,
- Float.NaN, null);
- assertTrue(fs.addNonNestedFeature(sf1));
-
- // co-located feature is ok
- SequenceFeature sf2 = new SequenceFeature(type, type, 10, 20,
- Float.NaN, null);
- assertTrue(fs.addNonNestedFeature(sf2));
-
- // overlap left is ok
- SequenceFeature sf3 = new SequenceFeature(type, type, 5, 15, Float.NaN,
- null);
- assertTrue(fs.addNonNestedFeature(sf3));
-
- // overlap right is ok
- SequenceFeature sf4 = new SequenceFeature(type, type, 15, 25,
- Float.NaN, null);
- assertTrue(fs.addNonNestedFeature(sf4));
-
- // add enclosing feature is not ok
- SequenceFeature sf5 = new SequenceFeature(type, type, 10, 21,
- Float.NaN, null);
- assertFalse(fs.addNonNestedFeature(sf5));
- SequenceFeature sf6 = new SequenceFeature(type, type, 4, 15, Float.NaN,
- null);
- assertFalse(fs.addNonNestedFeature(sf6));
- SequenceFeature sf7 = new SequenceFeature(type, type, 1, 50, Float.NaN,
- null);
- assertFalse(fs.addNonNestedFeature(sf7));
-
- // add enclosed feature is not ok
- SequenceFeature sf8 = new SequenceFeature(type, type, 10, 19,
- Float.NaN, null);
- assertFalse(fs.addNonNestedFeature(sf8));
- SequenceFeature sf9 = new SequenceFeature(type, type, 16, 25,
- Float.NaN, null);
- assertFalse(fs.addNonNestedFeature(sf9));
- SequenceFeature sf10 = new SequenceFeature(type, type, 7, 7, Float.NaN,
- null);
- assertFalse(fs.addNonNestedFeature(sf10));
- }
-
@Test(groups = "Functional")
public void testGetPositionalFeatures()
{
assertEquals(fs.getFeatureCount(true), 3);
assertTrue(fs.delete(sf1));
assertEquals(fs.getFeatureCount(true), 2);
- // FeatureStore should now only contain features in the NCList
- assertTrue(fs.nonNestedFeatures.isEmpty());
- assertEquals(fs.nestedFeatures.size(), 2);
+ assertEquals(fs.features.size(), 2);
assertFalse(fs.isEmpty());
assertTrue(fs.delete(sf2));
assertEquals(fs.getFeatureCount(true), 1);
public void testListContains()
{
assertFalse(FeatureStore.listContains(null, null));
- List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> features = new ArrayList<>();
assertFalse(FeatureStore.listContains(features, null));
SequenceFeature sf1 = new SequenceFeature("type1", "desc1", 20, 30, 3f,
public void testShiftFeatures()
{
FeatureStore fs = new FeatureStore();
- assertFalse(fs.shiftFeatures(1));
+ assertFalse(fs.shiftFeatures(0, 1)); // nothing to do
SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
fs.addFeature(sf1);
fs.addFeature(sf4);
/*
- * shift features right by 5
+ * shift all features right by 5
*/
- assertTrue(fs.shiftFeatures(5));
+ assertTrue(fs.shiftFeatures(0, 5));
// non-positional features untouched:
List<SequenceFeature> nonPos = fs.getNonPositionalFeatures();
* feature at [7-10] should be removed
* feature at [13-19] should become [1-4]
*/
- assertTrue(fs.shiftFeatures(-15));
+ assertTrue(fs.shiftFeatures(0, -15));
pos = fs.getPositionalFeatures();
assertEquals(pos.size(), 2);
SequenceFeatures.sortFeatures(pos, true);
assertEquals(pos.get(0).getEnd(), 4);
assertEquals(pos.get(1).getBegin(), 13);
assertEquals(pos.get(1).getEnd(), 22);
+
+ /*
+ * shift right by 4 from position 2 onwards
+ * feature at [1-4] unchanged, feature at [13-22] shifts
+ */
+ assertTrue(fs.shiftFeatures(2, 4));
+ pos = fs.getPositionalFeatures();
+ assertEquals(pos.size(), 2);
+ SequenceFeatures.sortFeatures(pos, true);
+ assertEquals(pos.get(0).getBegin(), 1);
+ assertEquals(pos.get(0).getEnd(), 4);
+ assertEquals(pos.get(1).getBegin(), 17);
+ assertEquals(pos.get(1).getEnd(), 26);
+
+ /*
+ * shift right by 4 from position 18 onwards
+ * should be no change
+ */
+ SequenceFeature f1 = pos.get(0);
+ SequenceFeature f2 = pos.get(1);
+ assertFalse(fs.shiftFeatures(18, 4)); // no update
+ pos = fs.getPositionalFeatures();
+ assertEquals(pos.size(), 2);
+ SequenceFeatures.sortFeatures(pos, true);
+ assertSame(pos.get(0), f1);
+ assertSame(pos.get(1), f2);
}
@Test(groups = "Functional")
assertEquals(features.size(), 2);
assertTrue(features.contains(sf1));
assertTrue(features.contains(sf2));
- assertTrue(store.nonNestedFeatures.contains(sf1));
- assertTrue(store.nestedFeatures.contains(sf2));
+ assertTrue(store.features.contains(sf1));
+ assertTrue(store.features.contains(sf2));
/*
* delete the first feature
+++ /dev/null
-package jalview.datamodel.features;
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertFalse;
-import static org.testng.Assert.assertSame;
-import static org.testng.Assert.assertTrue;
-
-import jalview.datamodel.ContiguousI;
-import jalview.datamodel.Range;
-import jalview.datamodel.SequenceFeature;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Random;
-
-import junit.extensions.PA;
-
-import org.testng.annotations.DataProvider;
-import org.testng.annotations.Test;
-
-public class NCListTest
-{
-
- private Random random = new Random(107);
-
- private Comparator<ContiguousI> sorter = new RangeComparator(true);
-
- /**
- * A basic sanity test of the constructor
- */
- @Test(groups = "Functional")
- public void testConstructor()
- {
- List<Range> ranges = new ArrayList<Range>();
- ranges.add(new Range(20, 20));
- ranges.add(new Range(10, 20));
- ranges.add(new Range(15, 30));
- ranges.add(new Range(10, 30));
- ranges.add(new Range(11, 19));
- ranges.add(new Range(10, 20));
- ranges.add(new Range(1, 100));
-
- NCList<Range> ncl = new NCList<Range>(ranges);
- String expected = "[1-100 [10-30 [10-20 [10-20 [11-19]]]], 15-30 [20-20]]";
- assertEquals(ncl.toString(), expected);
- assertTrue(ncl.isValid());
-
- Collections.reverse(ranges);
- ncl = new NCList<Range>(ranges);
- assertEquals(ncl.toString(), expected);
- assertTrue(ncl.isValid());
- }
-
- @Test(groups = "Functional")
- public void testFindOverlaps()
- {
- List<Range> ranges = new ArrayList<Range>();
- ranges.add(new Range(20, 50));
- ranges.add(new Range(30, 70));
- ranges.add(new Range(1, 100));
- ranges.add(new Range(70, 120));
-
- NCList<Range> ncl = new NCList<Range>(ranges);
-
- List<Range> overlaps = ncl.findOverlaps(121, 122);
- assertEquals(overlaps.size(), 0);
-
- overlaps = ncl.findOverlaps(21, 22);
- assertEquals(overlaps.size(), 2);
- assertEquals(((ContiguousI) overlaps.get(0)).getBegin(), 1);
- assertEquals(((ContiguousI) overlaps.get(0)).getEnd(), 100);
- assertEquals(((ContiguousI) overlaps.get(1)).getBegin(), 20);
- assertEquals(((ContiguousI) overlaps.get(1)).getEnd(), 50);
-
- overlaps = ncl.findOverlaps(110, 110);
- assertEquals(overlaps.size(), 1);
- assertEquals(((ContiguousI) overlaps.get(0)).getBegin(), 70);
- assertEquals(((ContiguousI) overlaps.get(0)).getEnd(), 120);
- }
-
- @Test(groups = "Functional")
- public void testAdd_onTheEnd()
- {
- List<Range> ranges = new ArrayList<Range>();
- ranges.add(new Range(20, 50));
- NCList<Range> ncl = new NCList<Range>(ranges);
- assertEquals(ncl.toString(), "[20-50]");
- assertTrue(ncl.isValid());
-
- ncl.add(new Range(60, 70));
- assertEquals(ncl.toString(), "[20-50, 60-70]");
- assertTrue(ncl.isValid());
- }
-
- @Test(groups = "Functional")
- public void testAdd_inside()
- {
- List<Range> ranges = new ArrayList<Range>();
- ranges.add(new Range(20, 50));
- NCList<Range> ncl = new NCList<Range>(ranges);
- assertEquals(ncl.toString(), "[20-50]");
- assertTrue(ncl.isValid());
-
- ncl.add(new Range(30, 40));
- assertEquals(ncl.toString(), "[20-50 [30-40]]");
- }
-
- @Test(groups = "Functional")
- public void testAdd_onTheFront()
- {
- List<Range> ranges = new ArrayList<Range>();
- ranges.add(new Range(20, 50));
- NCList<Range> ncl = new NCList<Range>(ranges);
- assertEquals(ncl.toString(), "[20-50]");
- assertTrue(ncl.isValid());
-
- ncl.add(new Range(5, 15));
- assertEquals(ncl.toString(), "[5-15, 20-50]");
- assertTrue(ncl.isValid());
- }
-
- @Test(groups = "Functional")
- public void testAdd_enclosing()
- {
- List<Range> ranges = new ArrayList<Range>();
- ranges.add(new Range(20, 50));
- ranges.add(new Range(30, 60));
- NCList<Range> ncl = new NCList<Range>(ranges);
- assertEquals(ncl.toString(), "[20-50, 30-60]");
- assertTrue(ncl.isValid());
- assertEquals(ncl.getStart(), 20);
-
- ncl.add(new Range(10, 70));
- assertEquals(ncl.toString(), "[10-70 [20-50, 30-60]]");
- assertTrue(ncl.isValid());
- }
-
- @Test(groups = "Functional")
- public void testAdd_spanning()
- {
- List<Range> ranges = new ArrayList<Range>();
- ranges.add(new Range(20, 40));
- ranges.add(new Range(60, 70));
- NCList<Range> ncl = new NCList<Range>(ranges);
- assertEquals(ncl.toString(), "[20-40, 60-70]");
- assertTrue(ncl.isValid());
-
- ncl.add(new Range(30, 50));
- assertEquals(ncl.toString(), "[20-40, 30-50, 60-70]");
- assertTrue(ncl.isValid());
-
- ncl.add(new Range(40, 65));
- assertEquals(ncl.toString(), "[20-40, 30-50, 40-65, 60-70]");
- assertTrue(ncl.isValid());
- }
-
- /**
- * Provides the scales for pseudo-random NCLists i.e. the range of the maximal
- * [0-scale] interval to be stored
- *
- * @return
- */
- @DataProvider(name = "scalesOfLife")
- public Object[][] getScales()
- {
- return new Object[][] { new Integer[] { 10 }, new Integer[] { 100 } };
- }
-
- /**
- * Do a number of pseudo-random (reproducible) builds of an NCList, to
- * exercise as many methods of the class as possible while generating the
- * range of possible structure topologies
- * <ul>
- * <li>verify that add adds an entry and increments size</li>
- * <li>...except where the entry is already contained (by equals test)</li>
- * <li>verify that the structure is valid at all stages of construction</li>
- * <li>generate, run and verify a range of overlap queries</li>
- * <li>tear down the structure by deleting entries, verifying correctness at
- * each stage</li>
- * </ul>
- */
- @Test(groups = "Functional", dataProvider = "scalesOfLife")
- public void test_pseudoRandom(Integer scale)
- {
- NCList<SequenceFeature> ncl = new NCList<SequenceFeature>();
- List<SequenceFeature> features = new ArrayList<SequenceFeature>(scale);
-
- testAdd_pseudoRandom(scale, ncl, features);
-
- /*
- * sort the list of added ranges - this doesn't affect the test,
- * just makes it easier to inspect the data in the debugger
- */
- Collections.sort(features, sorter);
-
- testFindOverlaps_pseudoRandom(ncl, scale, features);
-
- testDelete_pseudoRandom(ncl, features);
- }
-
- /**
- * Pick randomly selected entries to delete in turn, checking the NCList size
- * and validity at each stage, until it is empty
- *
- * @param ncl
- * @param features
- */
- protected void testDelete_pseudoRandom(NCList<SequenceFeature> ncl,
- List<SequenceFeature> features)
- {
- int deleted = 0;
-
- while (!features.isEmpty())
- {
- assertEquals(ncl.size(), features.size());
- int toDelete = random.nextInt(features.size());
- SequenceFeature entry = features.get(toDelete);
- assertTrue(ncl.contains(entry), String.format(
- "NCList doesn't contain entry [%d] '%s'!", deleted,
- entry.toString()));
-
- ncl.delete(entry);
- assertFalse(ncl.contains(entry), String.format(
- "NCList still contains deleted entry [%d] '%s'!", deleted,
- entry.toString()));
- features.remove(toDelete);
- deleted++;
-
- assertTrue(ncl.isValid(), String.format(
- "NCList invalid after %d deletions, last deleted was '%s'",
- deleted, entry.toString()));
-
- /*
- * brute force check that deleting one entry didn't delete any others
- */
- for (int i = 0; i < features.size(); i++)
- {
- SequenceFeature sf = features.get(i);
- assertTrue(ncl.contains(sf), String.format(
- "NCList doesn't contain entry [%d] %s after deleting '%s'!",
- i, sf.toString(), entry.toString()));
- }
- }
- assertEquals(ncl.size(), 0); // all gone
- }
-
- /**
- * Randomly generate entries and add them to the NCList, checking its validity
- * and size at each stage. A few entries should be duplicates (by equals test)
- * so not get added.
- *
- * @param scale
- * @param ncl
- * @param features
- */
- protected void testAdd_pseudoRandom(Integer scale,
- NCList<SequenceFeature> ncl,
- List<SequenceFeature> features)
- {
- int count = 0;
- final int size = 50;
-
- for (int i = 0; i < size; i++)
- {
- int r1 = random.nextInt(scale + 1);
- int r2 = random.nextInt(scale + 1);
- int from = Math.min(r1, r2);
- int to = Math.max(r1, r2);
-
- /*
- * choice of two feature values means that occasionally an identical
- * feature may be generated, in which case it should not be added
- */
- float value = (float) i % 2;
- SequenceFeature feature = new SequenceFeature("Pfam", "", from, to,
- value, "group");
-
- /*
- * add to NCList - with duplicate entries (by equals) disallowed
- */
- ncl.add(feature, false);
- if (features.contains(feature))
- {
- System.out.println("Duplicate feature generated "
- + feature.toString());
- }
- else
- {
- features.add(feature);
- count++;
- }
-
- /*
- * check list format is valid at each stage of its construction
- */
- assertTrue(ncl.isValid(),
- String.format("Failed for scale = %d, i=%d", scale, i));
- assertEquals(ncl.size(), count);
- }
- // System.out.println(ncl.prettyPrint());
- }
-
- /**
- * A helper method that generates pseudo-random range queries and veries that
- * findOverlaps returns the correct matches
- *
- * @param ncl
- * the NCList to query
- * @param scale
- * ncl maximal range is [0, scale]
- * @param features
- * a list of the ranges stored in ncl
- */
- protected void testFindOverlaps_pseudoRandom(NCList<SequenceFeature> ncl,
- int scale,
- List<SequenceFeature> features)
- {
- int halfScale = scale / 2;
- int minIterations = 20;
-
- /*
- * generates ranges in [-halfScale, scale+halfScale]
- * - some should be internal to [0, scale] P = 1/4
- * - some should lie before 0 P = 1/16
- * - some should lie after scale P = 1/16
- * - some should overlap left P = 1/4
- * - some should overlap right P = 1/4
- * - some should enclose P = 1/8
- *
- * 50 iterations give a 96% probability of including the
- * unlikeliest case; keep going until we have done all!
- */
- boolean inside = false;
- boolean enclosing = false;
- boolean before = false;
- boolean after = false;
- boolean overlapLeft = false;
- boolean overlapRight = false;
- boolean allCasesCovered = false;
-
- int i = 0;
- while (i < minIterations || !allCasesCovered)
- {
- i++;
- int r1 = random.nextInt((scale + 1) * 2);
- int r2 = random.nextInt((scale + 1) * 2);
- int from = Math.min(r1, r2) - halfScale;
- int to = Math.max(r1, r2) - halfScale;
-
- /*
- * ensure all cases of interest get covered
- */
- inside |= from >= 0 && to <= scale;
- enclosing |= from <= 0 && to >= scale;
- before |= to < 0;
- after |= from > scale;
- overlapLeft |= from < 0 && to >= 0 && to <= scale;
- overlapRight |= from >= 0 && from <= scale && to > scale;
- if (!allCasesCovered)
- {
- allCasesCovered |= inside && enclosing && before && after
- && overlapLeft && overlapRight;
- if (allCasesCovered)
- {
- System.out
- .println(String
- .format("Covered all findOverlaps cases after %d iterations for scale %d",
- i, scale));
- }
- }
-
- verifyFindOverlaps(ncl, from, to, features);
- }
- }
-
- /**
- * A helper method that verifies that overlaps found by interrogating an
- * NCList correctly match those found by brute force search
- *
- * @param ncl
- * @param from
- * @param to
- * @param features
- */
- protected void verifyFindOverlaps(NCList<SequenceFeature> ncl, int from,
- int to, List<SequenceFeature> features)
- {
- List<SequenceFeature> overlaps = ncl.findOverlaps(from, to);
-
- /*
- * check returned entries do indeed overlap from-to range
- */
- for (ContiguousI sf : overlaps)
- {
- int begin = sf.getBegin();
- int end = sf.getEnd();
- assertTrue(begin <= to && end >= from, String.format(
- "[%d, %d] does not overlap query range [%d, %d]", begin, end,
- from, to));
- }
-
- /*
- * check overlapping ranges are included in the results
- * (the test above already shows non-overlapping ranges are not)
- */
- for (ContiguousI sf : features)
- {
- int begin = sf.getBegin();
- int end = sf.getEnd();
- if (begin <= to && end >= from)
- {
- boolean found = overlaps.contains(sf);
- assertTrue(found, String.format(
- "[%d, %d] missing in query range [%d, %d]", begin, end,
- from, to));
- }
- }
- }
-
- @Test(groups = "Functional")
- public void testGetEntries()
- {
- List<Range> ranges = new ArrayList<Range>();
- Range r1 = new Range(20, 20);
- Range r2 = new Range(10, 20);
- Range r3 = new Range(15, 30);
- Range r4 = new Range(10, 30);
- Range r5 = new Range(11, 19);
- Range r6 = new Range(10, 20);
- ranges.add(r1);
- ranges.add(r2);
- ranges.add(r3);
- ranges.add(r4);
- ranges.add(r5);
- ranges.add(r6);
-
- NCList<Range> ncl = new NCList<Range>(ranges);
- Range r7 = new Range(1, 100);
- ncl.add(r7);
-
- List<Range> contents = ncl.getEntries();
- assertEquals(contents.size(), 7);
- assertTrue(contents.contains(r1));
- assertTrue(contents.contains(r2));
- assertTrue(contents.contains(r3));
- assertTrue(contents.contains(r4));
- assertTrue(contents.contains(r5));
- assertTrue(contents.contains(r6));
- assertTrue(contents.contains(r7));
-
- ncl = new NCList<Range>();
- assertTrue(ncl.getEntries().isEmpty());
- }
-
- @Test(groups = "Functional")
- public void testDelete()
- {
- List<Range> ranges = new ArrayList<Range>();
- Range r1 = new Range(20, 30);
- ranges.add(r1);
- NCList<Range> ncl = new NCList<Range>(ranges);
- assertTrue(ncl.getEntries().contains(r1));
-
- Range r2 = new Range(20, 30);
- assertFalse(ncl.delete(null)); // null argument
- assertFalse(ncl.delete(r2)); // never added
- assertTrue(ncl.delete(r1)); // success
- assertTrue(ncl.getEntries().isEmpty());
-
- /*
- * tests where object.equals() == true
- */
- NCList<SequenceFeature> features = new NCList<SequenceFeature>();
- SequenceFeature sf1 = new SequenceFeature("type", "desc", 1, 10, 2f,
- "group");
- SequenceFeature sf2 = new SequenceFeature("type", "desc", 1, 10, 2f,
- "group");
- features.add(sf1);
- assertEquals(sf1, sf2); // sf1.equals(sf2)
- assertFalse(features.delete(sf2)); // equality is not enough for deletion
- assertTrue(features.getEntries().contains(sf1)); // still there!
- assertTrue(features.delete(sf1));
- assertTrue(features.getEntries().isEmpty()); // gone now
-
- /*
- * test with duplicate objects in NCList
- */
- features.add(sf1);
- features.add(sf1);
- assertEquals(features.getEntries().size(), 2);
- assertSame(features.getEntries().get(0), sf1);
- assertSame(features.getEntries().get(1), sf1);
- assertTrue(features.delete(sf1)); // first match only is deleted
- assertTrue(features.contains(sf1));
- assertEquals(features.size(), 1);
- assertTrue(features.delete(sf1));
- assertTrue(features.getEntries().isEmpty());
- }
-
- @Test(groups = "Functional")
- public void testAdd_overlapping()
- {
- List<Range> ranges = new ArrayList<Range>();
- ranges.add(new Range(40, 50));
- ranges.add(new Range(20, 30));
- NCList<Range> ncl = new NCList<Range>(ranges);
- assertEquals(ncl.toString(), "[20-30, 40-50]");
- assertTrue(ncl.isValid());
-
- /*
- * add range overlapping internally
- */
- ncl.add(new Range(25, 35));
- assertEquals(ncl.toString(), "[20-30, 25-35, 40-50]");
- assertTrue(ncl.isValid());
-
- /*
- * add range overlapping last range
- */
- ncl.add(new Range(45, 55));
- assertEquals(ncl.toString(), "[20-30, 25-35, 40-50, 45-55]");
- assertTrue(ncl.isValid());
-
- /*
- * add range overlapping first range
- */
- ncl.add(new Range(15, 25));
- assertEquals(ncl.toString(), "[15-25, 20-30, 25-35, 40-50, 45-55]");
- assertTrue(ncl.isValid());
- }
-
- /**
- * Test the contains method (which uses object equals test)
- */
- @Test(groups = "Functional")
- public void testContains()
- {
- NCList<SequenceFeature> ncl = new NCList<SequenceFeature>();
- SequenceFeature sf1 = new SequenceFeature("type", "desc", 1, 10, 2f,
- "group");
- SequenceFeature sf2 = new SequenceFeature("type", "desc", 1, 10, 2f,
- "group");
- SequenceFeature sf3 = new SequenceFeature("type", "desc", 1, 10, 2f,
- "anothergroup");
- ncl.add(sf1);
-
- assertTrue(ncl.contains(sf1));
- assertTrue(ncl.contains(sf2)); // sf1.equals(sf2)
- assertFalse(ncl.contains(sf3)); // !sf1.equals(sf3)
-
- /*
- * make some deeper structure in the NCList
- */
- SequenceFeature sf4 = new SequenceFeature("type", "desc", 2, 9, 2f,
- "group");
- ncl.add(sf4);
- assertTrue(ncl.contains(sf4));
- SequenceFeature sf5 = new SequenceFeature("type", "desc", 4, 5, 2f,
- "group");
- SequenceFeature sf6 = new SequenceFeature("type", "desc", 6, 8, 2f,
- "group");
- ncl.add(sf5);
- ncl.add(sf6);
- assertTrue(ncl.contains(sf5));
- assertTrue(ncl.contains(sf6));
- }
-
- @Test(groups = "Functional")
- public void testIsValid()
- {
- List<Range> ranges = new ArrayList<Range>();
- Range r1 = new Range(40, 50);
- ranges.add(r1);
- NCList<Range> ncl = new NCList<Range>(ranges);
- assertTrue(ncl.isValid());
-
- Range r2 = new Range(42, 44);
- ncl.add(r2);
- assertTrue(ncl.isValid());
- Range r3 = new Range(46, 48);
- ncl.add(r3);
- assertTrue(ncl.isValid());
- Range r4 = new Range(43, 43);
- ncl.add(r4);
- assertTrue(ncl.isValid());
-
- assertEquals(ncl.toString(), "[40-50 [42-44 [43-43], 46-48]]");
- assertTrue(ncl.isValid());
-
- PA.setValue(r1, "start", 43);
- assertFalse(ncl.isValid()); // r2 not inside r1
- PA.setValue(r1, "start", 40);
- assertTrue(ncl.isValid());
-
- PA.setValue(r3, "start", 41);
- assertFalse(ncl.isValid()); // r3 should precede r2
- PA.setValue(r3, "start", 46);
- assertTrue(ncl.isValid());
-
- PA.setValue(r4, "start", 41);
- assertFalse(ncl.isValid()); // r4 not inside r2
- PA.setValue(r4, "start", 43);
- assertTrue(ncl.isValid());
-
- PA.setValue(r4, "start", 44);
- assertFalse(ncl.isValid()); // r4 has reverse range
- }
-
- @Test(groups = "Functional")
- public void testPrettyPrint()
- {
- /*
- * construct NCList from a list of ranges
- * they are sorted then assembled into NCList subregions
- * notice that 42-42 end up inside 41-46
- */
- List<Range> ranges = new ArrayList<Range>();
- ranges.add(new Range(40, 50));
- ranges.add(new Range(45, 55));
- ranges.add(new Range(40, 45));
- ranges.add(new Range(41, 46));
- ranges.add(new Range(42, 42));
- ranges.add(new Range(42, 42));
- NCList<Range> ncl = new NCList<Range>(ranges);
- assertTrue(ncl.isValid());
- assertEquals(ncl.toString(),
- "[40-50 [40-45], 41-46 [42-42 [42-42]], 45-55]");
- String expected = "40-50\n 40-45\n41-46\n 42-42\n 42-42\n45-55\n";
- assertEquals(ncl.prettyPrint(), expected);
-
- /*
- * repeat but now add ranges one at a time
- * notice that 42-42 end up inside 40-50 so we get
- * a different but equal valid NCList structure
- */
- ranges.clear();
- ncl = new NCList<Range>(ranges);
- ncl.add(new Range(40, 50));
- ncl.add(new Range(45, 55));
- ncl.add(new Range(40, 45));
- ncl.add(new Range(41, 46));
- ncl.add(new Range(42, 42));
- ncl.add(new Range(42, 42));
- assertTrue(ncl.isValid());
- assertEquals(ncl.toString(),
- "[40-50 [40-45 [42-42 [42-42]], 41-46], 45-55]");
- expected = "40-50\n 40-45\n 42-42\n 42-42\n 41-46\n45-55\n";
- assertEquals(ncl.prettyPrint(), expected);
- }
-
- /**
- * A test that shows different valid trees can be constructed from the same
- * set of ranges, depending on the order of construction
- */
- @Test(groups = "Functional")
- public void testConstructor_alternativeTrees()
- {
- List<Range> ranges = new ArrayList<Range>();
- ranges.add(new Range(10, 60));
- ranges.add(new Range(20, 30));
- ranges.add(new Range(40, 50));
-
- /*
- * constructor with greedy traversal of sorted ranges to build nested
- * containment lists results in 20-30 inside 10-60, 40-50 a sibling
- */
- NCList<Range> ncl = new NCList<Range>(ranges);
- assertEquals(ncl.toString(), "[10-60 [20-30], 40-50]");
- assertTrue(ncl.isValid());
-
- /*
- * adding ranges one at a time results in 40-50
- * a sibling of 20-30 inside 10-60
- */
- ncl = new NCList<Range>(new Range(10, 60));
- ncl.add(new Range(20, 30));
- ncl.add(new Range(40, 50));
- assertEquals(ncl.toString(), "[10-60 [20-30, 40-50]]");
- assertTrue(ncl.isValid());
- }
-}
+++ /dev/null
-package jalview.datamodel.features;
-
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertFalse;
-import static org.testng.Assert.assertTrue;
-
-import jalview.datamodel.Range;
-import jalview.datamodel.SequenceFeature;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import junit.extensions.PA;
-
-import org.testng.annotations.Test;
-
-public class NCNodeTest
-{
- @Test(groups = "Functional")
- public void testAdd()
- {
- Range r1 = new Range(10, 20);
- NCNode<Range> node = new NCNode<Range>(r1);
- assertEquals(node.getBegin(), 10);
- Range r2 = new Range(10, 15);
- node.add(r2);
-
- List<Range> contents = new ArrayList<Range>();
- node.getEntries(contents);
- assertEquals(contents.size(), 2);
- assertTrue(contents.contains(r1));
- assertTrue(contents.contains(r2));
- }
-
- @Test(
- groups = "Functional",
- expectedExceptions = { IllegalArgumentException.class })
- public void testAdd_invalidRangeStart()
- {
- Range r1 = new Range(10, 20);
- NCNode<Range> node = new NCNode<Range>(r1);
- assertEquals(node.getBegin(), 10);
- Range r2 = new Range(9, 15);
- node.add(r2);
- }
-
- @Test(
- groups = "Functional",
- expectedExceptions = { IllegalArgumentException.class })
- public void testAdd_invalidRangeEnd()
- {
- Range r1 = new Range(10, 20);
- NCNode<Range> node = new NCNode<Range>(r1);
- assertEquals(node.getBegin(), 10);
- Range r2 = new Range(12, 21);
- node.add(r2);
- }
-
- @Test(groups = "Functional")
- public void testGetEntries()
- {
- Range r1 = new Range(10, 20);
- NCNode<Range> node = new NCNode<Range>(r1);
- List<Range> entries = new ArrayList<Range>();
-
- node.getEntries(entries);
- assertEquals(entries.size(), 1);
- assertTrue(entries.contains(r1));
-
- // clearing the returned list does not affect the NCNode
- entries.clear();
- node.getEntries(entries);
- assertEquals(entries.size(), 1);
- assertTrue(entries.contains(r1));
-
- Range r2 = new Range(15, 18);
- node.add(r2);
- entries.clear();
- node.getEntries(entries);
- assertEquals(entries.size(), 2);
- assertTrue(entries.contains(r1));
- assertTrue(entries.contains(r2));
- }
-
- /**
- * Tests for the contains method (uses entry.equals() test)
- */
- @Test(groups = "Functional")
- public void testContains()
- {
- SequenceFeature sf1 = new SequenceFeature("type", "desc", 1, 10, 2f,
- "group");
- SequenceFeature sf2 = new SequenceFeature("type", "desc", 1, 10, 2f,
- "group");
- SequenceFeature sf3 = new SequenceFeature("type", "desc", 1, 10, 2f,
- "anothergroup");
- NCNode<SequenceFeature> node = new NCNode<SequenceFeature>(sf1);
-
- assertFalse(node.contains(null));
- assertTrue(node.contains(sf1));
- assertTrue(node.contains(sf2)); // sf1.equals(sf2)
- assertFalse(node.contains(sf3)); // !sf1.equals(sf3)
- }
-
- /**
- * Test method that checks for valid structure. Valid means that all
- * subregions (if any) lie within the root range, and that all subregions have
- * valid structure.
- */
- @Test(groups = "Functional")
- public void testIsValid()
- {
- Range r1 = new Range(10, 20);
- Range r2 = new Range(14, 15);
- Range r3 = new Range(16, 17);
- NCNode<Range> node = new NCNode<Range>(r1);
- node.add(r2);
- node.add(r3);
-
- /*
- * node has root range [10-20] and contains an
- * NCList of [14-15, 16-17]
- */
- assertTrue(node.isValid());
- PA.setValue(r1, "start", 15);
- assertFalse(node.isValid()); // r2 not within r1
- PA.setValue(r1, "start", 10);
- assertTrue(node.isValid());
- PA.setValue(r1, "end", 16);
- assertFalse(node.isValid()); // r3 not within r1
- PA.setValue(r1, "end", 20);
- assertTrue(node.isValid());
- PA.setValue(r3, "start", 12);
- assertFalse(node.isValid()); // r3 should precede r2
- }
-}
+++ /dev/null
-package jalview.datamodel.features;
-
-import static org.testng.Assert.assertEquals;
-
-import jalview.datamodel.ContiguousI;
-import jalview.datamodel.Range;
-
-import java.util.Comparator;
-
-import org.testng.annotations.Test;
-
-public class RangeComparatorTest
-{
-
- @Test(groups = "Functional")
- public void testCompare()
- {
- RangeComparator comp = new RangeComparator(true);
-
- // same position, same length
- assertEquals(comp.compare(10, 10, 20, 20), 0);
- // same position, len1 > len2
- assertEquals(comp.compare(10, 10, 20, 19), -1);
- // same position, len1 < len2
- assertEquals(comp.compare(10, 10, 20, 21), 1);
- // pos1 > pos2
- assertEquals(comp.compare(11, 10, 20, 20), 1);
- // pos1 < pos2
- assertEquals(comp.compare(10, 11, 20, 10), -1);
- }
-
- @Test(groups = "Functional")
- public void testCompare_byStart()
- {
- Comparator<ContiguousI> comp = RangeComparator.BY_START_POSITION;
-
- // same start position, same length
- assertEquals(comp.compare(new Range(10, 20), new Range(10, 20)), 0);
- // same start position, len1 > len2
- assertEquals(comp.compare(new Range(10, 20), new Range(10, 19)), -1);
- // same start position, len1 < len2
- assertEquals(comp.compare(new Range(10, 18), new Range(10, 20)), 1);
- // pos1 > pos2
- assertEquals(comp.compare(new Range(11, 20), new Range(10, 20)), 1);
- // pos1 < pos2
- assertEquals(comp.compare(new Range(10, 20), new Range(11, 20)), -1);
- }
-
- @Test(groups = "Functional")
- public void testCompare_byEnd()
- {
- Comparator<ContiguousI> comp = RangeComparator.BY_END_POSITION;
-
- // same end position, same length
- assertEquals(comp.compare(new Range(10, 20), new Range(10, 20)), 0);
- // same end position, len1 > len2
- assertEquals(comp.compare(new Range(10, 20), new Range(11, 20)), -1);
- // same end position, len1 < len2
- assertEquals(comp.compare(new Range(11, 20), new Range(10, 20)), 1);
- // end1 > end2
- assertEquals(comp.compare(new Range(10, 21), new Range(10, 20)), 1);
- // end1 < end2
- assertEquals(comp.compare(new Range(10, 20), new Range(10, 21)), -1);
- }
-}
public void testShiftFeatures()
{
SequenceFeatures store = new SequenceFeatures();
- assertFalse(store.shiftFeatures(1));
+ assertFalse(store.shiftFeatures(0, 1));
SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
store.add(sf1);
/*
* shift features right by 5
*/
- assertTrue(store.shiftFeatures(5));
+ assertTrue(store.shiftFeatures(0, 5));
// non-positional features untouched:
List<SequenceFeature> nonPos = store.getNonPositionalFeatures();
* feature at [7-10] should be removed
* feature at [13-19] should become [1-4]
*/
- assertTrue(store.shiftFeatures(-15));
+ assertTrue(store.shiftFeatures(0, -15));
pos = store.getPositionalFeatures();
assertEquals(pos.size(), 2);
SequenceFeatures.sortFeatures(pos, true);
assertEquals(pos.get(1).getBegin(), 13);
assertEquals(pos.get(1).getEnd(), 22);
assertEquals(pos.get(1).getType(), "Disulfide bond");
+
+ /*
+ * shift right by 4 from column 2
+ * feature at [1-4] should be unchanged
+ * feature at [13-22] should become [17-26]
+ */
+ assertTrue(store.shiftFeatures(2, 4));
+ pos = store.getPositionalFeatures();
+ assertEquals(pos.size(), 2);
+ SequenceFeatures.sortFeatures(pos, true);
+ assertEquals(pos.get(0).getBegin(), 1);
+ assertEquals(pos.get(0).getEnd(), 4);
+ assertEquals(pos.get(0).getType(), "Metal");
+ assertEquals(pos.get(1).getBegin(), 17);
+ assertEquals(pos.get(1).getEnd(), 26);
+ assertEquals(pos.get(1).getType(), "Disulfide bond");
+
+ /*
+ * shift right from column 18
+ * should be no updates
+ */
+ SequenceFeature f1 = pos.get(0);
+ SequenceFeature f2 = pos.get(1);
+ assertFalse(store.shiftFeatures(18, 6));
+ pos = store.getPositionalFeatures();
+ assertEquals(pos.size(), 2);
+ SequenceFeatures.sortFeatures(pos, true);
+ assertSame(pos.get(0), f1);
+ assertSame(pos.get(1), f2);
}
@Test(groups = "Functional")
assertTrue(store.isOntologyTerm("junk", new String[] {}));
assertTrue(store.isOntologyTerm("junk", (String[]) null));
}
+
+ @Test(groups = "Functional")
+ public void testDeleteAll()
+ {
+ SequenceFeaturesI store = new SequenceFeatures();
+ assertFalse(store.hasFeatures());
+ store.deleteAll();
+ assertFalse(store.hasFeatures());
+ store.add(new SequenceFeature("Cath", "Desc", 12, 20, 0f, "Group"));
+ store.add(new SequenceFeature("Pfam", "Desc", 6, 12, 2f, "Group2"));
+ assertTrue(store.hasFeatures());
+ store.deleteAll();
+ assertFalse(store.hasFeatures());
+ }
}
// exon at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("-");
genomic.addSequenceFeature(sf);
// exon (sub-type) at (start + exon_variant) length 101
sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("-");
genomic.addSequenceFeature(sf);
// exon belonging to a different transcript doesn't count
sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
- sf.setValue("Parent", "transcript:anotherOne");
+ sf.setValue("Parent", "anotherOne");
genomic.addSequenceFeature(sf);
// transcript feature doesn't count
// exon at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// exon (sub-type) at (start + exon_variant) length 101
sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// exon belonging to a different transcript doesn't count
sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
- sf.setValue("Parent", "transcript:anotherOne");
+ sf.setValue("Parent", "anotherOne");
genomic.addSequenceFeature(sf);
// transcript feature doesn't count
assertTrue(testee.retainFeature(sf, accId));
// other feature with desired parent is retained
- sf.setValue("Parent", "transcript:" + accId);
+ sf.setValue("Parent", accId);
assertTrue(testee.retainFeature(sf, accId));
// test is not case-sensitive
assertTrue(testee.retainFeature(sf, accId.toLowerCase()));
// feature with wrong parent is not retained
- sf.setValue("Parent", "transcript:XYZ");
+ sf.setValue("Parent", "XYZ");
assertFalse(testee.retainFeature(sf, accId));
}
// exon with wrong parent: not valid
SequenceFeature sf2 = new SequenceFeature("exon", "", 1, 2, 0f, null);
- sf2.setValue("Parent", "transcript:XYZ");
+ sf2.setValue("Parent", "XYZ");
seq.addSequenceFeature(sf2);
// exon with right parent is valid
SequenceFeature sf3 = new SequenceFeature("exon", "", 1, 2, 0f, null);
- sf3.setValue("Parent", "transcript:" + accId);
+ sf3.setValue("Parent", accId);
seq.addSequenceFeature(sf3);
// exon sub-type with right parent is valid
SequenceFeature sf4 = new SequenceFeature("coding_exon", "", 1, 2, 0f,
null);
- sf4.setValue("Parent", "transcript:" + accId);
+ sf4.setValue("Parent", accId);
seq.addSequenceFeature(sf4);
// transcript not valid:
SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
null);
- sf5.setValue("Parent", "transcript:" + accId);
+ sf5.setValue("Parent", accId);
seq.addSequenceFeature(sf5);
// CDS not valid:
SequenceFeature sf6 = new SequenceFeature("transcript", "", 1, 2, 0f,
null);
- sf6.setValue("Parent", "transcript:" + accId);
+ sf6.setValue("Parent", accId);
seq.addSequenceFeature(sf6);
List<SequenceFeature> sfs = new EnsemblCdna()
// CDS at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// CDS (sub-type) at (start + 10500) length 101
sf = new SequenceFeature("CDS_predicted", "", 10500, 10600, 0f, null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// CDS belonging to a different transcript doesn't count
sf = new SequenceFeature("CDS", "", 11500, 12600, 0f, null);
- sf.setValue("Parent", "transcript:anotherOne");
+ sf.setValue("Parent", "anotherOne");
genomic.addSequenceFeature(sf);
// exon feature doesn't count
assertFalse(testee.retainFeature(sf, accId));
// other feature with no parent is retained
- sf = new SequenceFeature("CDS_psequence_variantredicted", "", 20000,
+ sf = new SequenceFeature("anotherType", "", 20000,
20500, 0f, null);
assertTrue(testee.retainFeature(sf, accId));
// other feature with desired parent is retained
- sf.setValue("Parent", "transcript:" + accId);
+ sf.setValue("Parent", accId);
assertTrue(testee.retainFeature(sf, accId));
// feature with wrong parent is not retained
- sf.setValue("Parent", "transcript:XYZ");
+ sf.setValue("Parent", "XYZ");
assertFalse(testee.retainFeature(sf, accId));
}
// cds with wrong parent not valid
SequenceFeature sf2 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
- sf2.setValue("Parent", "transcript:XYZ");
+ sf2.setValue("Parent", "XYZ");
seq.addSequenceFeature(sf2);
// cds with right parent is valid
SequenceFeature sf3 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
- sf3.setValue("Parent", "transcript:" + accId);
+ sf3.setValue("Parent", accId);
seq.addSequenceFeature(sf3);
// cds sub-type with right parent is valid
SequenceFeature sf4 = new SequenceFeature("CDS_predicted", "", 1, 2, 0f,
null);
- sf4.setValue("Parent", "transcript:" + accId);
+ sf4.setValue("Parent", accId);
seq.addSequenceFeature(sf4);
// transcript not valid:
SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
null);
- sf5.setValue("Parent", "transcript:" + accId);
+ sf5.setValue("Parent", accId);
seq.addSequenceFeature(sf5);
// exon not valid:
SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
- sf6.setValue("Parent", "transcript:" + accId);
+ sf6.setValue("Parent", accId);
seq.addSequenceFeature(sf6);
List<SequenceFeature> sfs = new EnsemblCds().getIdentifyingFeatures(seq,
// gene at (start + 10500) length 101
SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
null);
- sf.setValue("ID", "gene:" + geneId);
+ sf.setValue("id", geneId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// gene at (start + 10500) length 101
SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
null);
- sf.setValue("ID", "gene:" + geneId);
+ sf.setValue("id", geneId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// transcript feature
SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
20500, 0f, null);
- sf1.setValue("Parent", "gene:" + geneId);
- sf1.setValue("transcript_id", "transcript1");
+ sf1.setValue("Parent", geneId);
+ sf1.setValue("id", "transcript1");
genomic.addSequenceFeature(sf1);
// transcript sub-type feature
SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500,
0f, null);
- sf2.setValue("Parent", "gene:" + geneId);
- sf2.setValue("transcript_id", "transcript2");
+ sf2.setValue("Parent", geneId);
+ sf2.setValue("id", "transcript2");
genomic.addSequenceFeature(sf2);
// NMD_transcript_variant treated like transcript in Ensembl
SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
22000, 22500, 0f, null);
// id matching should not be case-sensitive
- sf3.setValue("Parent", "gene:" + geneId.toLowerCase());
- sf3.setValue("transcript_id", "transcript3");
+ sf3.setValue("Parent", geneId.toLowerCase());
+ sf3.setValue("id", "transcript3");
genomic.addSequenceFeature(sf3);
// transcript for a different gene - ignored
SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500,
0f, null);
- sf4.setValue("Parent", "gene:XYZ");
- sf4.setValue("transcript_id", "transcript4");
+ sf4.setValue("Parent", "XYZ");
+ sf4.setValue("id", "transcript4");
genomic.addSequenceFeature(sf4);
EnsemblGene testee = new EnsemblGene();
EnsemblGene testee = new EnsemblGene();
SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
null);
- sf.setValue("ID", "gene:" + geneId);
+ sf.setValue("id", geneId);
assertFalse(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null);
- sf.setValue("Parent", "gene:" + geneId);
+ sf.setValue("Parent", geneId);
assertTrue(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
null);
- sf.setValue("Parent", "gene:" + geneId);
+ sf.setValue("Parent", geneId);
assertTrue(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
0f, null);
- sf.setValue("Parent", "gene:" + geneId);
+ sf.setValue("Parent", geneId);
assertTrue(testee.retainFeature(sf, geneId));
- sf.setValue("Parent", "gene:XYZ");
+ sf.setValue("Parent", "ßXYZ");
assertFalse(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
seq.addSequenceFeature(sf1);
// gene with wrong ID not valid
- SequenceFeature sf2 = new SequenceFeature("gene", "", 1, 2, 0f, null);
- sf2.setValue("ID", "gene:XYZ");
+ SequenceFeature sf2 = new SequenceFeature("gene", "a", 1, 2, 0f, null);
+ sf2.setValue("id", "XYZ");
seq.addSequenceFeature(sf2);
// gene with right ID is valid
- SequenceFeature sf3 = new SequenceFeature("gene", "", 1, 2, 0f, null);
- sf3.setValue("ID", "gene:" + accId);
+ SequenceFeature sf3 = new SequenceFeature("gene", "b", 1, 2, 0f, null);
+ sf3.setValue("id", accId);
seq.addSequenceFeature(sf3);
// gene sub-type with right ID is valid
SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
- sf4.setValue("ID", "gene:" + accId);
+ sf4.setValue("id", accId);
seq.addSequenceFeature(sf4);
// transcript not valid:
SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, null);
- sf5.setValue("ID", "gene:" + accId);
+ sf5.setValue("id", accId);
seq.addSequenceFeature(sf5);
// exon not valid:
SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
- sf6.setValue("ID", "gene:" + accId);
+ sf6.setValue("id", accId);
seq.addSequenceFeature(sf6);
List<SequenceFeature> sfs = new EnsemblGene()
// transcript at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
20500, 0f, null);
- sf.setValue("ID", "transcript:" + transcriptId);
+ sf.setValue("id", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// transcript (sub-type) at (start + 10500) length 101
sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
- sf.setValue("ID", "transcript:" + transcriptId);
+ sf.setValue("id", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// although strictly it is a sequence_variant in SO
sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
0f, null);
- sf.setValue("ID", "transcript:" + transcriptId);
+ sf.setValue("id", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// transcript with a different ID doesn't count
sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
- sf.setValue("ID", "transcript:anotherOne");
+ sf.setValue("id", "anotherOne");
genomic.addSequenceFeature(sf);
// parent of transcript feature doesn't count
assertTrue(testee.retainFeature(sf, accId));
// other feature with correct parent is kept
- sf.setValue("Parent", "transcript:" + accId);
+ sf.setValue("Parent", accId);
assertTrue(testee.retainFeature(sf, accId));
// other feature with wrong parent is not kept
- sf.setValue("Parent", "transcript:XYZ");
+ sf.setValue("Parent", "XYZ");
assertFalse(testee.retainFeature(sf, accId));
}
seq.addSequenceFeature(sf1);
// transcript with wrong ID not valid
- SequenceFeature sf2 = new SequenceFeature("transcript", "", 1, 2, 0f,
+ // NB change desc to avoid rejection of duplicate feature!
+ SequenceFeature sf2 = new SequenceFeature("transcript", "a", 1, 2, 0f,
null);
- sf2.setValue("ID", "transcript");
+ sf2.setValue("id", "transcript");
seq.addSequenceFeature(sf2);
// transcript with right ID is valid
- SequenceFeature sf3 = new SequenceFeature("transcript", "", 1, 2, 0f,
+ SequenceFeature sf3 = new SequenceFeature("transcript", "b", 1, 2, 0f,
null);
- sf3.setValue("ID", "transcript:" + accId);
+ sf3.setValue("id", accId);
seq.addSequenceFeature(sf3);
// transcript sub-type with right ID is valid
SequenceFeature sf4 = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
- sf4.setValue("ID", "transcript:" + accId);
+ sf4.setValue("id", accId);
seq.addSequenceFeature(sf4);
// Ensembl treats NMD_transcript_variant as if a transcript
SequenceFeature sf5 = new SequenceFeature("NMD_transcript_variant", "",
1, 2, 0f, null);
- sf5.setValue("ID", "transcript:" + accId);
+ sf5.setValue("id", accId);
seq.addSequenceFeature(sf5);
// gene not valid:
SequenceFeature sf6 = new SequenceFeature("gene", "", 1, 2, 0f, null);
- sf6.setValue("ID", "transcript:" + accId);
+ sf6.setValue("id", accId);
seq.addSequenceFeature(sf6);
// exon not valid:
SequenceFeature sf7 = new SequenceFeature("exon", "", 1, 2, 0f, null);
- sf7.setValue("ID", "transcript:" + accId);
+ sf7.setValue("id", accId);
seq.addSequenceFeature(sf7);
List<SequenceFeature> sfs = new EnsemblGenome()
// verify attributes string is updated with reverse complement
assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
}
-
- @Test(groups = "Functional")
- public void testSortFeatures()
- {
- SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
- SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
- SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
- SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
- List<SequenceFeature> sfs = Arrays.asList(new SequenceFeature[] { sf1,
- sf2, sf3, sf4 });
-
- // sort by start position ascending (forward strand)
- // sf2 and sf3 tie and should not be reordered by sorting
- SequenceFeatures.sortFeatures(sfs, true);
- assertSame(sfs.get(0), sf2);
- assertSame(sfs.get(1), sf3);
- assertSame(sfs.get(2), sf1);
- assertSame(sfs.get(3), sf4);
-
- // sort by end position descending (reverse strand)
- SequenceFeatures.sortFeatures(sfs, false);
- assertSame(sfs.get(0), sf1);
- assertSame(sfs.get(1), sf3);
- assertSame(sfs.get(2), sf2);
- assertSame(sfs.get(3), sf4);
- }
}
fail("Expected exception");
} catch (IOException e)
{
- System.out.println(
- "Caught IOException in testCreateFastaSequenceIndex");
- e.printStackTrace();
- // expected
+ // we expect an IO Exception because the pgmB.fasta.fai exists, since it
+ // was checked it in.
}
/*
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "External" })
public void testLaunchAndExit()
{
final StructureManager structureManager = new StructureManager(true);
*/
package jalview.gui;
+import static org.junit.Assert.assertNotEquals;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotSame;
* seq1 feature in columns 1-5 is hidden
* seq2 feature in columns 6-10 is shown
*/
- FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f);
+ FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
+ 0f, 10f);
fc.setAboveThreshold(true);
fc.setThreshold(5f);
alignFrame.getFeatureRenderer().setColour("Metal", fc);
sp.valueChanged(22);
assertEquals(av2.getResidueShading().getConservationInc(), 22);
}
+
+ /**
+ * Verify that making a New View preserves the dataset reference for the
+ * alignment. Otherwise, see a 'duplicate jar entry' reference when trying to
+ * save alignments with multiple views, and codon mappings will not be shared
+ * across all panels in a split frame.
+ *
+ * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
+ */
+ @Test(groups = "Functional")
+ public void testNewView_dsRefPreserved()
+ {
+ AlignViewport av = af.getViewport();
+ AlignmentI al = av.getAlignment();
+ AlignmentI original_ds = al.getDataset();
+ af.newView_actionPerformed(null);
+ assertNotEquals("New view didn't select the a new panel", av,
+ af.getViewport());
+ org.testng.Assert.assertEquals(original_ds,
+ af.getViewport().getAlignment().getDataset(),
+ "Dataset was not preserved in new view");
+ }
}
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNotSame;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
+import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.PIDColourScheme;
import jalview.structure.StructureSelectionManager;
* Test for JAL-1306 - conservation thread should run even when only Quality
* (and not Conservation) is enabled in Preferences
*/
- @Test(groups = { "Functional" })
+ @Test(groups = { "Functional" }, timeOut=2000)
public void testUpdateConservation_qualityOnly()
{
Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
Boolean.FALSE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignmentAnnotation[] anns = af.viewport.getAlignment()
+
+ /*
+ * wait for Conservation thread to complete
+ */
+ AlignViewport viewport = af.getViewport();
+ synchronized (this)
+ {
+ while (viewport.getAlignmentConservationAnnotation() != null)
+ {
+ try
+ {
+ wait(50);
+ } catch (InterruptedException e)
+ {
+ }
+ }
+ }
+ AlignmentAnnotation[] anns = viewport.getAlignment()
.getAlignmentAnnotation();
assertNotNull("No annotations found", anns);
assertEquals("More than one annotation found", 1, anns.length);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
ColourSchemeI cs = new PIDColourScheme();
- af.getViewport().setGlobalColourScheme(cs);
- assertFalse(af.getViewport().getResidueShading()
+ AlignViewport viewport = af.getViewport();
+ viewport.setGlobalColourScheme(cs);
+ assertFalse(viewport.getResidueShading()
.conservationApplied());
+
+ /*
+ * JAL-3201 groups have their own ColourSchemeI instances
+ */
+ AlignmentI aln = viewport.getAlignment();
+ SequenceGroup sg1 = new SequenceGroup();
+ sg1.addSequence(aln.getSequenceAt(0), false);
+ sg1.addSequence(aln.getSequenceAt(2), false);
+ SequenceGroup sg2 = new SequenceGroup();
+ sg2.addSequence(aln.getSequenceAt(1), false);
+ sg2.addSequence(aln.getSequenceAt(3), false);
+ aln.addGroup(sg1);
+ aln.addGroup(sg2);
+ viewport.setColourAppliesToAllGroups(true);
+ viewport.setGlobalColourScheme(new ClustalxColourScheme());
+ ColourSchemeI cs0 = viewport.getGlobalColourScheme();
+ ColourSchemeI cs1 = sg1.getColourScheme();
+ ColourSchemeI cs2 = sg2.getColourScheme();
+ assertTrue(cs0 instanceof ClustalxColourScheme);
+ assertTrue(cs1 instanceof ClustalxColourScheme);
+ assertTrue(cs2 instanceof ClustalxColourScheme);
+ assertNotSame(cs0, cs1);
+ assertNotSame(cs0, cs2);
+ assertNotSame(cs1, cs2);
}
@Test(groups = { "Functional" })
/**
* Test that update layout reverts to original (unwrapped) values for endRes
- * and endSeq when switching from wrapped to unwrapped mode (JAL-2739)
+ * when switching from wrapped back to unwrapped mode (JAL-2739)
*/
@Test(groups = "Functional")
public void TestUpdateLayout_endRes()
af.alignPanel.getAlignViewport().setWrapAlignment(true);
af.alignPanel.updateLayout();
- // endRes changes
+ // endRes has changed
assertNotEquals(ranges.getEndRes(), endres);
// unwrap
af.alignPanel.getAlignViewport().setWrapAlignment(false);
af.alignPanel.updateLayout();
- // endRes and endSeq back to original values
+ // endRes back to original value
assertEquals(ranges.getEndRes(), endres);
}
--- /dev/null
+package jalview.gui;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+
+import org.testng.annotations.Test;
+
+public class AnnotationLabelsTest
+{
+ @Test(groups = "Functional")
+ public void testGetTooltip()
+ {
+ assertNull(AnnotationLabels.getTooltip(null));
+
+ /*
+ * simple description only
+ */
+ AlignmentAnnotation ann = new AlignmentAnnotation("thelabel", "thedesc",
+ null);
+ String expected = "<html>thedesc</html>";
+ assertEquals(AnnotationLabels.getTooltip(ann), expected);
+
+ /*
+ * description needing html encoding
+ * (no idea why '<' is encoded but '>' is not)
+ */
+ ann.description = "TCoffee scores < 56 and > 28";
+ expected = "<html>TCoffee scores < 56 and > 28</html>";
+ assertEquals(AnnotationLabels.getTooltip(ann), expected);
+
+ /*
+ * description already html formatted
+ */
+ ann.description = "<html>hello world</html>";
+ assertEquals(AnnotationLabels.getTooltip(ann), ann.description);
+
+ /*
+ * simple description and score
+ */
+ ann.description = "hello world";
+ ann.setScore(2.34d);
+ expected = "<html>hello world<br/> Score: 2.34</html>";
+ assertEquals(AnnotationLabels.getTooltip(ann), expected);
+
+ /*
+ * html description and score
+ */
+ ann.description = "<html>hello world</html>";
+ ann.setScore(2.34d);
+ expected = "<html>hello world<br/> Score: 2.34</html>";
+ assertEquals(AnnotationLabels.getTooltip(ann), expected);
+
+ /*
+ * score, no description
+ */
+ ann.description = " ";
+ assertEquals(AnnotationLabels.getTooltip(ann),
+ "<html> Score: 2.34</html>");
+ ann.description = null;
+ assertEquals(AnnotationLabels.getTooltip(ann),
+ "<html> Score: 2.34</html>");
+
+ /*
+ * sequenceref, simple description
+ */
+ ann.description = "Count < 12";
+ ann.sequenceRef = new Sequence("Seq1", "MLRIQST");
+ ann.hasScore = false;
+ ann.score = Double.NaN;
+ expected = "<html>Seq1 : Count < 12</html>";
+ assertEquals(AnnotationLabels.getTooltip(ann), expected);
+
+ /*
+ * sequenceref, html description, score
+ */
+ ann.description = "<html>Score < 4.8</html>";
+ ann.sequenceRef = new Sequence("Seq1", "MLRIQST");
+ ann.setScore(-2.1D);
+ expected = "<html>Seq1 : Score < 4.8<br/> Score: -2.1</html>";
+ assertEquals(AnnotationLabels.getTooltip(ann), expected);
+
+ /*
+ * no score, null description
+ */
+ ann.description = null;
+ ann.hasScore = false;
+ ann.score = Double.NaN;
+ assertNull(AnnotationLabels.getTooltip(ann));
+
+ /*
+ * no score, empty description, sequenceRef
+ */
+ ann.description = "";
+ assertEquals(AnnotationLabels.getTooltip(ann), "<html>Seq1 :</html>");
+
+ /*
+ * no score, empty description, no sequenceRef
+ */
+ ann.sequenceRef = null;
+ assertNull(AnnotationLabels.getTooltip(ann));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetStatusMessage()
+ {
+ assertNull(AnnotationLabels.getStatusMessage(null, null));
+
+ /*
+ * simple label
+ */
+ AlignmentAnnotation aa = new AlignmentAnnotation("IUPredWS Short",
+ "Protein disorder", null);
+ assertEquals(AnnotationLabels.getStatusMessage(aa, null),
+ "IUPredWS Short");
+
+ /*
+ * with sequence ref
+ */
+ aa.setSequenceRef(new Sequence("FER_CAPAA", "MIGRKQL"));
+ assertEquals(AnnotationLabels.getStatusMessage(aa, null),
+ "FER_CAPAA : IUPredWS Short");
+
+ /*
+ * with graph group (degenerate, one annotation only)
+ */
+ aa.graphGroup = 1;
+ AlignmentAnnotation aa2 = new AlignmentAnnotation("IUPredWS Long",
+ "Protein disorder", null);
+ assertEquals(
+ AnnotationLabels.getStatusMessage(aa, new AlignmentAnnotation[]
+ { aa, aa2 }), "FER_CAPAA : IUPredWS Short");
+
+ /*
+ * graph group with two members; note labels are appended in
+ * reverse order (matching rendering order on screen)
+ */
+ aa2.graphGroup = 1;
+ assertEquals(
+ AnnotationLabels.getStatusMessage(aa, new AlignmentAnnotation[]
+ { aa, aa2 }), "FER_CAPAA : IUPredWS Long, IUPredWS Short");
+
+ /*
+ * graph group with no sequence ref
+ */
+ aa.sequenceRef = null;
+ assertEquals(
+ AnnotationLabels.getStatusMessage(aa, new AlignmentAnnotation[]
+ { aa, aa2 }), "IUPredWS Long, IUPredWS Short");
+ }
+}
--- /dev/null
+package jalview.gui;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.AlignmentAnnotation;
+
+import org.testng.annotations.Test;
+
+public class AnnotationPanelTest
+{
+
+ @Test(groups = "Functional")
+ public void testGetRowIndex()
+ {
+ assertEquals(AnnotationPanel.getRowIndex(0, null), -1);
+
+ AlignmentAnnotation[] anns = new AlignmentAnnotation[] {};
+ assertEquals(AnnotationPanel.getRowIndex(0, anns), -1);
+
+ AlignmentAnnotation ann1 = new AlignmentAnnotation(null, null, null);
+ AlignmentAnnotation ann2 = new AlignmentAnnotation(null, null, null);
+ AlignmentAnnotation ann3 = new AlignmentAnnotation(null, null, null);
+ ann1.visible = true;
+ ann2.visible = true;
+ ann3.visible = true;
+ ann1.height = 10;
+ ann2.height = 20;
+ ann3.height = 30;
+ anns = new AlignmentAnnotation[] { ann1, ann2, ann3 };
+
+ assertEquals(AnnotationPanel.getRowIndex(0, anns), 0);
+ assertEquals(AnnotationPanel.getRowIndex(9, anns), 0);
+ assertEquals(AnnotationPanel.getRowIndex(10, anns), 1);
+ assertEquals(AnnotationPanel.getRowIndex(29, anns), 1);
+ assertEquals(AnnotationPanel.getRowIndex(30, anns), 2);
+ assertEquals(AnnotationPanel.getRowIndex(59, anns), 2);
+ assertEquals(AnnotationPanel.getRowIndex(60, anns), -1);
+
+ ann2.visible = false;
+ assertEquals(AnnotationPanel.getRowIndex(0, anns), 0);
+ assertEquals(AnnotationPanel.getRowIndex(9, anns), 0);
+ assertEquals(AnnotationPanel.getRowIndex(10, anns), 2);
+ assertEquals(AnnotationPanel.getRowIndex(39, anns), 2);
+ assertEquals(AnnotationPanel.getRowIndex(40, anns), -1);
+
+ ann1.visible = false;
+ assertEquals(AnnotationPanel.getRowIndex(0, anns), 2);
+ assertEquals(AnnotationPanel.getRowIndex(29, anns), 2);
+ assertEquals(AnnotationPanel.getRowIndex(30, anns), -1);
+ }
+}
--- /dev/null
+package jalview.gui;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertSame;
+
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.ScoreModelI;
+import jalview.bin.Cache;
+
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class CalculationChooserTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ // read-only Jalview properties
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.applicationProperties.setProperty("BLOSUM62_PCA_FOR_NUCLEOTIDE",
+ Boolean.FALSE.toString());
+ }
+
+ @Test(groups = "Functional")
+ public void testGetApplicableScoreModels()
+ {
+ ScoreModels models = ScoreModels.getInstance();
+ ScoreModelI blosum62 = models.getBlosum62();
+ ScoreModelI pam250 = models.getPam250();
+ ScoreModelI dna = models.getDefaultModel(false);
+
+ /*
+ * peptide models for PCA
+ */
+ List<ScoreModelI> filtered = CalculationChooser
+ .getApplicableScoreModels(false, true);
+ assertEquals(filtered.size(), 4);
+ assertSame(filtered.get(0), blosum62);
+ assertSame(filtered.get(1), pam250);
+ assertEquals(filtered.get(2).getName(), "PID");
+ assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
+
+ /*
+ * peptide models for Tree are the same
+ */
+ filtered = CalculationChooser.getApplicableScoreModels(false, false);
+ assertEquals(filtered.size(), 4);
+ assertSame(filtered.get(0), blosum62);
+ assertSame(filtered.get(1), pam250);
+ assertEquals(filtered.get(2).getName(), "PID");
+ assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
+
+ /*
+ * nucleotide models for PCA
+ */
+ filtered = CalculationChooser.getApplicableScoreModels(true, true);
+ assertEquals(filtered.size(), 3);
+ assertSame(filtered.get(0), dna);
+ assertEquals(filtered.get(1).getName(), "PID");
+ assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
+
+ /*
+ * nucleotide models for Tree are the same
+ */
+ filtered = CalculationChooser.getApplicableScoreModels(true, false);
+ assertEquals(filtered.size(), 3);
+ assertSame(filtered.get(0), dna);
+ assertEquals(filtered.get(1).getName(), "PID");
+ assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
+
+ /*
+ * enable inclusion of BLOSUM62 for nucleotide PCA (JAL-2962)
+ */
+ Cache.applicationProperties.setProperty("BLOSUM62_PCA_FOR_NUCLEOTIDE",
+ Boolean.TRUE.toString());
+
+ /*
+ * nucleotide models for Tree are unchanged
+ */
+ filtered = CalculationChooser.getApplicableScoreModels(true, false);
+ assertEquals(filtered.size(), 3);
+ assertSame(filtered.get(0), dna);
+ assertEquals(filtered.get(1).getName(), "PID");
+ assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
+
+ /*
+ * nucleotide models for PCA add BLOSUM62 as last option
+ */
+ filtered = CalculationChooser.getApplicableScoreModels(true, true);
+ assertEquals(filtered.size(), 4);
+ assertSame(filtered.get(0), dna);
+ assertEquals(filtered.get(1).getName(), "PID");
+ assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
+ assertSame(filtered.get(3), blosum62);
+ }
+}
--- /dev/null
+package jalview.gui;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertSame;
+import static org.testng.Assert.assertTrue;
+
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.MessageManager;
+
+import java.util.Enumeration;
+import java.util.Iterator;
+
+import javax.swing.AbstractButton;
+import javax.swing.ButtonGroup;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class ColourMenuHelperTest
+{
+ /**
+ * Use a properties file with a user-defined colour scheme
+ */
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ }
+
+ @Test(groups = "Functional")
+ public void testAddMenuItems_peptide()
+ {
+ SequenceI s1 = new Sequence("s1", "KFRQSILM");
+ AlignmentI al = new Alignment(new SequenceI[] { s1 });
+ JMenu menu = new JMenu();
+
+ ButtonGroup bg = ColourMenuHelper.addMenuItems(menu, null, al, false);
+ Enumeration<AbstractButton> bgElements = bg.getElements();
+
+ /*
+ * first entry is 'No Colour' option
+ */
+ JMenuItem item = menu.getItem(0);
+ assertEquals(item.getName(), ResidueColourScheme.NONE);
+ assertEquals(item.getText(), MessageManager.getString("label.none"));
+ AbstractButton bgItem = bgElements.nextElement();
+ assertSame(bgItem, item);
+
+ /*
+ * check that each registered colour scheme is in the menu,
+ * and in the button group;
+ * nucleotide-only schemes should be disabled menu items
+ */
+ Iterator<ColourSchemeI> colourSchemes = ColourSchemes.getInstance()
+ .getColourSchemes().iterator();
+ final int items = menu.getItemCount();
+ for (int i = 1; i < items; i++)
+ {
+ item = menu.getItem(i);
+ bgItem = bgElements.nextElement();
+ assertSame(bgItem, item);
+ ColourSchemeI cs = colourSchemes.next();
+ String name = cs.getSchemeName();
+ assertEquals(item.getName(), name);
+ boolean enabled = item.isEnabled();
+ assertEquals(enabled, cs.isApplicableTo(al));
+ if (cs instanceof NucleotideColourScheme) // nucleotide only
+ {
+ assertFalse(enabled);
+ }
+ if (cs instanceof ClustalxColourScheme) // peptide only
+ {
+ assertTrue(enabled);
+ }
+ if (cs instanceof PIDColourScheme) // nucleotide or peptide
+ {
+ assertTrue(enabled);
+ }
+
+ /*
+ * check i18n for display name
+ */
+ String label = MessageManager.getStringOrReturn("label.colourScheme_",
+ name.toLowerCase().replace(" ", "_"));
+ assertEquals(item.getText(), label);
+ }
+
+ /*
+ * check nothing left over
+ */
+ assertFalse(colourSchemes.hasNext());
+ assertFalse(bgElements.hasMoreElements());
+ }
+
+ @Test(groups = "Functional")
+ public void testAddMenuItems_nucleotide()
+ {
+ SequenceI s1 = new Sequence("s1", "GAATAATCCATAACAG");
+ AlignmentI al = new Alignment(new SequenceI[] { s1 });
+ JMenu menu = new JMenu();
+ AlignFrame af = new AlignFrame(al, 500, 500);
+
+ /*
+ * menu for SequenceGroup excludes 'User Defined Colour'
+ */
+ PopupMenu popup = new PopupMenu(af.alignPanel, s1, null);
+ ButtonGroup bg = ColourMenuHelper.addMenuItems(menu, popup, al, false);
+ Enumeration<AbstractButton> bgElements = bg.getElements();
+
+ /*
+ * first entry is 'No Colour' option
+ */
+ JMenuItem item = menu.getItem(0);
+ assertEquals(item.getName(), ResidueColourScheme.NONE);
+ assertEquals(item.getText(), MessageManager.getString("label.none"));
+ AbstractButton bgItem = bgElements.nextElement();
+ assertSame(bgItem, item);
+
+ /*
+ * check that each registered colour scheme is in the menu,
+ * and in the button group;
+ * nucleotide-only schemes should be disabled menu items
+ */
+ Iterator<ColourSchemeI> colourSchemes = ColourSchemes.getInstance()
+ .getColourSchemes().iterator();
+ final int items = menu.getItemCount();
+ for (int i = 1; i < items; i++)
+ {
+ item = menu.getItem(i);
+ bgItem = bgElements.nextElement();
+ assertSame(bgItem, item);
+ ColourSchemeI cs = colourSchemes.next();
+ String name = cs.getSchemeName();
+ assertEquals(item.getName(), name);
+ boolean enabled = item.isEnabled();
+ assertEquals(enabled, cs.isApplicableTo(al));
+ if (cs instanceof NucleotideColourScheme) // nucleotide only
+ {
+ assertTrue(enabled);
+ }
+ if (cs instanceof ClustalxColourScheme) // peptide only
+ {
+ assertFalse(enabled);
+ }
+ if (cs instanceof PIDColourScheme) // nucleotide or peptide
+ {
+ assertTrue(enabled);
+ }
+
+ /*
+ * check i18n for display name
+ */
+ String label = MessageManager.getStringOrReturn("label.colourScheme_",
+ name.toLowerCase().replace(" ", "_"));
+ assertEquals(item.getText(), label);
+ }
+
+ /*
+ * check nothing left over
+ */
+ assertFalse(colourSchemes.hasNext());
+ assertFalse(bgElements.hasMoreElements());
+ }
+
+ /**
+ * 'Simple only' mode constructs colour menu for structures
+ * <ul>
+ * <li>no 'No Colour' option</li>
+ * <li>only simple colour schemes (colour per residue)</li>
+ * </ul>
+ */
+ @Test(groups = "Functional")
+ public void testAddMenuItems_simpleOnly()
+ {
+ SequenceI s1 = new Sequence("s1", "KFRQSILM");
+ AlignmentI al = new Alignment(new SequenceI[] { s1 });
+ JMenu menu = new JMenu();
+
+ ButtonGroup bg = ColourMenuHelper.addMenuItems(menu, null, al, true);
+ Enumeration<AbstractButton> bgElements = bg.getElements();
+
+ /*
+ * check that only 'simple' colour schemes are included
+ */
+ Iterator<ColourSchemeI> colourSchemes = ColourSchemes.getInstance()
+ .getColourSchemes().iterator();
+ int i = 0;
+ while (colourSchemes.hasNext())
+ {
+ ColourSchemeI cs = colourSchemes.next();
+ if (!cs.isSimple())
+ {
+ continue;
+ }
+ JMenuItem item = menu.getItem(i++);
+ AbstractButton bgItem = bgElements.nextElement();
+ assertSame(bgItem, item);
+ }
+
+ /*
+ * check nothing left over
+ */
+ assertEquals(i, menu.getItemCount());
+ assertFalse(bgElements.hasMoreElements());
+ }
+
+ /*
+ * menu for AlignFrame includes 'User Defined Colour'
+ */
+ @Test(groups = "Functional")
+ public void testAddMenuItems_forAlignFrame()
+ {
+ SequenceI s1 = new Sequence("s1", "KFRQSILM");
+ AlignmentI al = new Alignment(new SequenceI[] { s1 });
+ AlignFrame af = new AlignFrame(al, 500, 500);
+ JMenu menu = new JMenu();
+
+ ButtonGroup bg = ColourMenuHelper.addMenuItems(menu, af, al, false);
+ Enumeration<AbstractButton> bgElements = bg.getElements();
+
+ /*
+ * check that each registered colour scheme is in the menu,
+ * (skipping over No Colour which is the first menu item),
+ * and in the button group
+ */
+ bgElements.nextElement(); // skip No Colour
+ Iterator<ColourSchemeI> colourSchemes = ColourSchemes.getInstance()
+ .getColourSchemes().iterator();
+ final int items = menu.getItemCount();
+ for (int i = 1; i < items - 1; i++)
+ {
+ JMenuItem item = menu.getItem(i);
+ AbstractButton bgItem = bgElements.nextElement();
+ assertSame(bgItem, item);
+ ColourSchemeI cs = colourSchemes.next();
+ assertEquals(item.getName(), cs.getSchemeName());
+ }
+
+ /*
+ * check menu also has User Defined Colour
+ */
+ assertFalse(colourSchemes.hasNext());
+ JMenuItem item = menu.getItem(items - 1);
+ AbstractButton bgItem = bgElements.nextElement();
+ assertSame(bgItem, item);
+ assertEquals(item.getName(), ResidueColourScheme.USER_DEFINED_MENU);
+ assertEquals(item.getText(),
+ MessageManager.getString("action.user_defined"));
+ }
+}
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.schemes.FeatureColour;
+import jalview.schemes.FeatureColourTest;
import jalview.util.matcher.Condition;
import java.awt.Color;
fr.setColour("type2", byLabel);
// type3: by score above threshold
- FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
- 10);
+ FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
+ Color.BLUE, null, 1, 10);
byScore.setAboveThreshold(true);
byScore.setThreshold(2f);
fr.setColour("type3", byScore);
fr.setColour("type4", byAF);
// type5: by attribute CSQ:PolyPhen below threshold
- FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
- 1, 10);
+ FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
+ Color.BLUE, null, 1, 10);
byPolyPhen.setBelowThreshold(true);
byPolyPhen.setThreshold(3f);
byPolyPhen.setAttributeName("CSQ", "PolyPhen");
});
seq.addSequenceFeature(sf);
}
+
+ /**
+ * @see FeatureColourTest#testGetDescription()
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testGetColorTooltip() throws IOException
+ {
+ assertNull(FeatureSettings.getColorTooltip(null, false));
+
+ /*
+ * simple colour
+ */
+ FeatureColourI fc = new FeatureColour(Color.black);
+ String simpleTooltip = "Click to edit, right-click for menu";
+ assertEquals(FeatureSettings.getColorTooltip(fc, true), simpleTooltip);
+ assertNull(FeatureSettings.getColorTooltip(fc, false));
+
+ /*
+ * graduated colour tooltip includes description of colour
+ */
+ fc.setColourByLabel(true);
+ assertEquals(FeatureSettings.getColorTooltip(fc, false),
+ "<html>By Label</html>");
+ assertEquals(FeatureSettings.getColorTooltip(fc, true),
+ "<html>By Label<br>" + simpleTooltip + "</br></html>");
+
+ /*
+ * graduated colour with threshold is html-encoded
+ */
+ fc = new FeatureColour(null, Color.red, Color.blue, null, 2f, 10f);
+ fc.setBelowThreshold(true);
+ fc.setThreshold(4f);
+ assertEquals(FeatureSettings.getColorTooltip(fc, false),
+ "<html>By Score (< 4.0)</html>");
+ assertEquals(FeatureSettings.getColorTooltip(fc, true),
+ "<html>By Score (< 4.0)<br>" + simpleTooltip
+ + "</br></html>");
+
+ fc.setAboveThreshold(true);
+ assertEquals(FeatureSettings.getColorTooltip(fc, false),
+ "<html>By Score (> 4.0)</html>");
+ assertEquals(FeatureSettings.getColorTooltip(fc, true),
+ "<html>By Score (> 4.0)<br>" + simpleTooltip
+ + "</br></html>");
+ }
}
package jalview.gui;
import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
import jalview.analysis.AlignmentGenerator;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
+import java.awt.event.MouseEvent;
import java.io.File;
import java.io.IOException;
import java.io.PrintStream;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class FreeUpMemoryTest
{
private static final int ONE_MB = 1000 * 1000;
{
Jalview.main(new String[] { "-nonews", "-props",
"test/jalview/testProps.jvprops" });
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
- Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("SHOW_QUALITY",
- Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
- Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("SHOW_OCCUPANCY",
- Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
- Boolean.TRUE.toString());
+ String True = Boolean.TRUE.toString();
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", True);
+ Cache.applicationProperties.setProperty("SHOW_QUALITY", True);
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION", True);
+ Cache.applicationProperties.setProperty("SHOW_OCCUPANCY", True);
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY", True);
}
/**
protected void checkUsedMemory(long expectedMax)
{
/*
- * request garbage collection and wait briefly for it to run;
+ * request garbage collection and wait for it to run;
* NB there is no guarantee when, or whether, it will do so
+ * wait time depends on JRE/processor, generous allowance here
*/
System.gc();
- waitFor(100);
+ waitFor(1500);
/*
* a second gc() call should not be necessary - but it is!
* the test passes with it, and fails without it
*/
System.gc();
- waitFor(100);
+ waitFor(1500);
/*
* check used memory is 'reasonably low'
}
/*
+ * open an Overview window
+ */
+ af.overviewMenuItem_actionPerformed(null);
+ assertNotNull(af.alignPanel.overviewPanel);
+
+ /*
+ * exercise the pop-up menu in the Overview Panel (JAL-2864)
+ */
+ Object[] args = new Object[] {
+ new MouseEvent(af, 0, 0, 0, 0, 0, 1, true) };
+ PA.invokeMethod(af.alignPanel.overviewPanel,
+ "showPopupMenu(java.awt.event.MouseEvent)", args);
+
+ /*
* set a selection group - potential memory leak if it retains
* a reference to the alignment
*/
--- /dev/null
+package jalview.gui;
+
+import static org.testng.Assert.assertTrue;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.awt.event.MouseEvent;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class ScalePanelTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(groups = "Functional")
+ public void testPreventNegativeStartColumn()
+ {
+ SequenceI seq1 = new Sequence("Seq1", "MATRESS");
+ SequenceI seq2 = new Sequence("Seq2", "MADNESS");
+ AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
+
+ AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
+ al.getHeight());
+ ScalePanel scalePanel = new ScalePanel(
+ alignFrame.getViewport(), alignFrame.alignPanel
+ );
+
+ MouseEvent mouse = new MouseEvent(
+ scalePanel, 0, 1, 0, 4, 0, 1, false
+ );
+ scalePanel.mousePressed(mouse);
+ scalePanel.mouseDragged(mouse);
+
+ // simulate dragging selection leftwards beyond the sequences giving
+ // negative X
+ mouse = new MouseEvent(scalePanel, 0, 1, 0, -30, 0, 1, false);
+
+ scalePanel.mouseReleased(mouse);
+
+ SequenceGroup sg = scalePanel.av.getSelectionGroup();
+ int startCol = sg.getStartRes();
+
+ assertTrue(startCol >= 0);
+
+
+ }
+
+}
import java.awt.Font;
import java.awt.FontMetrics;
-import junit.extensions.PA;
-
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class SeqCanvasTest
{
/**
assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 3);
/*
- * reduce canvas height by 1 pixel - should not be enough height
- * to draw 3 widths
+ * reduce canvas height by 1 pixel
+ * - should not be enough height to draw 3 widths
*/
canvasHeight -= 1;
testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
canvasWidth += 8;
wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
canvasHeight);
- assertEquals(wrappedWidth, 27);
+ assertEquals(wrappedWidth, 27); // 8px not enough
canvasWidth += 1;
wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
canvasHeight);
- assertEquals(wrappedWidth, 28);
+ assertEquals(wrappedWidth, 28); // 9px is enough
/*
* now West but not East scale - lose 39 pixels or 4 columns
canvasWidth += 2;
wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
canvasHeight);
- assertEquals(wrappedWidth, 24);
+ assertEquals(wrappedWidth, 24); // 2px not enough
canvasWidth += 1;
wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
canvasHeight);
- assertEquals(wrappedWidth, 25);
+ assertEquals(wrappedWidth, 25); // 3px is enough
/*
* turn off scales left and right, make width exactly 157 columns
2 * charHeight);
int repeatingHeight = (int) PA.getValue(testee, "wrappedRepeatHeightPx");
assertEquals(repeatingHeight, charHeight * (2 + al.getHeight())
- + annotationHeight);
+ + SeqCanvas.SEQS_ANNOTATION_GAP + annotationHeight);
assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 1);
/*
- * repeat height is 17 * (2 + 15) = 289 + annotationHeight = 507
- * make canvas height 2 * 289 + 3 * charHeight so just enough to
- * draw 2 widths and the first sequence of a third
+ * repeat height is 17 * (2 + 15) = 289 + 3 + annotationHeight = 510
+ * make canvas height 2 of these plus 3 charHeights
+ * so just enough to draw 2 widths, gap + scale + the first sequence of a third
*/
- canvasHeight = charHeight * (17 * 2 + 3) + 2 * annotationHeight;
+ canvasHeight = charHeight * (17 * 2 + 3)
+ + 2 * (annotationHeight + SeqCanvas.SEQS_ANNOTATION_GAP);
testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 3);
* reduce height to enough for 2 widths and not quite a third
* i.e. two repeating heights + spacer + sequence - 1 pixel
*/
- canvasHeight = charHeight * (16 * 2 + 2) + 2 * annotationHeight - 1;
+ canvasHeight = charHeight * (16 * 2 + 2)
+ + 2 * (annotationHeight + SeqCanvas.SEQS_ANNOTATION_GAP) - 1;
testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 2);
package jalview.gui;
import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.commands.EditCommand.Edit;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.SeqPanel.MousePos;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.util.MessageManager;
+import java.awt.Event;
+import java.awt.EventQueue;
+import java.awt.event.MouseEvent;
+import java.lang.reflect.InvocationTargetException;
+
+import javax.swing.JLabel;
+
+import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class SeqPanelTest
{
AlignFrame af;
assertEquals(
alignFrame.alignPanel.getSeqPanel().setStatusMessage(
visAl.getSequenceAt(1), 1, 1), 2);
- assertEquals(alignFrame.statusBar.getText(),
+ assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
"Sequence 2 ID: Seq2 Residue: ALA (2)");
assertEquals(
alignFrame.alignPanel.getSeqPanel().setStatusMessage(
visAl.getSequenceAt(1), 4, 1), 3);
- assertEquals(alignFrame.statusBar.getText(),
+ assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
"Sequence 2 ID: Seq2 Residue: GLU (3)");
// no status message at a gap, returns next residue position to the right
assertEquals(
alignFrame.alignPanel.getSeqPanel().setStatusMessage(
visAl.getSequenceAt(1), 2, 1), 3);
- assertEquals(alignFrame.statusBar.getText(), "Sequence 2 ID: Seq2");
+ assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
+ "Sequence 2 ID: Seq2");
assertEquals(
alignFrame.alignPanel.getSeqPanel().setStatusMessage(
visAl.getSequenceAt(1), 3, 1), 3);
- assertEquals(alignFrame.statusBar.getText(), "Sequence 2 ID: Seq2");
+ assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
+ "Sequence 2 ID: Seq2");
}
@Test(groups = "Functional")
assertEquals(
alignFrame.alignPanel.getSeqPanel().setStatusMessage(
visAl.getSequenceAt(1), 1, 1), 2);
- assertEquals(alignFrame.statusBar.getText(),
+ assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
"Sequence 2 ID: Seq2 Residue: B (2)");
}
+
+ @Test(groups = "Functional")
+ public void testGetEditStatusMessage()
+ {
+ assertNull(SeqPanel.getEditStatusMessage(null));
+
+ EditCommand edit = new EditCommand(); // empty
+ assertNull(SeqPanel.getEditStatusMessage(edit));
+
+ SequenceI[] seqs = new SequenceI[] { new Sequence("a", "b") };
+
+ // 1 gap
+ edit.addEdit(edit.new Edit(Action.INSERT_GAP, seqs, 1, 1, '-'));
+ String expected = MessageManager.formatMessage("label.insert_gap", "1");
+ assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
+
+ // 3 more gaps makes +4
+ edit.addEdit(edit.new Edit(Action.INSERT_GAP, seqs, 1, 3, '-'));
+ expected = MessageManager.formatMessage("label.insert_gaps", "4");
+ assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
+
+ // 2 deletes makes + 2
+ edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-'));
+ expected = MessageManager.formatMessage("label.insert_gaps", "2");
+ assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
+
+ // 2 more deletes makes 0 - no text
+ edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-'));
+ assertNull(SeqPanel.getEditStatusMessage(edit));
+
+ // 1 more delete makes 1 delete
+ edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-'));
+ expected = MessageManager.formatMessage("label.delete_gap", "1");
+ assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
+
+ // 1 more delete makes 2 deletes
+ edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-'));
+ expected = MessageManager.formatMessage("label.delete_gaps", "2");
+ assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
+ }
+
+ /**
+ * Tests that simulate 'locked editing', where an inserted gap is balanced by
+ * a gap deletion in the selection group, and vice versa
+ */
+ @Test(groups = "Functional")
+ public void testGetEditStatusMessage_lockedEditing()
+ {
+ EditCommand edit = new EditCommand(); // empty
+ SequenceI[] seqs = new SequenceI[] { new Sequence("a", "b") };
+
+ // 1 gap inserted, balanced by 1 delete
+ Edit e1 = edit.new Edit(Action.INSERT_GAP, seqs, 1, 1, '-');
+ edit.addEdit(e1);
+ Edit e2 = edit.new Edit(Action.DELETE_GAP, seqs, 5, 1, '-');
+ e2.setSystemGenerated(true);
+ edit.addEdit(e2);
+ String expected = MessageManager.formatMessage("label.insert_gap", "1");
+ assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
+
+ // 2 more gaps makes +3
+ Edit e3 = edit.new Edit(Action.INSERT_GAP, seqs, 1, 2, '-');
+ edit.addEdit(e3);
+ Edit e4 = edit.new Edit(Action.DELETE_GAP, seqs, 5, 2, '-');
+ e4.setSystemGenerated(true);
+ edit.addEdit(e4);
+ expected = MessageManager.formatMessage("label.insert_gaps", "3");
+ assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
+
+ // 2 deletes makes + 1
+ Edit e5 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-');
+ edit.addEdit(e5);
+ Edit e6 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 2, '-');
+ e6.setSystemGenerated(true);
+ edit.addEdit(e6);
+ expected = MessageManager.formatMessage("label.insert_gap", "1");
+ assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
+
+ // 1 more delete makes 0 - no text
+ Edit e7 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-');
+ edit.addEdit(e7);
+ Edit e8 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 1, '-');
+ e8.setSystemGenerated(true);
+ edit.addEdit(e8);
+ expected = MessageManager.formatMessage("label.insert_gaps", "2");
+ assertNull(SeqPanel.getEditStatusMessage(edit));
+
+ // 1 more delete makes 1 delete
+ Edit e9 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-');
+ edit.addEdit(e9);
+ Edit e10 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 1, '-');
+ e10.setSystemGenerated(true);
+ edit.addEdit(e10);
+ expected = MessageManager.formatMessage("label.delete_gap", "1");
+ assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
+
+ // 2 more deletes makes 3 deletes
+ Edit e11 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-');
+ edit.addEdit(e11);
+ Edit e12 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 2, '-');
+ e12.setSystemGenerated(true);
+ edit.addEdit(e12);
+ expected = MessageManager.formatMessage("label.delete_gaps", "3");
+ assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
+ }
+
+ public void testFindMousePosition_unwrapped()
+ {
+ String seqData = ">Seq1\nAACDE\n>Seq2\nAA--E\n";
+ AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(seqData,
+ DataSourceType.PASTE);
+ AlignViewportI av = alignFrame.getViewport();
+ av.setShowAnnotation(true);
+ av.setWrapAlignment(false);
+ final int charHeight = av.getCharHeight();
+ final int charWidth = av.getCharWidth();
+ // sanity checks:
+ assertTrue(charHeight > 0);
+ assertTrue(charWidth > 0);
+ assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
+
+ SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
+ int x = 0;
+ int y = 0;
+
+ /*
+ * mouse at top left of unwrapped panel
+ */
+ MouseEvent evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y,
+ 0, 0, 0, false, 0);
+ MousePos pos = testee.findMousePosition(evt);
+ assertEquals(pos.column, 0);
+ assertEquals(pos.seqIndex, 0);
+ assertEquals(pos.annotationIndex, -1);
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void tearDown()
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ @Test(groups = "Functional")
+ public void testFindMousePosition_wrapped_annotations()
+ {
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "true");
+ Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
+ AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ AlignViewportI av = alignFrame.getViewport();
+ av.setScaleAboveWrapped(false);
+ av.setScaleLeftWrapped(false);
+ av.setScaleRightWrapped(false);
+ alignFrame.alignPanel.paintAlignment(false, false);
+ waitForSwing(); // for Swing thread
+
+ final int charHeight = av.getCharHeight();
+ final int charWidth = av.getCharWidth();
+ final int alignmentHeight = av.getAlignment().getHeight();
+
+ // sanity checks:
+ assertTrue(charHeight > 0);
+ assertTrue(charWidth > 0);
+ assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
+
+ SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
+ int x = 0;
+ int y = 0;
+
+ /*
+ * mouse at top left of wrapped panel; there is a gap of charHeight
+ * above the alignment
+ */
+ MouseEvent evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y,
+ 0, 0, 0, false, 0);
+ MousePos pos = testee.findMousePosition(evt);
+ assertEquals(pos.column, 0);
+ assertEquals(pos.seqIndex, -1); // above sequences
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at bottom of gap above
+ */
+ y = charHeight - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, -1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor over top of first sequence
+ */
+ y = charHeight;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 0);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at bottom of first sequence
+ */
+ y = 2 * charHeight - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 0);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at top of second sequence
+ */
+ y = 2 * charHeight;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at bottom of second sequence
+ */
+ y = 3 * charHeight - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at bottom of last sequence
+ */
+ y = charHeight * (1 + alignmentHeight) - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, alignmentHeight - 1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor below sequences, in 3-pixel gap above annotations
+ * method reports index of nearest sequence above
+ */
+ y += 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, alignmentHeight - 1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor still in the gap above annotations, now at the bottom of it
+ */
+ y += SeqCanvas.SEQS_ANNOTATION_GAP - 1; // 3-1 = 2
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, alignmentHeight - 1);
+ assertEquals(pos.annotationIndex, -1);
+
+ AlignmentAnnotation[] annotationRows = av.getAlignment()
+ .getAlignmentAnnotation();
+ for (int n = 0; n < annotationRows.length; n++)
+ {
+ /*
+ * cursor at the top of the n'th annotation
+ */
+ y += 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, alignmentHeight - 1);
+ assertEquals(pos.annotationIndex, n); // over n'th annotation
+
+ /*
+ * cursor at the bottom of the n'th annotation
+ */
+ y += annotationRows[n].height - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, alignmentHeight - 1);
+ assertEquals(pos.annotationIndex, n);
+ }
+
+ /*
+ * cursor in gap between wrapped widths
+ */
+ y += 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, -1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at bottom of gap between wrapped widths
+ */
+ y += charHeight - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, -1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at top of first sequence, second wrapped width
+ */
+ y += 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 0);
+ assertEquals(pos.annotationIndex, -1);
+ }
+
+ @Test(groups = "Functional")
+ public void testFindMousePosition_wrapped_scaleAbove()
+ {
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "true");
+ Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
+ AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ AlignViewportI av = alignFrame.getViewport();
+ av.setScaleAboveWrapped(true);
+ av.setScaleLeftWrapped(false);
+ av.setScaleRightWrapped(false);
+ alignFrame.alignPanel.paintAlignment(false, false);
+ waitForSwing();
+
+ final int charHeight = av.getCharHeight();
+ final int charWidth = av.getCharWidth();
+ final int alignmentHeight = av.getAlignment().getHeight();
+
+ // sanity checks:
+ assertTrue(charHeight > 0);
+ assertTrue(charWidth > 0);
+ assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
+
+ SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
+ int x = 0;
+ int y = 0;
+
+ /*
+ * mouse at top left of wrapped panel; there is a gap of charHeight
+ * above the alignment
+ */
+ MouseEvent evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y,
+ 0, 0, 0, false, 0);
+ MousePos pos = testee.findMousePosition(evt);
+ assertEquals(pos.column, 0);
+ assertEquals(pos.seqIndex, -1); // above sequences
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at bottom of gap above
+ * two charHeights including scale panel
+ */
+ y = 2 * charHeight - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, -1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor over top of first sequence
+ */
+ y += 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 0);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at bottom of first sequence
+ */
+ y += charHeight - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 0);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at top of second sequence
+ */
+ y += 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at bottom of second sequence
+ */
+ y += charHeight - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at bottom of last sequence
+ * (scale + gap + sequences)
+ */
+ y = charHeight * (2 + alignmentHeight) - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, alignmentHeight - 1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor below sequences, in 3-pixel gap above annotations
+ */
+ y += 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, alignmentHeight - 1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor still in the gap above annotations, now at the bottom of it
+ * method reports index of nearest sequence above
+ */
+ y += SeqCanvas.SEQS_ANNOTATION_GAP - 1; // 3-1 = 2
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, alignmentHeight - 1);
+ assertEquals(pos.annotationIndex, -1);
+
+ AlignmentAnnotation[] annotationRows = av.getAlignment().getAlignmentAnnotation();
+ for (int n = 0; n < annotationRows.length; n++)
+ {
+ /*
+ * cursor at the top of the n'th annotation
+ */
+ y += 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, alignmentHeight - 1);
+ assertEquals(pos.annotationIndex, n); // over n'th annotation
+
+ /*
+ * cursor at the bottom of the n'th annotation
+ */
+ y += annotationRows[n].height - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, alignmentHeight - 1);
+ assertEquals(pos.annotationIndex, n);
+ }
+
+ /*
+ * cursor in gap between wrapped widths
+ */
+ y += 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, -1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at bottom of gap between wrapped widths
+ */
+ y += charHeight - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, -1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at top of scale, second wrapped width
+ */
+ y += 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, -1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at bottom of scale, second wrapped width
+ */
+ y += charHeight - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, -1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at top of first sequence, second wrapped width
+ */
+ y += 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 0);
+ assertEquals(pos.annotationIndex, -1);
+ }
+
+ @Test(groups = "Functional")
+ public void testFindMousePosition_wrapped_noAnnotations()
+ {
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "false");
+ Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
+ AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ AlignViewportI av = alignFrame.getViewport();
+ av.setScaleAboveWrapped(false);
+ av.setScaleLeftWrapped(false);
+ av.setScaleRightWrapped(false);
+ alignFrame.alignPanel.paintAlignment(false, false);
+ waitForSwing();
+
+ final int charHeight = av.getCharHeight();
+ final int charWidth = av.getCharWidth();
+ final int alignmentHeight = av.getAlignment().getHeight();
+
+ // sanity checks:
+ assertTrue(charHeight > 0);
+ assertTrue(charWidth > 0);
+ assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
+
+ SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
+ int x = 0;
+ int y = 0;
+
+ /*
+ * mouse at top left of wrapped panel; there is a gap of charHeight
+ * above the alignment
+ */
+ MouseEvent evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y,
+ 0, 0, 0, false, 0);
+ MousePos pos = testee.findMousePosition(evt);
+ assertEquals(pos.column, 0);
+ assertEquals(pos.seqIndex, -1); // above sequences
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor over top of first sequence
+ */
+ y = charHeight;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 0);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at bottom of last sequence
+ */
+ y = charHeight * (1 + alignmentHeight) - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, alignmentHeight - 1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor below sequences, at top of charHeight gap between widths
+ */
+ y += 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, -1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor below sequences, at top of charHeight gap between widths
+ */
+ y += charHeight - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, -1);
+ assertEquals(pos.annotationIndex, -1);
+
+ /*
+ * cursor at the top of the first sequence, second width
+ */
+ y += 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+ false, 0);
+ pos = testee.findMousePosition(evt);
+ assertEquals(pos.seqIndex, 0);
+ assertEquals(pos.annotationIndex, -1);
+ }
+
+ @Test(groups = "Functional")
+ public void testFindColumn_unwrapped()
+ {
+ Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "false");
+ AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
+ int x = 0;
+ final int charWidth = alignFrame.getViewport().getCharWidth();
+ assertTrue(charWidth > 0); // sanity check
+ assertEquals(alignFrame.getViewport().getRanges().getStartRes(), 0);
+
+ /*
+ * mouse at top left of unwrapped panel
+ */
+ MouseEvent evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0,
+ 0, 0, 0, false, 0);
+ assertEquals(testee.findColumn(evt), 0);
+
+ /*
+ * not quite one charWidth across
+ */
+ x = charWidth-1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0,
+ 0, 0, 0, false, 0);
+ assertEquals(testee.findColumn(evt), 0);
+
+ /*
+ * one charWidth across
+ */
+ x = charWidth;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
+ false, 0);
+ assertEquals(testee.findColumn(evt), 1);
+
+ /*
+ * two charWidths across
+ */
+ x = 2 * charWidth;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
+ false, 0);
+ assertEquals(testee.findColumn(evt), 2);
+
+ /*
+ * limited to last column of seqcanvas
+ */
+ x = 20000;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
+ false, 0);
+ SeqCanvas seqCanvas = alignFrame.alignPanel.getSeqPanel().seqCanvas;
+ int w = seqCanvas.getWidth();
+ // limited to number of whole columns, base 0
+ int expected = w / charWidth - 1;
+ assertEquals(testee.findColumn(evt), expected);
+
+ /*
+ * hide columns 5-10 (base 1)
+ */
+ alignFrame.getViewport().hideColumns(4, 9);
+ x = 5 * charWidth + 2;
+ // x is in 6th visible column, absolute column 12, or 11 base 0
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
+ false, 0);
+ assertEquals(testee.findColumn(evt), 11);
+ }
+
+ @Test(groups = "Functional")
+ public void testFindColumn_wrapped()
+ {
+ Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
+ AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ AlignViewport av = alignFrame.getViewport();
+ av.setScaleAboveWrapped(false);
+ av.setScaleLeftWrapped(false);
+ av.setScaleRightWrapped(false);
+ alignFrame.alignPanel.paintAlignment(false, false);
+ // need to wait for repaint to finish!
+ waitForSwing();
+ SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
+ int x = 0;
+ final int charWidth = av.getCharWidth();
+ assertTrue(charWidth > 0); // sanity check
+ assertEquals(av.getRanges().getStartRes(), 0);
+
+ /*
+ * mouse at top left of wrapped panel, no West (left) scale
+ */
+ MouseEvent evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0,
+ 0, 0, 0, false, 0);
+ assertEquals(testee.findColumn(evt), 0);
+
+ /*
+ * not quite one charWidth across
+ */
+ x = charWidth-1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0,
+ 0, 0, 0, false, 0);
+ assertEquals(testee.findColumn(evt), 0);
+
+ /*
+ * one charWidth across
+ */
+ x = charWidth;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
+ false, 0);
+ assertEquals(testee.findColumn(evt), 1);
+
+ /*
+ * x over scale left (before drawn columns) results in -1
+ */
+ av.setScaleLeftWrapped(true);
+ alignFrame.alignPanel.paintAlignment(false, false);
+ waitForSwing();
+ SeqCanvas seqCanvas = testee.seqCanvas;
+ int labelWidth = (int) PA.getValue(seqCanvas, "labelWidthWest");
+ assertTrue(labelWidth > 0);
+ x = labelWidth - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
+ false, 0);
+ assertEquals(testee.findColumn(evt), -1);
+
+ x = labelWidth;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
+ false, 0);
+ assertEquals(testee.findColumn(evt), 0);
+
+ /*
+ * x over right edge of last residue (including scale left)
+ */
+ int residuesWide = av.getRanges().getViewportWidth();
+ assertTrue(residuesWide > 0);
+ x = labelWidth + charWidth * residuesWide - 1;
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
+ false, 0);
+ assertEquals(testee.findColumn(evt), residuesWide - 1);
+
+ /*
+ * x over scale right (beyond drawn columns) results in -1
+ */
+ av.setScaleRightWrapped(true);
+ alignFrame.alignPanel.paintAlignment(false, false);
+ waitForSwing();
+ labelWidth = (int) PA.getValue(seqCanvas, "labelWidthEast");
+ assertTrue(labelWidth > 0);
+ int residuesWide2 = av.getRanges().getViewportWidth();
+ assertTrue(residuesWide2 > 0);
+ assertTrue(residuesWide2 < residuesWide); // available width reduced
+ x += 1; // just over left edge of scale right
+ evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
+ false, 0);
+ assertEquals(testee.findColumn(evt), -1);
+
+ // todo add startRes offset, hidden columns
+
+ }
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ /*
+ * use read-only test properties file
+ */
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Jalview.main(new String[] { "-nonews" });
+ }
+
+ /**
+ * waits for Swing event dispatch queue to empty
+ */
+ synchronized void waitForSwing()
+ {
+ try
+ {
+ EventQueue.invokeAndWait(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ }
+ });
+ } catch (InterruptedException | InvocationTargetException e)
+ {
+ e.printStackTrace();
+ }
+ }
}
}
}
- AlignmentI readAlignmentFile(File f)
+ protected AlignmentI readAlignmentFile(File f)
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
--- /dev/null
+package jalview.io;
+
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.List;
+import java.util.TreeMap;
+
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class BackupFilesTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ private static boolean actuallyDeleteTmpFiles = true;
+ private static String testDir = "examples";
+
+ private static String testBasename = "backupfilestest";
+
+ private static String testExt = ".fa";
+
+ private static String testFilename = testBasename + testExt;
+
+
+ private static String testFile = testDir + File.separatorChar
+ + testFilename;
+
+ private static String newBasename = testBasename + "Temp";
+
+ private static String newFilename = newBasename + testExt;
+
+ private static String newFile = testDir + File.separatorChar
+ + newFilename;
+
+ private static String sequenceName = "BACKUP_FILES";
+
+ private static String sequenceDescription = "backupfiles";
+
+ private static String sequenceData = "AAAARG";
+
+ private static String suffix = "_BACKUPTEST-%n";
+
+ private static int digits = 8;
+
+ private static int rollMax = 2;
+
+ private AlignFrame af;
+
+ // read and save with backupfiles disabled
+ @Test(groups = { "Functional" })
+ public void noBackupsEnabledTest() throws Exception
+ {
+ // set BACKUPFILES_ENABLED to false (i.e. turn off BackupFiles feature -- no
+ // backup files to be made when saving)
+ setBackupFilesOptions(false, true, true);
+
+ // init the newFile and backups (i.e. make sure newFile exists on its own
+ // and has no backups
+ initNewFileForTesting();
+
+ // now save again
+ save();
+
+ // check no backup files
+ File[] backupFiles = getBackupFiles();
+ Assert.assertTrue(backupFiles.length == 0);
+ }
+
+ // save keeping all backup files
+ @Test(groups = { "Functional" })
+ public void backupsEnabledNoRollMaxTest() throws Exception
+ {
+ // Enable BackupFiles and set noMax so all backupfiles get kept
+ setBackupFilesOptions(true, false, true);
+
+ // init the newFile and backups (i.e. make sure newFile exists on its own
+ // and has no backups)
+ initNewFileForTesting();
+
+ // now save a few times again. No rollMax so should have more than two
+ // backup files
+ int numSaves = 10;
+ for (int i = 0; i < numSaves; i++)
+ {
+ save();
+ }
+
+ // check 10 backup files
+ HashMap correctindexmap = new HashMap();
+ correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-00000001");
+ correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-00000002");
+ correctindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-00000003");
+ correctindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-00000004");
+ correctindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-00000005");
+ correctindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-00000006");
+ correctindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-00000007");
+ correctindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-00000008");
+ correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-00000009");
+ correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-00000010");
+ HashMap wrongindexmap = new HashMap();
+ wrongindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-1");
+ wrongindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-00000002");
+ wrongindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-00000003");
+ wrongindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-00000004");
+ wrongindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-00000005");
+ wrongindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-00000006");
+ wrongindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-00000007");
+ wrongindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-00000008");
+ wrongindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-00000009");
+ wrongindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-00000010");
+ int[] indexes2 = { 3, 4, 5, 6, 7, 8, 9, 10 };
+ int[] indexes3 = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 };
+ Assert.assertTrue(checkBackupFiles(correctindexmap));
+ Assert.assertFalse(checkBackupFiles(wrongindexmap));
+ Assert.assertFalse(checkBackupFiles(indexes2));
+ Assert.assertFalse(checkBackupFiles(indexes3));
+ }
+
+ // save keeping only the last rollMax (2) backup files
+ @Test(groups = { "Functional" })
+ public void backupsEnabledRollMaxTest() throws Exception
+ {
+ // Enable BackupFiles and set noMax so all backupfiles get kept
+ setBackupFilesOptions(true, false, false);
+
+ // init the newFile and backups (i.e. make sure newFile exists on its own
+ // and has no backups)
+ initNewFileForTesting();
+
+ // now save a few times again. No rollMax so should have more than two
+ // backup files
+ int numSaves = 10;
+ for (int i = 0; i < numSaves; i++)
+ {
+ save();
+ }
+
+ // check there are "rollMax" backup files and they are all saved correctly
+ // check 10 backup files
+ HashMap correctindexmap = new HashMap();
+ correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-00000009");
+ correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-00000010");
+ int[] indexes2 = { 10 };
+ int[] indexes3 = { 8, 9, 10 };
+ Assert.assertTrue(checkBackupFiles(correctindexmap));
+ Assert.assertFalse(checkBackupFiles(indexes2));
+ Assert.assertFalse(checkBackupFiles(indexes3));
+ }
+
+ // save keeping only the last rollMax (2) backup files
+ @Test(groups = { "Functional" })
+ public void backupsEnabledReverseRollMaxTest() throws Exception
+ {
+ // Enable BackupFiles and set noMax so all backupfiles get kept
+ setBackupFilesOptions(true, true, false);
+
+ // init the newFile and backups (i.e. make sure newFile exists on its own
+ // and has no backups)
+ initNewFileForTesting();
+
+ // now save a few times again. No rollMax so should have more than two
+ // backup files
+ int numSaves = 10;
+ for (int i = 0; i < numSaves; i++)
+ {
+ save();
+ }
+
+ // check there are "rollMax" backup files and they are all saved correctly
+ // check 10 backup files
+ HashMap correctindexmap = new HashMap();
+ correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-00000001");
+ correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-00000002");
+ int[] indexes2 = { 1 };
+ int[] indexes3 = { 1, 2, 3 };
+ Assert.assertTrue(checkBackupFiles(correctindexmap));
+ Assert.assertFalse(checkBackupFiles(indexes2));
+ Assert.assertFalse(checkBackupFiles(indexes3));
+ }
+
+ private void setBackupFilesOptions()
+ {
+ setBackupFilesOptions(true, false, false);
+ }
+
+ private void setBackupFilesOptions(boolean enabled, boolean reverse,
+ boolean noMax)
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+
+ Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
+ Boolean.toString(enabled));
+ Cache.applicationProperties.setProperty(BackupFiles.SUFFIX, suffix);
+ Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
+ Integer.toString(digits));
+ Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
+ Boolean.toString(reverse));
+ Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
+ Boolean.toString(noMax));
+ Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
+ Integer.toString(rollMax));
+ Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
+ "false");
+ }
+
+ private void save()
+ {
+ if (af != null)
+ {
+ af.saveAlignment(newFile, jalview.io.FileFormat.Fasta);
+ }
+ }
+
+ // this runs cleanTmpFiles and then writes the newFile once as a starting
+ // point for all tests
+ private void initNewFileForTesting() throws Exception
+ {
+ cleanupTmpFiles();
+
+ AppletFormatAdapter afa = new AppletFormatAdapter();
+ AlignmentI al = afa.readFile(testFile, DataSourceType.FILE,
+ jalview.io.FileFormat.Fasta);
+ List<SequenceI> l = al.getSequences();
+
+ // check this is right
+ if (l.size() != 1)
+ {
+ throw new Exception("single sequence from '" + testFile
+ + "' not read in correctly (should be a single short sequence). List<SequenceI> size is wrong.");
+ }
+ SequenceI s = l.get(0);
+ Sequence ref = new Sequence(sequenceName, sequenceData);
+ ref.setDescription(sequenceDescription);
+ if (!sequencesEqual(s, ref))
+ {
+ throw new Exception("single sequence from '" + testFile
+ + "' not read in correctly (should be a single short sequence). SequenceI name, description or data is wrong.");
+ }
+ // save alignment file to new filename -- this doesn't test backups disabled
+ // yet as this file shouldn't already exist
+ af = new AlignFrame(al, 0, 0);
+ af.saveAlignment(newFile, jalview.io.FileFormat.Fasta);
+ }
+
+ // this deletes the newFile (if it exists) and any saved backup file for it
+ @AfterClass(alwaysRun = true)
+ private void cleanupTmpFiles()
+ {
+ File newfile = new File(newFile);
+ if (newfile.exists())
+ {
+ newfile.delete();
+ }
+ File[] tmpFiles = getBackupFiles(newFile, suffix, digits);
+ for (int i = 0; i < tmpFiles.length; i++)
+ {
+ if (actuallyDeleteTmpFiles)
+ {
+ tmpFiles[i].delete();
+ }
+ else
+ {
+ System.out.println("Pretending to delete " + tmpFiles[i].getPath());
+ }
+ }
+ }
+
+ private static File[] getBackupFiles(String f, String s, int i)
+ {
+ TreeMap<Integer, File> bfTreeMap = BackupFiles.getBackupFilesAsTreeMap(f,
+ s, i);
+ File[] backupFiles = new File[bfTreeMap.size()];
+ bfTreeMap.values().toArray(backupFiles);
+ return backupFiles;
+ }
+
+ private static File[] getBackupFiles()
+ {
+ return getBackupFiles(newFile, suffix, digits);
+ }
+
+ private static boolean checkBackupFiles(HashMap<Integer, String> indexmap)
+ throws IOException
+ {
+ TreeMap<Integer, File> map = BackupFiles.getBackupFilesAsTreeMap(newFile,
+ suffix, digits);
+ Enumeration<Integer> indexesenum = Collections
+ .enumeration(indexmap.keySet());
+ while (indexesenum.hasMoreElements())
+ {
+ int i = indexesenum.nextElement();
+ String indexfilename = indexmap.get(i);
+ if (!map.containsKey(i))
+ {
+ return false;
+ }
+ File f = map.get(i);
+ if (!filesContentEqual(newFile, f.getPath()))
+ {
+ return false;
+ }
+ map.remove(i);
+ if (f == null)
+ {
+ return false;
+ }
+ if (!f.getName().equals(indexfilename))
+ {
+ return false;
+ }
+ }
+ // should be nothing left in map
+ if (map.size() > 0)
+ {
+ return false;
+ }
+
+ return true;
+ }
+
+ private static boolean checkBackupFiles(int[] indexes) throws IOException
+ {
+ TreeMap<Integer, File> map = BackupFiles.getBackupFilesAsTreeMap(newFile,
+ suffix, digits);
+ for (int m = 0; m < indexes.length; m++)
+ {
+ int i = indexes[m];
+ if (!map.containsKey(i))
+ {
+ return false;
+ }
+ File f = map.get(i);
+ if (!filesContentEqual(newFile, f.getPath()))
+ {
+ return false;
+ }
+ map.remove(i);
+ if (f == null)
+ {
+ return false;
+ }
+ // check the filename -- although this uses the same code to forumulate the filename so not much of a test!
+ String filename = BackupFilenameParts.getBackupFilename(i,
+ newBasename + testExt, suffix, digits);
+ if (!filename.equals(f.getName()))
+ {
+ System.out.println("Supposed filename '" + filename
+ + "' not equal to actual filename '" + f.getName() + "'");
+ return false;
+ }
+ }
+ // should be nothing left in map
+ if (map.size() > 0)
+ {
+ return false;
+ }
+
+ return true;
+ }
+
+ private static String[] getBackupFilesAsStrings()
+ {
+ File[] files = getBackupFiles(newFile, suffix, digits);
+ String[] filenames = new String[files.length];
+ for (int i = 0; i < files.length; i++)
+ {
+ filenames[i] = files[i].getPath();
+ }
+ return filenames;
+ }
+
+ public static boolean sequencesEqual(SequenceI s1, SequenceI s2) {
+ if (s1 == null && s2 == null) {
+ return true;
+ } else if (s1 == null || s2 == null) {
+ return false;
+ }
+ return (s1.getName().equals(s2.getName())
+ && s1.getDescription().equals(s2.getDescription())
+ && Arrays.equals(s1.getSequence(), s2.getSequence()));
+ }
+
+ public static boolean filesContentEqual(String fileName1,
+ String fileName2) throws IOException
+ {
+ Path file1 = Paths.get(fileName1);
+ Path file2 = Paths.get(fileName2);
+ byte[] bytes1 = Files.readAllBytes(file1);
+ byte[] bytes2 = Files.readAllBytes(file2);
+ return Arrays.equals(bytes1, bytes2);
+ }
+
+}
import jalview.schemes.FeatureColour;
import jalview.structure.StructureSelectionManager;
import jalview.util.matcher.Condition;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
import java.awt.Color;
import java.io.File;
import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
* first with no features displayed, exclude non-positional features
*/
FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
- Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
- List<String> visibleGroups = new ArrayList<>(
- Arrays.asList(new String[] {}));
- String exported = featuresFile.printJalviewFormat(
- al.getSequencesArray(), visible, null, visibleGroups, false);
+ String exported = featuresFile
+ .printJalviewFormat(al.getSequencesArray(), fr, false);
String expected = "No Features Visible";
assertEquals(expected, exported);
/*
- * include non-positional features
+ * include non-positional features, but still no positional features
*/
- visibleGroups.add("uniprot");
- exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
- visible, null, visibleGroups, true);
- expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
- + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
- + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n" // NaN is not output
- + "\nSTARTGROUP\tuniprot\nENDGROUP\tuniprot\n";
+ fr.setGroupVisibility("uniprot", true);
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ true);
+ expected = "\nSTARTGROUP\tuniprot\n"
+ + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
+ + "ENDGROUP\tuniprot\n\n"
+ + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
+ + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
assertEquals(expected, exported);
/*
*/
fr.setVisible("METAL");
fr.setVisible("GAMMA-TURN");
- visible = fr.getDisplayedFeatureCols();
- exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
- visible, null, visibleGroups, false);
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ false);
expected = "METAL\tcc9900\n"
+ "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
+ "\nSTARTGROUP\tuniprot\n"
* now set Pfam visible
*/
fr.setVisible("Pfam");
- visible = fr.getDisplayedFeatureCols();
- exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
- visible, null, visibleGroups, false);
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ false);
/*
- * features are output within group, ordered by sequence and by type
+ * features are output within group, ordered by sequence and type
*/
expected = "METAL\tcc9900\n"
+ "Pfam\tff0000\n"
+ "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
+ "ENDGROUP\tuniprot\n"
- // null / empty group features output after features in named
- // groups:
+ // null / empty group features are output after named groups
+ + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
+ + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
+ assertEquals(expected, exported);
+
+ /*
+ * hide uniprot group
+ */
+ fr.setGroupVisibility("uniprot", false);
+ expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
+ + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
+ + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
+ + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ false);
+ assertEquals(expected, exported);
+
+ /*
+ * include non-positional (overrides group not shown)
+ */
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ true);
+ expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
+ + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
+ + "\nSTARTGROUP\tuniprot\n"
+ + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
+ + "ENDGROUP\tuniprot\n"
+ + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
+ "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
+ + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
+ "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
assertEquals(expected, exported);
}
* no features
*/
FeaturesFile featuresFile = new FeaturesFile();
- FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
- Map<String, FeatureColourI> visible = new HashMap<>();
- List<String> visibleGroups = new ArrayList<>(
- Arrays.asList(new String[] {}));
+ FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
+ .getFeatureRenderer();
String exported = featuresFile.printGffFormat(al.getSequencesArray(),
- visible, visibleGroups, false);
+ fr, false);
String gffHeader = "##gff-version 2\n";
assertEquals(gffHeader, exported);
- exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
- visibleGroups, true);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ true);
assertEquals(gffHeader, exported);
/*
al.getSequenceAt(1).addSequenceFeature(sf);
/*
+ * 'discover' features then hide all feature types
+ */
+ fr.findAllFeatures(true);
+ FeatureSettingsBean[] data = new FeatureSettingsBean[4];
+ FeatureColourI fc = new FeatureColour(Color.PINK);
+ data[0] = new FeatureSettingsBean("Domain", fc, null, false);
+ data[1] = new FeatureSettingsBean("METAL", fc, null, false);
+ data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
+ data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
+ fr.setFeaturePriority(data);
+
+ /*
* with no features displayed, exclude non-positional features
*/
- exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
- visibleGroups, false);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false);
assertEquals(gffHeader, exported);
/*
* include non-positional features
*/
- visibleGroups.add("Uniprot");
- exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
- visibleGroups, true);
+ fr.setGroupVisibility("Uniprot", true);
+ fr.setGroupVisibility("s3dm", false);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ true);
String expected = gffHeader
+ "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
assertEquals(expected, exported);
*/
fr.setVisible("METAL");
fr.setVisible("GAMMA-TURN");
- visible = fr.getDisplayedFeatureCols();
- exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
- visibleGroups, false);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false);
// METAL feature has null group: description used for column 2
expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
assertEquals(expected, exported);
/*
* set s3dm group visible
*/
- visibleGroups.add("s3dm");
- exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
- visibleGroups, false);
+ fr.setGroupVisibility("s3dm", true);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false);
// METAL feature has null group: description used for column 2
expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
+ "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
* now set Pfam visible
*/
fr.setVisible("Pfam");
- visible = fr.getDisplayedFeatureCols();
- exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
- visibleGroups, false);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false);
// Pfam feature columns include strand(+), phase(2), attributes
expected = gffHeader
+ "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
featureFilters.put("pfam", filter2);
visible.put("foobar", new FeatureColour(Color.blue));
ff.outputFeatureFilters(sb, visible, featureFilters);
- String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n\n";
+ String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
assertEquals(expected, sb.toString());
}
+
+ /**
+ * Output as GFF should not include features which are not visible due to
+ * colour threshold or feature filter settings
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testPrintGffFormat_withFilters() throws Exception
+ {
+ File f = new File("examples/uniref50.fa");
+ AlignmentI al = readAlignmentFile(f);
+ AlignFrame af = new AlignFrame(al, 500, 500);
+ SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
+ null);
+ sf1.setValue("clin_sig", "Likely Pathogenic");
+ sf1.setValue("AF", "24");
+ al.getSequenceAt(0).addSequenceFeature(sf1);
+ SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
+ null);
+ sf2.setValue("clin_sig", "Benign");
+ sf2.setValue("AF", "46");
+ al.getSequenceAt(0).addSequenceFeature(sf2);
+
+ FeaturesFile featuresFile = new FeaturesFile();
+ FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
+ final String gffHeader = "##gff-version 2\n";
+
+ fr.setVisible("METAL");
+ fr.setColour("METAL", new FeatureColour(Color.PINK));
+ String exported = featuresFile.printGffFormat(al.getSequencesArray(),
+ fr, false);
+ String expected = gffHeader
+ + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
+ + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
+ assertEquals(expected, exported);
+
+ /*
+ * now threshold to Score > 1.1 - should exclude sf2
+ */
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
+ Color.white, 0f, 2f);
+ fc.setAboveThreshold(true);
+ fc.setThreshold(1.1f);
+ fr.setColour("METAL", fc);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false);
+ expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
+ assertEquals(expected, exported);
+
+ /*
+ * remove threshold and check sf2 is exported
+ */
+ fc.setAboveThreshold(false);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false);
+ expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
+ + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
+ assertEquals(expected, exported);
+
+ /*
+ * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
+ */
+ FeatureMatcherSetI filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
+ "clin_sig"));
+ fr.setFeatureFilter("METAL", filter);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false);
+ expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
+ assertEquals(expected, exported);
+ }
+
+ /**
+ * Output as Jalview should not include features which are not visible due to
+ * colour threshold or feature filter settings
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testPrintJalviewFormat_withFilters() throws Exception
+ {
+ File f = new File("examples/uniref50.fa");
+ AlignmentI al = readAlignmentFile(f);
+ AlignFrame af = new AlignFrame(al, 500, 500);
+ SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
+ "grp1");
+ sf1.setValue("clin_sig", "Likely Pathogenic");
+ sf1.setValue("AF", "24");
+ al.getSequenceAt(0).addSequenceFeature(sf1);
+ SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
+ "grp2");
+ sf2.setValue("clin_sig", "Benign");
+ sf2.setValue("AF", "46");
+ al.getSequenceAt(0).addSequenceFeature(sf2);
+
+ FeaturesFile featuresFile = new FeaturesFile();
+ FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
+ fr.findAllFeatures(true);
+
+ fr.setVisible("METAL");
+ fr.setColour("METAL", new FeatureColour(Color.PINK));
+ String exported = featuresFile.printJalviewFormat(
+ al.getSequencesArray(),
+ fr, false);
+ String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
+ + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
+ + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
+ + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
+ + "ENDGROUP\tgrp2\n";
+ assertEquals(expected, exported);
+
+ /*
+ * now threshold to Score > 1.1 - should exclude sf2
+ * (and there should be no empty STARTGROUP/ENDGROUP output)
+ */
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
+ Color.white, 0f, 2f);
+ fc.setAboveThreshold(true);
+ fc.setThreshold(1.1f);
+ fr.setColour("METAL", fc);
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ false);
+ expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
+ + "STARTGROUP\tgrp1\n"
+ + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
+ + "ENDGROUP\tgrp1\n";
+ assertEquals(expected, exported);
+
+ /*
+ * remove threshold and check sf2 is exported
+ */
+ fc.setAboveThreshold(false);
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ false);
+ expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
+ + "STARTGROUP\tgrp1\n"
+ + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
+ + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
+ + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
+ + "ENDGROUP\tgrp2\n";
+ assertEquals(expected, exported);
+
+ /*
+ * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
+ */
+ FeatureMatcherSetI filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
+ "clin_sig"));
+ fr.setFeatureFilter("METAL", filter);
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ false);
+ expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
+ expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
+ + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
+ + "STARTGROUP\tgrp2\n"
+ + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
+ + "ENDGROUP\tgrp2\n";
+ assertEquals(expected, exported);
+ }
}
import java.io.IOException;
import java.net.MalformedURLException;
+import org.testng.annotations.AfterMethod;
import org.testng.annotations.Test;
public class ScoreMatrixFileTest
{
+ @AfterMethod(alwaysRun=true)
+ public void tearDownAfterTest()
+ {
+ ScoreModels.getInstance().reset();
+ }
+
/**
* Test a successful parse of a (small) score matrix file
*
import java.awt.Color;
import java.util.Map;
-import junit.extensions.PA;
-
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class SequenceAnnotationReportTest
{
/*
* then with colour by an attribute the feature lacks
*/
- FeatureColourI fc = new FeatureColour(Color.white, Color.black, 5, 10);
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
+ null, 5, 10);
fc.setAttributeName("Pfam");
fr.setColour("METAL", fc);
sb.setLength(0);
FeatureRendererModel fr = new FeatureRenderer(null);
Map<String, float[][]> minmax = fr.getMinMax();
- FeatureColourI fc = new FeatureColour(Color.white, Color.blue, 12, 22);
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.blue,
+ null, 12, 22);
fc.setAttributeName("clinical_significance");
fr.setColour("METAL", fc);
minmax.put("METAL", new float[][] { { 0f, 1f }, null });
// with showDbRefs = true, colour Variant features by clinical_significance
sb.setLength(0);
- FeatureColourI fc = new FeatureColour(Color.green, Color.pink, 2, 3);
+ FeatureColourI fc = new FeatureColour(null, Color.green, Color.pink,
+ null, 2, 3);
fc.setAttributeName("clinical_significance");
fr.setColour("Variant", fc);
sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
cacheBox.updateCache();
try
{
- // This 1ms delay is essential to prevent the
- // assertion below from executing before
- // cacheBox.updateCache() finishes updating the cache
- Thread.sleep(100);
+ // This delay is to let
+ // cacheBox.updateCache() finish updating the cache
+ Thread.sleep(200);
} catch (InterruptedException e)
{
e.printStackTrace();
#---JalviewX Properties File---
#Fri Apr 25 09:54:25 BST 2014
+#
+BACKUPFILES_ROLL_MAX=2
+BACKUPFILES_REVERSE_ORDER=false
+BACKUPFILES_SUFFIX=_BACKUPFILESTESTTMP%n
+BACKUPFILES_CONFIRM_DELETE_OLD=false
+BACKUPFILES_NO_MAX=false
+BACKUPFILES_ENABLED=true
+BACKUPFILES_SUFFIX_DIGITS=8
SCREEN_Y=768
SCREEN_X=936
SHOW_WSDISCOVERY_ERRORS=true
// insertion G/GA is transferred to nucleotide but not to peptide
"17\t45051613\t.\tG\tGA,C\t1666.64\tRF\tAC=15;AF=3.0e-03,2.0e-03" };
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public void setUp()
{
/*
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
- assertEquals(sf.getScore(), 4.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 4.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,C");
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
sf = geneFeatures.get(1);
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 5.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 5.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,T");
sf = geneFeatures.get(2);
assertEquals(sf.getBegin(), 4);
assertEquals(sf.getEnd(), 4);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 2.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
sf = geneFeatures.get(3);
assertEquals(sf.getBegin(), 4);
assertEquals(sf.getEnd(), 4);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 3.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA");
/*
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 2.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
sf = transcriptFeatures.get(1);
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 3.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA");
/*
assertEquals(sf.getBegin(), 24);
assertEquals(sf.getEnd(), 24);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 5.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 5.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "T,A");
/*
assertEquals(sf.getBegin(), 24);
assertEquals(sf.getEnd(), 24);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 4.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 4.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "T,G");
/*
assertEquals(sf.getBegin(), 22);
assertEquals(sf.getEnd(), 22);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 2.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "C,G");
/*
assertEquals(sf.getBegin(), 21);
assertEquals(sf.getEnd(), 21);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 3.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GT");
/*
assertEquals(sf.getBegin(), 16);
assertEquals(sf.getEnd(), 16);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 3.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GT");
/*
assertEquals(sf.getBegin(), 17);
assertEquals(sf.getEnd(), 17);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 2.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "C,G");
/*
SequenceFeature sf = geneFeatures.get(0);
assertEquals(sf.getBegin(), 1);
assertEquals(sf.getEnd(), 1);
- assertEquals(sf.getScore(), 0.1f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.1f, DELTA);
assertEquals(sf.getValue("alleles"), "C,A");
// gene features include Consequence for all transcripts
Map map = (Map) sf.getValue("CSQ");
sf = geneFeatures.get(1);
assertEquals(sf.getBegin(), 5);
assertEquals(sf.getEnd(), 5);
- assertEquals(sf.getScore(), 0.2f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.2f, DELTA);
assertEquals(sf.getValue("alleles"), "C,T");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = geneFeatures.get(2);
assertEquals(sf.getBegin(), 9);
assertEquals(sf.getEnd(), 11); // deletion over 3 positions
- assertEquals(sf.getScore(), 0.3f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.3f, DELTA);
assertEquals(sf.getValue("alleles"), "CGG,C");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = geneFeatures.get(3);
assertEquals(sf.getBegin(), 13);
assertEquals(sf.getEnd(), 13);
- assertEquals(sf.getScore(), 0.5f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.5f, DELTA);
assertEquals(sf.getValue("alleles"), "C,T");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = geneFeatures.get(4);
assertEquals(sf.getBegin(), 13);
assertEquals(sf.getEnd(), 13);
- assertEquals(sf.getScore(), 0.4f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.4f, DELTA);
assertEquals(sf.getValue("alleles"), "C,G");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = geneFeatures.get(5);
assertEquals(sf.getBegin(), 17);
assertEquals(sf.getEnd(), 17);
- assertEquals(sf.getScore(), 0.7f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA);
assertEquals(sf.getValue("alleles"), "A,G");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = geneFeatures.get(6);
assertEquals(sf.getBegin(), 17);
assertEquals(sf.getEnd(), 17); // insertion
- assertEquals(sf.getScore(), 0.6f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA);
assertEquals(sf.getValue("alleles"), "A,AC");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = transcriptFeatures.get(0);
assertEquals(sf.getBegin(), 3);
assertEquals(sf.getEnd(), 3);
- assertEquals(sf.getScore(), 0.2f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.2f, DELTA);
assertEquals(sf.getValue("alleles"), "C,T");
// transcript features only have Consequence for that transcripts
map = (Map) sf.getValue("CSQ");
sf = transcriptFeatures.get(1);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
- assertEquals(sf.getScore(), 0.7f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA);
assertEquals(sf.getValue("alleles"), "A,G");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
sf = transcriptFeatures.get(2);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
- assertEquals(sf.getScore(), 0.6f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA);
assertEquals(sf.getValue("alleles"), "A,AC");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
sf = transcriptFeatures.get(0);
assertEquals(sf.getBegin(), 7);
assertEquals(sf.getEnd(), 7);
- assertEquals(sf.getScore(), 0.5f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.5f, DELTA);
assertEquals(sf.getValue("alleles"), "C,T");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
sf = transcriptFeatures.get(1);
assertEquals(sf.getBegin(), 7);
assertEquals(sf.getEnd(), 7);
- assertEquals(sf.getScore(), 0.4f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.4f, DELTA);
assertEquals(sf.getValue("alleles"), "C,G");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
sf = transcriptFeatures.get(2);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
- assertEquals(sf.getScore(), 0.7f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA);
assertEquals(sf.getValue("alleles"), "A,G");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
sf = transcriptFeatures.get(3);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
- assertEquals(sf.getScore(), 0.6f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA);
assertEquals(sf.getValue("alleles"), "A,AC");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
package jalview.math;
import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotSame;
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertTrue;
}
}
Matrix m1 = new Matrix(in);
+
Matrix m2 = (Matrix) m1.copy();
assertNotSame(m1, m2);
assertTrue(matrixEquals(m1, m2));
+ assertNull(m2.d);
+ assertNull(m2.e);
+
+ /*
+ * now add d and e vectors and recopy
+ */
+ m1.d = Arrays.copyOf(in[2], in[2].length);
+ m1.e = Arrays.copyOf(in[4], in[4].length);
+ m2 = (Matrix) m1.copy();
+ assertNotSame(m2.d, m1.d);
+ assertNotSame(m2.e, m1.e);
+ assertEquals(m2.d, m1.d);
+ assertEquals(m2.e, m1.e);
}
/**
assertMatricesMatch(m1, m2);
}
- private void assertMatricesMatch(MatrixI m1, MatrixI m2)
+ public static void assertMatricesMatch(MatrixI m1, MatrixI m2)
{
if (m1.height() != m2.height())
{
}
}
}
- ArrayAsserts.assertArrayEquals(m1.getD(), m2.getD(), 0.00001d);
- ArrayAsserts.assertArrayEquals(m1.getE(), m2.getE(), 0.00001d);
+ ArrayAsserts.assertArrayEquals("D vector", m1.getD(), m2.getD(),
+ 0.00001d);
+ ArrayAsserts.assertArrayEquals("E vector", m1.getE(), m2.getE(),
+ 0.00001d);
}
@Test(groups = "Functional")
values[0][0] = -1d;
assertEquals(m.getValue(0, 0), 1d, DELTA); // unchanged
}
+
+ @Test(groups = "Functional")
+ public void testEquals()
+ {
+ double[][] values = new double[][] { { 1, 2, 3 }, { 4, 5, 6 } };
+ Matrix m1 = new Matrix(values);
+ double[][] values2 = new double[][] { { 1, 2, 3 }, { 4, 5, 6 } };
+ Matrix m2 = new Matrix(values2);
+
+ double delta = 0.0001d;
+ assertTrue(m1.equals(m1, delta));
+ assertTrue(m1.equals(m2, delta));
+ assertTrue(m2.equals(m1, delta));
+
+ double[][] values3 = new double[][] { { 1, 2, 3 }, { 4, 5, 7 } };
+ m2 = new Matrix(values3);
+ assertFalse(m1.equals(m2, delta));
+ assertFalse(m2.equals(m1, delta));
+
+ // must be same shape
+ values2 = new double[][] { { 1, 2, 3 } };
+ m2 = new Matrix(values2);
+ assertFalse(m2.equals(m1, delta));
+
+ assertFalse(m1.equals(null, delta));
+ }
}
--- /dev/null
+package jalview.math;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.math.RotatableMatrix.Axis;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+public class RotatableMatrixTest
+{
+ private RotatableMatrix rm;
+
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ rm = new RotatableMatrix();
+
+ /*
+ * 0.5 1.0 1.5
+ * 1.0 2.0 3.0
+ * 1.5 3.0 4.5
+ */
+ for (int i = 1; i <= 3; i++)
+ {
+ for (int j = 1; j <= 3; j++)
+ {
+ rm.setValue(i - 1, j - 1, i * j / 2f);
+ }
+ }
+ }
+
+ @Test(groups = "Functional")
+ public void testPreMultiply()
+ {
+ float[][] pre = new float[3][3];
+ int i = 1;
+ for (int j = 0; j < 3; j++)
+ {
+ for (int k = 0; k < 3; k++)
+ {
+ pre[j][k] = i++;
+ }
+ }
+
+ rm.preMultiply(pre);
+
+ /*
+ * check rm[i, j] is now the product of the i'th row of pre
+ * and the j'th column of (original) rm
+ */
+ for (int j = 0; j < 3; j++)
+ {
+ for (int k = 0; k < 3; k++)
+ {
+ float expected = 0f;
+ for (int l = 0; l < 3; l++)
+ {
+ float rm_l_k = (l + 1) * (k + 1) / 2f;
+ expected += pre[j][l] * rm_l_k;
+ }
+ assertEquals(rm.getValue(j, k), expected,
+ String.format("[%d, %d]", j, k));
+ }
+ }
+ }
+
+ @Test(groups = "Functional")
+ public void testVectorMultiply()
+ {
+ float[] result = rm.vectorMultiply(new float[] { 2f, 3f, 4.5f });
+
+ // vector times first column of matrix
+ assertEquals(result[0], 2f * 0.5f + 3f * 1f + 4.5f * 1.5f);
+
+ // vector times second column of matrix
+ assertEquals(result[1], 2f * 1.0f + 3f * 2f + 4.5f * 3f);
+
+ // vector times third column of matrix
+ assertEquals(result[2], 2f * 1.5f + 3f * 3f + 4.5f * 4.5f);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetRotation()
+ {
+ float theta = 60f;
+ double cosTheta = Math.cos((theta * Math.PI / 180f));
+ double sinTheta = Math.sin((theta * Math.PI / 180f));
+
+ /*
+ * sanity check that sin(60) = sqrt(3) / 2, cos(60) = 1/2
+ */
+ double delta = 0.0001d;
+ assertEquals(cosTheta, 0.5f, delta);
+ assertEquals(sinTheta, Math.sqrt(3d) / 2d, delta);
+
+ /*
+ * so far so good, now verify rotations
+ * @see https://en.wikipedia.org/wiki/Rotation_matrix#Basic_rotations
+ */
+
+ /*
+ * 60 degrees about X axis should be
+ * 1 0 0
+ * 0 cos -sin
+ * 0 sin cos
+ * but code applies the negative of this
+ * nb cos(-x) = cos(x), sin(-x) = -sin(x)
+ */
+ float[][] rot = RotatableMatrix.getRotation(theta, Axis.X);
+ assertEquals(rot[0][0], 1f, delta);
+ assertEquals(rot[0][1], 0f, delta);
+ assertEquals(rot[0][2], 0f, delta);
+ assertEquals(rot[1][0], 0f, delta);
+ assertEquals(rot[1][1], cosTheta, delta);
+ assertEquals(rot[1][2], sinTheta, delta);
+ assertEquals(rot[2][0], 0f, delta);
+ assertEquals(rot[2][1], -sinTheta, delta);
+ assertEquals(rot[2][2], cosTheta, delta);
+
+ /*
+ * 60 degrees about Y axis should be
+ * cos 0 sin
+ * 0 1 0
+ * -sin 0 cos
+ * but code applies the negative of this
+ */
+ rot = RotatableMatrix.getRotation(theta, Axis.Y);
+ assertEquals(rot[0][0], cosTheta, delta);
+ assertEquals(rot[0][1], 0f, delta);
+ assertEquals(rot[0][2], -sinTheta, delta);
+ assertEquals(rot[1][0], 0f, delta);
+ assertEquals(rot[1][1], 1f, delta);
+ assertEquals(rot[1][2], 0f, delta);
+ assertEquals(rot[2][0], sinTheta, delta);
+ assertEquals(rot[2][1], 0f, delta);
+ assertEquals(rot[2][2], cosTheta, delta);
+
+ /*
+ * 60 degrees about Z axis should be
+ * cos -sin 0
+ * sin cos 0
+ * 0 0 1
+ * - and it is!
+ */
+ rot = RotatableMatrix.getRotation(theta, Axis.Z);
+ assertEquals(rot[0][0], cosTheta, delta);
+ assertEquals(rot[0][1], -sinTheta, delta);
+ assertEquals(rot[0][2], 0f, delta);
+ assertEquals(rot[1][0], sinTheta, delta);
+ assertEquals(rot[1][1], cosTheta, delta);
+ assertEquals(rot[1][2], 0f, delta);
+ assertEquals(rot[2][0], 0f, delta);
+ assertEquals(rot[2][1], 0f, delta);
+ assertEquals(rot[2][2], 1f, delta);
+ }
+}
import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
+import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.gui.Desktop;
import jalview.gui.FeatureRenderer;
import jalview.gui.JvOptionPane;
+import jalview.gui.PCAPanel;
import jalview.gui.PopupMenu;
import jalview.gui.SliderPanel;
import jalview.io.DataSourceType;
import java.util.List;
import java.util.Map;
+import javax.swing.JInternalFrame;
+
import org.testng.Assert;
import org.testng.AssertJUnit;
import org.testng.annotations.BeforeClass;
assertNotNull(af, "Didn't read input file " + inFile);
int olddsann = countDsAnn(af.getViewport());
assertTrue(olddsann > 0, "Didn't find any dataset annotations");
- af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices
- .toString());
+ af.changeColour_actionPerformed(
+ JalviewColourScheme.RNAHelices.toString());
assertTrue(
- af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour,
+ af.getViewport()
+ .getGlobalColourScheme() instanceof RNAHelicesColour,
"Couldn't apply RNA helices colourscheme");
assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
"Failed to store as a project.");
af.closeMenuItem_actionPerformed(true);
af = null;
- af = new FileLoader()
- .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile,
+ DataSourceType.FILE);
assertNotNull(af, "Failed to import new project");
int newdsann = countDsAnn(af.getViewport());
assertEquals(olddsann, newdsann,
"Differing numbers of dataset sequence annotation\nOriginally "
+ olddsann + " and now " + newdsann);
- System.out
- .println("Read in same number of annotations as originally present ("
+ System.out.println(
+ "Read in same number of annotations as originally present ("
+ olddsann + ")");
assertTrue(
- af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour,
+ af.getViewport()
+ .getGlobalColourScheme() instanceof RNAHelicesColour,
"RNA helices colourscheme was not applied on import.");
}
@Test(groups = { "Functional" })
public void testTCoffeeScores() throws Exception
{
- String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
+ String inFile = "examples/uniref50.fa",
+ inAnnot = "examples/uniref50.score_ascii";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
DataSourceType.FILE);
assertNotNull(af, "Didn't read input file " + inFile);
af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
- assertSame(af.getViewport().getGlobalColourScheme().getClass(),
+ AlignViewport viewport = af.getViewport();
+ assertSame(viewport.getGlobalColourScheme().getClass(),
TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
- assertNotNull(ColourSchemeProperty.getColourScheme(af.getViewport()
- .getAlignment(), af.getViewport().getGlobalColourScheme()
- .getSchemeName()), "Recognise T-Coffee score from string");
+ assertNotNull(
+ ColourSchemeProperty.getColourScheme(viewport,
+ viewport.getAlignment(),
+ viewport.getGlobalColourScheme()
+ .getSchemeName()),
+ "Recognise T-Coffee score from string");
assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
"Failed to store as a project.");
af.closeMenuItem_actionPerformed(true);
af = null;
- af = new FileLoader()
- .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile,
+ DataSourceType.FILE);
assertNotNull(af, "Failed to import new project");
assertSame(af.getViewport().getGlobalColourScheme().getClass(),
TCoffeeColourScheme.class,
"Didn't set T-coffee colourscheme for imported project.");
- System.out
- .println("T-Coffee score shading successfully recovered from project.");
+ System.out.println(
+ "T-Coffee score shading successfully recovered from project.");
}
@Test(groups = { "Functional" })
public void testColourByAnnotScores() throws Exception
{
- String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
+ String inFile = "examples/uniref50.fa",
+ inAnnot = "examples/testdata/uniref50_iupred.jva";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
.getSequenceAt(0).getAnnotation("IUPredWS (Short)");
assertTrue(
- aa != null && aa.length > 0,
+ aa != null && aa.length > 0,
"Didn't find any IUPred annotation to use to shade alignment.");
AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null,
AnnotationColourGradient.ABOVE_THRESHOLD);
- AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0],
- null, AnnotationColourGradient.BELOW_THRESHOLD);
+ AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0], null,
+ AnnotationColourGradient.BELOW_THRESHOLD);
cs.setSeqAssociated(true);
gcs.setSeqAssociated(true);
af.changeColour(cs);
"Failed to store as a project.");
af.closeMenuItem_actionPerformed(true);
af = null;
- af = new FileLoader()
- .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile,
+ DataSourceType.FILE);
assertNotNull(af, "Failed to import new project");
// check for group and alignment colourschemes
ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
- ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
- .get(0).getColourScheme();
+ ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups().get(0)
+ .getColourScheme();
assertNotNull(_rcs, "Didn't recover global colourscheme");
assertTrue(_rcs instanceof AnnotationColourGradient,
"Didn't recover annotation colour global scheme");
boolean diffseqcols = false, diffgseqcols = false;
SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
- for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
+ for (int p = 0, pSize = af.getViewport().getAlignment()
+ .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
{
if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
.findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
}
}
assertTrue(diffseqcols, "Got Different sequence colours");
- System.out
- .println("Per sequence colourscheme (Background) successfully applied and recovered.");
+ System.out.println(
+ "Per sequence colourscheme (Background) successfully applied and recovered.");
assertNotNull(_rgcs, "Didn't recover group colourscheme");
assertTrue(_rgcs instanceof AnnotationColourGradient,
assertTrue(__rcs.isSeqAssociated(),
"Group Annotation colourscheme wasn't sequence associated");
- for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
+ for (int p = 0, pSize = af.getViewport().getAlignment()
+ .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
{
- if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs
- .findColour(sqs[2].getCharAt(p), p, sqs[2], null, 0f))
+ if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
+ 0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
+ 0f))
{
diffgseqcols = true;
}
}
assertTrue(diffgseqcols, "Got Different group sequence colours");
- System.out
- .println("Per sequence (Group) colourscheme successfully applied and recovered.");
+ System.out.println(
+ "Per sequence (Group) colourscheme successfully applied and recovered.");
}
@Test(groups = { "Functional" })
public void gatherViewsHere() throws Exception
{
- int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
- .getAlignFrames().length;
+ int origCount = Desktop.getAlignFrames() == null ? 0
+ : Desktop.getAlignFrames().length;
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
sq.findPosition(p);
try
{
- assertTrue(
- (alaa.annotations[p] == null && refan.annotations[p] == null)
- || alaa.annotations[p].value == refan.annotations[p].value,
+ assertTrue((alaa.annotations[p] == null
+ && refan.annotations[p] == null)
+ || alaa.annotations[p].value == refan.annotations[p].value,
"Mismatch at alignment position " + p);
} catch (NullPointerException q)
{
- Assert.fail("Mismatch of alignment annotations at position "
- + p + " Ref seq ann: " + refan.annotations[p]
+ Assert.fail("Mismatch of alignment annotations at position " + p
+ + " Ref seq ann: " + refan.annotations[p]
+ " alignment " + alaa.annotations[p]);
}
}
AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
groups.getAlignViewport().setViewStyle(structureStyle);
- AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
- .getViewStyle()));
- Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
- .getViewStyle()));
+ AssertJUnit.assertFalse(
+ groupStyle.sameStyle(groups.getAlignViewport().getViewStyle()));
+ Assert.assertTrue(structureStyle
+ .sameStyle(groups.getAlignViewport().getViewStyle()));
}
// check FileLoader returned a reference to the one alignFrame that is
// actually on the Desktop
- assertSame(
- af,
- Desktop.getAlignFrameFor(af.getViewport()),
+ assertSame(af, Desktop.getAlignFrameFor(af.getViewport()),
"Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window");
Desktop.explodeViews(af);
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
DataSourceType.FILE);
Assert.assertNotNull(af);
+ Assert.assertEquals(Desktop.getAlignFrames().length,
+ Desktop.getAlignmentPanels(
+ af.getViewport().getSequenceSetId()).length);
Assert.assertEquals(
- Desktop.getAlignFrames().length,
- Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
- Assert.assertEquals(
- Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
+ Desktop.getAlignmentPanels(
+ af.getViewport().getSequenceSetId()).length,
oldviews);
}
assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test"));
assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST"));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test"));
- assertTrue(Jalview2XML
- .isVersionStringLaterThan(null, "Automated Build"));
+ assertTrue(
+ Jalview2XML.isVersionStringLaterThan(null, "Automated Build"));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
"Automated Build"));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
n++;
}
- File tfile = File
- .createTempFile("testStoreAndRecoverGroupReps", ".jvp");
+ File tfile = File.createTempFile("testStoreAndRecoverGroupReps",
+ ".jvp");
try
{
new Jalview2XML(false).saveState(tfile);
*/
List<String> hidden = hiddenSeqNames.get(ap.getViewName());
HiddenSequences hs = alignment.getHiddenSequences();
- assertEquals(
- hidden.size(),
- hs.getSize(),
+ assertEquals(hidden.size(), hs.getSize(),
"wrong number of restored hidden sequences in "
+ ap.getViewName());
}
pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile);
pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile);
pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile);
- Assert.assertEquals(seqs[0].getDatasetSequence().getAllPDBEntries()
- .get(0), pdbEntries[0]);
- Assert.assertEquals(seqs[1].getDatasetSequence().getAllPDBEntries()
- .get(0), pdbEntries[1]);
- Assert.assertEquals(seqs[2].getDatasetSequence().getAllPDBEntries()
- .get(0), pdbEntries[2]);
- Assert.assertEquals(seqs[3].getDatasetSequence().getAllPDBEntries()
- .get(0), pdbEntries[3]);
+ Assert.assertEquals(
+ seqs[0].getDatasetSequence().getAllPDBEntries().get(0),
+ pdbEntries[0]);
+ Assert.assertEquals(
+ seqs[1].getDatasetSequence().getAllPDBEntries().get(0),
+ pdbEntries[1]);
+ Assert.assertEquals(
+ seqs[2].getDatasetSequence().getAllPDBEntries().get(0),
+ pdbEntries[2]);
+ Assert.assertEquals(
+ seqs[3].getDatasetSequence().getAllPDBEntries().get(0),
+ pdbEntries[3]);
File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
try
/*
* Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
*/
+ av.setColourAppliesToAllGroups(false);
af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
af.abovePIDThreshold_actionPerformed(true);
sg.setEndRes(25);
av.setSelectionGroup(sg);
PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
- popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
- .toString());
+ popupMenu.changeColour_actionPerformed(
+ JalviewColourScheme.Strand.toString());
assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
assertEquals(al.getGroups().size(), 1);
assertSame(al.getGroups().get(0), sg);
fr.setColour("type2", byLabel);
// type3: by score above threshold
- FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
- 10);
+ FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
+ Color.BLUE, null, 1, 10);
byScore.setAboveThreshold(true);
byScore.setThreshold(2f);
fr.setColour("type3", byScore);
fr.setColour("type4", byAF);
// type5: by attribute CSQ:PolyPhen below threshold
- FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
- 1, 10);
+ FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
+ Color.BLUE, null, 1, 10);
byPolyPhen.setBelowThreshold(true);
byPolyPhen.setThreshold(3f);
byPolyPhen.setAttributeName("CSQ", "PolyPhen");
*/
af.closeMenuItem_actionPerformed(true);
af = null;
- af = new FileLoader()
- .LoadFileWaitTillLoaded(filePath, DataSourceType.FILE);
+ af = new FileLoader().LoadFileWaitTillLoaded(filePath,
+ DataSourceType.FILE);
assertNotNull(af, "Failed to import new project");
/*
addFeature(seq, featureType, score++);
addFeature(seq, featureType, score);
}
+
+ /**
+ * pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
+ * view (JAL-3171) this test ensures we can import and merge those views
+ */
+ @Test(groups = { "Functional" })
+ public void testMergeDatasetsforViews() throws IOException
+ {
+ // simple project - two views on one alignment
+ AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
+ "examples/testdata/projects/twoViews.jvp", DataSourceType.FILE);
+ assertNotNull(af);
+ assertTrue(af.getAlignPanels().size() > 1);
+ verifyDs(af);
+ }
+
+ /**
+ * pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
+ * view (JAL-3171) this test ensures we can import and merge those views This
+ * is a more complex project
+ */
+ @Test(groups = { "Functional" })
+ public void testMergeDatasetsforManyViews() throws IOException
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ // complex project - one dataset, several views on several alignments
+ AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
+ "examples/testdata/projects/manyViews.jvp",
+ DataSourceType.FILE);
+ assertNotNull(af);
+
+ AlignmentI ds = null;
+ for (AlignFrame alignFrame : Desktop.getAlignFrames())
+ {
+ if (ds == null)
+ {
+ ds = verifyDs(alignFrame);
+ }
+ else
+ {
+ // check that this frame's dataset matches the last
+ assertTrue(ds == verifyDs(alignFrame));
+ }
+ }
+ }
+
+ private AlignmentI verifyDs(AlignFrame af)
+ {
+ AlignmentI ds = null;
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ if (ds == null)
+ {
+ ds = ap.getAlignment().getDataset();
+ }
+ else
+ {
+ assertTrue(ap.getAlignment().getDataset() == ds,
+ "Dataset was not the same for imported 2.10.5 project with several alignment views");
+ }
+ }
+ return ds;
+ }
+
+ @Test(groups = "Functional")
+ public void testPcaViewAssociation() throws IOException
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ final String PCAVIEWNAME = "With PCA";
+ // create a new tempfile
+ File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp");
+
+ {
+ String exampleFile = "examples/uniref50.fa";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
+ DataSourceType.FILE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+ AlignmentPanel origView = (AlignmentPanel) af.getAlignPanels().get(0);
+ AlignmentPanel newview = af.newView(PCAVIEWNAME, true);
+ // create another for good measure
+ af.newView("Not the PCA View", true);
+ PCAPanel pcaPanel = new PCAPanel(origView, "BLOSUM62",
+ new SimilarityParams(true, true, true, false));
+ // we're in the test exec thread, so we can just run synchronously here
+ pcaPanel.run();
+
+ // now switch the linked view
+ pcaPanel.selectAssociatedView(newview);
+
+ assertTrue(pcaPanel.getAlignViewport() == newview.getAlignViewport(),
+ "PCA should be associated with 'With PCA' view: test is broken");
+
+ // now save and reload project
+ Jalview2XML jv2xml = new jalview.project.Jalview2XML(false);
+ tempfile.delete();
+ jv2xml.saveState(tempfile);
+ assertTrue(jv2xml.errorMessage == null,
+ "Failed to save dummy project with PCA: test broken");
+ }
+
+ // load again.
+ Desktop.instance.closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ tempfile.getCanonicalPath(), DataSourceType.FILE);
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+ // PCA and the tabbed alignment view should be the only two windows on the
+ // desktop
+ assertEquals(frames.length, 2,
+ "PCA and the tabbed alignment view should be the only two windows on the desktop");
+ PCAPanel pcaPanel = (PCAPanel) frames[frames[0] == af ? 1 : 0];
+
+ AlignmentViewPanel restoredNewView = null;
+ for (AlignmentViewPanel alignpanel : Desktop.getAlignmentPanels(null))
+ {
+ if (alignpanel.getAlignViewport() == pcaPanel.getAlignViewport())
+ {
+ restoredNewView = alignpanel;
+ }
+ }
+ assertEquals(restoredNewView.getViewName(), PCAVIEWNAME);
+ assertTrue(
+ restoredNewView.getAlignViewport() == pcaPanel
+ .getAlignViewport(),
+ "Didn't restore correct view association for the PCA view");
+ }
}
*/
Color min = new Color(100, 50, 150);
Color max = new Color(200, 0, 100);
- FeatureColourI fc = new FeatureColour(min, max, 0, 10);
+ FeatureColourI fc = new FeatureColour(null, min, max, null, 0, 10);
fr.setColour("kd", fc);
fr.featuresAdded();
av.setShowSequenceFeatures(true);
*/
Color min = new Color(100, 50, 150);
Color max = new Color(200, 0, 100);
- FeatureColourI fc = new FeatureColour(min, max, 0, 10);
+ FeatureColourI fc = new FeatureColour(null, min, max, null, 0, 10);
fc.setAboveThreshold(true);
fc.setThreshold(5f);
fr.setColour(kdFeature, fc);
* give "Type3" features a graduated colour scheme
* - first with no threshold
*/
- FeatureColourI gc = new FeatureColour(Color.yellow, Color.red, null, 0f,
- 10f);
+ FeatureColourI gc = new FeatureColour(Color.green, Color.yellow,
+ Color.red, null, 0f, 10f);
fr.getFeatureColours().put("Type3", gc);
features = fr.findFeaturesAtColumn(seq, 8);
assertTrue(features.contains(sf4));
SequenceI seq = av.getAlignment().getSequenceAt(0);
SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
"group1");
- seq.addSequenceFeature(sf1);
SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, 2f,
"group2");
- seq.addSequenceFeature(sf2);
SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, 3f,
"group3");
- seq.addSequenceFeature(sf3);
SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, 4f,
"group4");
- seq.addSequenceFeature(sf4);
SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, 5f,
"group4");
+ seq.addSequenceFeature(sf1);
+ seq.addSequenceFeature(sf2);
+ seq.addSequenceFeature(sf3);
+ seq.addSequenceFeature(sf4);
seq.addSequenceFeature(sf5);
fr.findAllFeatures(true);
assertTrue(features.contains(sf5));
/*
- * hide groups 2 and 3 makes no difference to this method
+ * features in hidden groups are removed
*/
fr.setGroupVisibility("group2", false);
fr.setGroupVisibility("group3", false);
features = seq.getSequenceFeatures();
fr.filterFeaturesForDisplay(features);
- assertEquals(features.size(), 3);
+ assertEquals(features.size(), 2);
assertTrue(features.contains(sf1) || features.contains(sf4));
assertFalse(features.contains(sf1) && features.contains(sf4));
- assertTrue(features.contains(sf2) || features.contains(sf3));
- assertFalse(features.contains(sf2) && features.contains(sf3));
+ assertFalse(features.contains(sf2));
+ assertFalse(features.contains(sf3));
assertTrue(features.contains(sf5));
/*
* graduated colour by score, no threshold, no score
*
*/
- FeatureColourI gc = new FeatureColour(Color.yellow, Color.red,
- Color.green, 1f, 11f);
+ FeatureColourI gc = new FeatureColour(Color.red, Color.yellow,
+ Color.red, Color.green, 1f, 11f);
fr.getFeatureColours().put("Cath", gc);
assertEquals(fr.getColour(sf1), Color.green);
* threshold is min-max; now score 6 is 1/6 of the way from 5 to 11
* or from yellow(255, 255, 0) to red(255, 0, 0)
*/
- gc = new FeatureColour(Color.yellow, Color.red, Color.green, 5f, 11f);
+ gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
+ 5f, 11f);
fr.getFeatureColours().put("Cath", gc);
gc.setAutoScaled(false); // this does little other than save a checkbox setting!
assertEquals(fr.getColour(sf2), new Color(255, 213, 0));
* colour by feature attribute value
* first with no value held
*/
- gc = new FeatureColour(Color.yellow, Color.red, Color.green, 1f, 11f);
+ gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
+ 1f, 11f);
fr.getFeatureColours().put("Cath", gc);
gc.setAttributeName("AF");
assertEquals(fr.getColour(sf2), Color.green);
csqData.put("Feature", "ENST01234");
assertEquals(fr.getColour(sf2), expected);
}
+
+ @Test(groups = "Functional")
+ public void testIsVisible()
+ {
+ String seqData = ">s1\nMLQGIFPRS\n";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
+ DataSourceType.PASTE);
+ AlignViewportI av = af.getViewport();
+ FeatureRenderer fr = new FeatureRenderer(av);
+ SequenceI seq = av.getAlignment().getSequenceAt(0);
+ SequenceFeature sf = new SequenceFeature("METAL", "Desc", 10, 10, 1f,
+ "Group");
+ sf.setValue("AC", "11");
+ sf.setValue("CLIN_SIG", "Likely Pathogenic");
+ seq.addSequenceFeature(sf);
+
+ assertFalse(fr.isVisible(null));
+
+ /*
+ * initial state FeatureRenderer hasn't 'found' feature
+ * and so its feature type has not yet been set visible
+ */
+ assertFalse(fr.getDisplayedFeatureCols().containsKey("METAL"));
+ assertFalse(fr.isVisible(sf));
+
+ fr.findAllFeatures(true);
+ assertTrue(fr.isVisible(sf));
+
+ /*
+ * feature group not visible
+ */
+ fr.setGroupVisibility("Group", false);
+ assertFalse(fr.isVisible(sf));
+ fr.setGroupVisibility("Group", true);
+ assertTrue(fr.isVisible(sf));
+
+ /*
+ * feature score outwith colour threshold (score > 2)
+ */
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
+ Color.white, 0, 10);
+ fc.setAboveThreshold(true);
+ fc.setThreshold(2f);
+ fr.setColour("METAL", fc);
+ assertFalse(fr.isVisible(sf)); // score 1 is not above threshold 2
+ fc.setBelowThreshold(true);
+ assertTrue(fr.isVisible(sf)); // score 1 is below threshold 2
+
+ /*
+ * colour with threshold on attribute AC (value is 11)
+ */
+ fc.setAttributeName("AC");
+ assertFalse(fr.isVisible(sf)); // value 11 is not below threshold 2
+ fc.setAboveThreshold(true);
+ assertTrue(fr.isVisible(sf)); // value 11 is above threshold 2
+
+ fc.setAttributeName("AF"); // attribute AF is absent in sf
+ assertTrue(fr.isVisible(sf)); // feature is not excluded by threshold
+
+ FeatureMatcherSetI filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byAttribute(Condition.Contains, "pathogenic",
+ "CLIN_SIG"));
+ fr.setFeatureFilter("METAL", filter);
+ assertTrue(fr.isVisible(sf)); // feature matches filter
+ filter.and(FeatureMatcher.byScore(Condition.LE, "0.4"));
+ assertFalse(fr.isVisible(sf)); // feature doesn't match filter
+ }
}
Color result = testee.shadeCalculation(ann, col);
assertEquals(result, expected, "for column " + col);
}
+
+ /*
+ * test for boundary case threshold == graphMax (JAL-3206)
+ */
+ float thresh = ann.threshold.value;
+ ann.threshold.value = ann.graphMax;
+ Color result = testee.shadeCalculation(ann, WIDTH - 1);
+ assertEquals(result, maxColour);
+ testee.setThresholdIsMinMax(false);
+ result = testee.shadeCalculation(ann, WIDTH - 1);
+ assertEquals(result, maxColour);
+ ann.threshold.value = thresh; // reset
}
/**
Color result = testee.shadeCalculation(ann, col);
assertEquals(result, expected, "for column " + col);
}
+
+ /*
+ * test for boundary case threshold == graphMin (JAL-3206)
+ */
+ float thresh = ann.threshold.value;
+ ann.threshold.value = ann.graphMin;
+ Color result = testee.shadeCalculation(ann, 0);
+ assertEquals(result, minColour);
+ testee.setThresholdIsMinMax(false);
+ result = testee.shadeCalculation(ann, 0);
+ assertEquals(result, minColour);
+ ann.threshold.value = thresh; // reset
}
/**
{
AnnotationColourGradient testee = new AnnotationColourGradient(ann,
minColour, maxColour, AnnotationColourGradient.ABOVE_THRESHOLD);
- testee = (AnnotationColourGradient) testee.getInstance(al, null);
+ testee = (AnnotationColourGradient) testee.getInstance(null, al);
for (int col = 0; col < WIDTH; col++)
{
Color result = testee.findColour('a', col, seq);
/*
- * expect white below threshold of 5
+ * expect white at or below threshold of 5
*/
- Color expected = col < 5 ? Color.white : new Color(50 + 10 * col,
+ Color expected = col <= 5 ? Color.white
+ : new Color(50 + 10 * col,
200 - 10 * col,
150 + 10 * col);
assertEquals(result, expected, "for column " + col);
for (int col = 0; col < WIDTH; col++)
{
/*
- * colours for values >= threshold are graduated
+ * colours for values > threshold are graduated
* range is 6-10 so steps of 100/5 = 20
*/
int factor = col - THRESHOLD_FIVE;
- Color expected = col < 5 ? Color.white : new Color(50 + 20 * factor,
+ Color expected = col <= 5 ? Color.white
+ : new Color(50 + 20 * factor,
200 - 20 * factor,
150 + 20 * factor);
Color result = testee.findColour('a', col, seq);
{
AnnotationColourGradient testee = new AnnotationColourGradient(ann,
minColour, maxColour, AnnotationColourGradient.BELOW_THRESHOLD);
- testee = (AnnotationColourGradient) testee.getInstance(al, null);
+ testee = (AnnotationColourGradient) testee.getInstance(null, al);
for (int col = 0; col < WIDTH; col++)
{
Color result = testee.findColour('a', col, seq);
- Color expected = col > 5 ? Color.white : new Color(50 + 10 * col,
+ Color expected = col >= 5 ? Color.white
+ : new Color(50 + 10 * col,
200 - 10 * col, 150 + 10 * col);
assertEquals(result, expected, "for column " + col);
}
for (int col = 0; col < WIDTH; col++)
{
/*
- * colours for values <= threshold are graduated
+ * colours for values < threshold are graduated
* range is 0-5 so steps of 100/5 = 20
*/
- Color expected = col > 5 ? Color.white : new Color(50 + 20 * col,
+ Color expected = col >= 5 ? Color.white
+ : new Color(50 + 20 * col,
200 - 20 * col, 150 + 20 * col);
Color result = testee.findColour('a', col, seq);
assertEquals(result, expected, "for column " + col);
{
AnnotationColourGradient testee = new AnnotationColourGradient(ann,
minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
- testee = (AnnotationColourGradient) testee.getInstance(al, null);
+ testee = (AnnotationColourGradient) testee.getInstance(null, al);
for (int col = 0; col < WIDTH; col++)
{
{
AnnotationColourGradient testee = new AnnotationColourGradient(ann,
minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
- testee = (AnnotationColourGradient) testee.getInstance(al, null);
+ testee = (AnnotationColourGradient) testee.getInstance(null, al);
/*
* flag corresponding to 'use original colours' checkbox
SequenceI seq = new Sequence("Seq1", "abcd");
AlignmentI al = new Alignment(new SequenceI[] { seq });
// the strings here correspond to JalviewColourScheme.toString() values
- ColourSchemeI cs = ColourSchemeProperty.getColourScheme(al, "Clustal");
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(null, al,
+ "Clustal");
assertTrue(cs instanceof ClustalxColourScheme);
// not case-sensitive
- cs = ColourSchemeProperty.getColourScheme(al, "CLUSTAL");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "CLUSTAL");
assertTrue(cs instanceof ClustalxColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "clustal");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "clustal");
assertTrue(cs instanceof ClustalxColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Blosum62");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Blosum62");
assertTrue(cs instanceof Blosum62ColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "% Identity");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "% Identity");
assertTrue(cs instanceof PIDColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Zappo");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Zappo");
assertTrue(cs instanceof ZappoColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Taylor");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Taylor");
assertTrue(cs instanceof TaylorColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Hydrophobic");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Hydrophobic");
assertTrue(cs instanceof HydrophobicColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Helix Propensity");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Helix Propensity");
assertTrue(cs instanceof HelixColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Strand Propensity");
+ cs = ColourSchemeProperty.getColourScheme(null, al,
+ "Strand Propensity");
assertTrue(cs instanceof StrandColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Turn Propensity");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Turn Propensity");
assertTrue(cs instanceof TurnColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Buried Index");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Buried Index");
assertTrue(cs instanceof BuriedColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Nucleotide");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Nucleotide");
assertTrue(cs instanceof NucleotideColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Purine/Pyrimidine");
+ cs = ColourSchemeProperty.getColourScheme(null, al,
+ "Purine/Pyrimidine");
assertTrue(cs instanceof PurinePyrimidineColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "T-Coffee Scores");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "T-Coffee Scores");
assertTrue(cs instanceof TCoffeeColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "RNA Helices");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "RNA Helices");
assertTrue(cs instanceof RNAHelicesColour);
// 'None' is a special value
- assertNull(ColourSchemeProperty.getColourScheme(al, "None"));
- assertNull(ColourSchemeProperty.getColourScheme(al, "none"));
+ assertNull(ColourSchemeProperty.getColourScheme(null, al, "None"));
+ assertNull(ColourSchemeProperty.getColourScheme(null, al, "none"));
// default is to convert the name into a fixed colour
- cs = ColourSchemeProperty.getColourScheme(al, "elephants");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "elephants");
assertTrue(cs instanceof UserColourScheme);
/*
* explicit aa colours
*/
UserColourScheme ucs = (UserColourScheme) ColourSchemeProperty
- .getColourScheme(al,
+ .getColourScheme(null, al,
"R,G=red;C=blue;c=green;Q=10,20,30;S,T=11ffdd");
assertEquals(ucs.findColour('H'), Color.white);
assertEquals(ucs.findColour('R'), Color.red);
import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
+import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.AnnotatedCollectionI;
}
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
{
final ColourSchemeI cs1 = ColourSchemes.getInstance()
.getColourScheme(JalviewColourScheme.Taylor.toString(),
}
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
{
- return new MyClustal(sg, hiddenRepSequences);
+ return new MyClustal(sg, view.getHiddenRepSequences());
}
@Override
+++ /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.schemes;
-
-import static org.testng.AssertJUnit.assertTrue;
-
-import jalview.gui.JvOptionPane;
-
-import java.util.Map;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class DnaCodonTests
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- @Test(groups = { "Functional" })
- public void testAmbiguityCodeGeneration()
- {
- assertTrue(ResidueProperties.ambiguityCodes.size() > 0);
- }
-
- @Test(groups = { "Functional" })
- public void testAmbiguityCodon()
- {
- for (String ac : ResidueProperties.ambiguityCodes.keySet())
- {
- assertTrue("Couldn't resolve GGN as glycine codon",
- ResidueProperties.codonHash2.get("GG" + ac).equals("G"));
- }
- }
-
- @Test(groups = { "Functional" })
- public void regenerateCodonTable()
- {
- for (Map.Entry<String, String> codon : ResidueProperties.codonHash2
- .entrySet())
- {
- System.out.println("ResidueProperties.codonHash2.set(\""
- + codon.getKey() + "\", \"" + codon.getValue() + "\");");
- }
- }
-}
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-import junit.extensions.PA;
-
public class FeatureColourTest
{
}
@Test(groups = { "Functional" })
+ public void testConstructors()
+ {
+ FeatureColourI fc = new FeatureColour();
+ assertNull(fc.getColour());
+ assertTrue(fc.isSimpleColour());
+ assertFalse(fc.isColourByLabel());
+ assertFalse(fc.isGraduatedColour());
+ assertFalse(fc.isColourByAttribute());
+ assertEquals(Color.white, fc.getMinColour());
+ assertEquals(Color.black, fc.getMaxColour());
+
+ fc = new FeatureColour(Color.RED);
+ assertEquals(Color.red, fc.getColour());
+ assertTrue(fc.isSimpleColour());
+ assertFalse(fc.isColourByLabel());
+ assertFalse(fc.isGraduatedColour());
+ assertFalse(fc.isColourByAttribute());
+ assertEquals(ColorUtils.bleachColour(Color.RED, 0.9f),
+ fc.getMinColour());
+ assertEquals(Color.RED, fc.getMaxColour());
+
+ }
+
+ @Test(groups = { "Functional" })
public void testCopyConstructor()
{
/*
/*
* min-max colour
*/
- fc = new FeatureColour(Color.gray, Color.black, 10f, 20f);
+ fc = new FeatureColour(null, Color.gray, Color.black, Color.gray, 10f,
+ 20f);
fc.setAboveThreshold(true);
fc.setThreshold(12f);
fc1 = new FeatureColour(fc);
/*
* min-max-noValue colour
*/
- fc = new FeatureColour(Color.gray, Color.black, Color.green, 10f, 20f);
+ fc = new FeatureColour(Color.red, Color.gray, Color.black, Color.green,
+ 10f, 20f);
fc.setAboveThreshold(true);
fc.setThreshold(12f);
fc1 = new FeatureColour(fc);
assertTrue(fc1.isGraduatedColour());
assertFalse(fc1.isColourByLabel());
+ assertFalse(fc1.isSimpleColour());
assertFalse(fc1.isColourByAttribute());
assertNull(fc1.getAttributeName());
assertTrue(fc1.isAboveThreshold());
assertEquals(Color.gray, fc1.getMinColour());
assertEquals(Color.black, fc1.getMaxColour());
assertEquals(Color.green, fc1.getNoColour());
+ assertEquals(Color.red, fc1.getColour());
assertEquals(10f, fc1.getMin());
assertEquals(20f, fc1.getMax());
/*
* colour by attribute (value)
*/
- fc = new FeatureColour(Color.gray, Color.black, Color.green, 10f, 20f);
+ fc = new FeatureColour(Color.yellow, Color.gray, Color.black,
+ Color.green, 10f, 20f);
fc.setAboveThreshold(true);
fc.setThreshold(12f);
fc.setAttributeName("AF");
assertTrue(fc1.isGraduatedColour());
assertFalse(fc1.isColourByLabel());
assertTrue(fc1.isColourByAttribute());
+ assertFalse(fc1.isSimpleColour());
assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
assertTrue(fc1.isAboveThreshold());
assertEquals(12f, fc1.getThreshold());
assertEquals(Color.gray, fc1.getMinColour());
assertEquals(Color.black, fc1.getMaxColour());
assertEquals(Color.green, fc1.getNoColour());
+ assertEquals(Color.yellow, fc1.getColour());
assertEquals(10f, fc1.getMin());
assertEquals(20f, fc1.getMax());
}
@Test(groups = { "Functional" })
- public void testCopyConstructor_minMax()
- {
- /*
- * graduated colour
- */
- FeatureColour fc = new FeatureColour(Color.BLUE, Color.RED, 1f, 5f);
- assertTrue(fc.isGraduatedColour());
- assertFalse(fc.isColourByLabel());
- assertFalse(fc.isColourByAttribute());
- assertNull(fc.getAttributeName());
- assertEquals(1f, fc.getMin());
- assertEquals(5f, fc.getMax());
-
- /*
- * update min-max bounds
- */
- FeatureColour fc1 = new FeatureColour(fc, 2f, 6f);
- assertTrue(fc1.isGraduatedColour());
- assertFalse(fc1.isColourByLabel());
- assertFalse(fc1.isColourByAttribute());
- assertNull(fc1.getAttributeName());
- assertEquals(2f, fc1.getMin());
- assertEquals(6f, fc1.getMax());
- assertFalse((boolean) PA.getValue(fc1, "isHighToLow"));
-
- /*
- * update min-max bounds - high to low
- */
- fc1 = new FeatureColour(fc, 23f, 16f);
- assertTrue(fc1.isGraduatedColour());
- assertFalse(fc1.isColourByLabel());
- assertFalse(fc1.isColourByAttribute());
- assertNull(fc1.getAttributeName());
- assertEquals(23f, fc1.getMin());
- assertEquals(16f, fc1.getMax());
- assertTrue((boolean) PA.getValue(fc1, "isHighToLow"));
-
- /*
- * graduated colour by attribute
- */
- fc1.setAttributeName("AF");
- fc1 = new FeatureColour(fc1, 13f, 36f);
- assertTrue(fc1.isGraduatedColour());
- assertFalse(fc1.isColourByLabel());
- assertTrue(fc1.isColourByAttribute());
- assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
- assertEquals(13f, fc1.getMin());
- assertEquals(36f, fc1.getMax());
- assertFalse((boolean) PA.getValue(fc1, "isHighToLow"));
-
- /*
- * colour by label
- */
- fc = new FeatureColour(Color.BLUE, Color.RED, 1f, 5f);
- fc.setColourByLabel(true);
- assertFalse(fc.isGraduatedColour());
- assertTrue(fc.isColourByLabel());
- assertFalse(fc.isColourByAttribute());
- assertNull(fc.getAttributeName());
- assertEquals(1f, fc.getMin());
- assertEquals(5f, fc.getMax());
-
- /*
- * update min-max bounds
- */
- fc1 = new FeatureColour(fc, 2f, 6f);
- assertFalse(fc1.isGraduatedColour());
- assertTrue(fc1.isColourByLabel());
- assertFalse(fc1.isColourByAttribute());
- assertNull(fc1.getAttributeName());
- assertEquals(2f, fc1.getMin());
- assertEquals(6f, fc1.getMax());
-
- /*
- * colour by attribute text
- */
- fc1.setAttributeName("AC");
- fc1 = new FeatureColour(fc1, 13f, 36f);
- assertFalse(fc1.isGraduatedColour());
- assertTrue(fc1.isColourByLabel());
- assertTrue(fc1.isColourByAttribute());
- assertArrayEquals(new String[] { "AC" }, fc1.getAttributeName());
- assertEquals(13f, fc1.getMin());
- assertEquals(36f, fc1.getMax());
- }
-
- @Test(groups = { "Functional" })
public void testGetColor_simpleColour()
{
FeatureColour fc = new FeatureColour(Color.RED);
* score 0 to 100
* gray(128, 128, 128) to red(255, 0, 0)
*/
- FeatureColour fc = new FeatureColour(Color.GRAY, Color.RED, 0f, 100f);
+ FeatureColour fc = new FeatureColour(null, Color.GRAY, Color.RED, null,
+ 0f, 100f);
// feature score is 75 which is 3/4 of the way from GRAY to RED
SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 75f,
null);
public void testGetColor_aboveBelowThreshold()
{
// gradient from [50, 150] from WHITE(255, 255, 255) to BLACK(0, 0, 0)
- FeatureColour fc = new FeatureColour(Color.WHITE, Color.BLACK, 50f,
- 150f);
+ FeatureColour fc = new FeatureColour(null, Color.WHITE, Color.BLACK,
+ Color.white, 50f, 150f);
SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 70f,
null);
* graduated colour by score, no threshold
* - default constructor sets noValueColor = minColor
*/
- fc = new FeatureColour(Color.GREEN, Color.RED, 12f, 25f);
+ fc = new FeatureColour(null, Color.GREEN, Color.RED, Color.GREEN, 12f,
+ 25f);
String greenHex = Format.getHexString(Color.GREEN);
String expected = String.format(
"domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
/*
* graduated colour by score, no threshold, no value gets min colour
*/
- fc = new FeatureColour(Color.GREEN, Color.RED, Color.GREEN, 12f, 25f);
+ fc = new FeatureColour(Color.RED, Color.GREEN, Color.RED, Color.GREEN,
+ 12f, 25f);
expected = String.format(
"domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
redHex);
/*
* graduated colour by score, no threshold, no value gets max colour
*/
- fc = new FeatureColour(Color.GREEN, Color.RED, Color.RED, 12f, 25f);
+ fc = new FeatureColour(Color.RED, Color.GREEN, Color.RED, Color.RED,
+ 12f, 25f);
expected = String.format(
"domain\tscore|%s|%s|noValueMax|abso|12.0|25.0|none", greenHex,
redHex);
* graduated colour based on attribute value for AF
* given a min-max range of 0-100
*/
- FeatureColour fc = new FeatureColour(new Color(50, 100, 150),
- new Color(150, 200, 250), Color.yellow, 0f, 100f);
+ FeatureColour fc = new FeatureColour(Color.white,
+ new Color(50, 100, 150), new Color(150, 200, 250), Color.yellow,
+ 0f, 100f);
String attName = "AF";
fc.setAttributeName(attName);
Color expected = new Color(70, 120, 170);
assertEquals(expected, fc.getColor(sf));
}
+
+ @Test(groups = { "Functional" })
+ public void testIsOutwithThreshold()
+ {
+ FeatureColourI fc = new FeatureColour(Color.red);
+ SequenceFeature sf = new SequenceFeature("METAL", "desc", 10, 12, 1.2f, "grp");
+ assertFalse(fc.isOutwithThreshold(null));
+ assertFalse(fc.isOutwithThreshold(sf));
+
+ fc = new FeatureColour(null, Color.white, Color.black, Color.green, 0f,
+ 10f);
+ assertFalse(fc.isOutwithThreshold(sf)); // no threshold
+
+ fc.setAboveThreshold(true);
+ fc.setThreshold(1f);
+ assertFalse(fc.isOutwithThreshold(sf)); // feature score 1.2 is above 1
+
+ fc.setThreshold(2f);
+ assertTrue(fc.isOutwithThreshold(sf)); // feature score 1.2 is not above 2
+
+ fc.setBelowThreshold(true);
+ assertFalse(fc.isOutwithThreshold(sf)); // feature score 1.2 is below 2
+
+ fc.setThreshold(1f);
+ assertTrue(fc.isOutwithThreshold(sf)); // feature score 1.2 is not below 1
+
+ /*
+ * with attribute value threshold
+ */
+ fc.setAttributeName("AC");
+ assertFalse(fc.isOutwithThreshold(sf)); // missing attribute AC is ignored
+
+ sf.setValue("AC", "-1");
+ assertFalse(fc.isOutwithThreshold(sf)); // value -1 is below 1
+
+ sf.setValue("AC", "1");
+ assertTrue(fc.isOutwithThreshold(sf)); // value 1 is not below 1
+
+ sf.setValue("AC", "junk");
+ assertFalse(fc.isOutwithThreshold(sf)); // bad value is ignored
+ }
+
+ /**
+ * Test description of feature colour suitable for a tooltip
+ */
+ @Test(groups = { "Functional" })
+ public void testGetDescription()
+ {
+ /*
+ * plain colour
+ */
+ FeatureColour fc = new FeatureColour(Color.RED);
+ assertEquals(
+ String.format("r=%d,g=%d,b=%d", Color.RED.getRed(),
+ Color.red.getGreen(), Color.red.getBlue()),
+ fc.getDescription());
+
+ /*
+ * colour by label (no threshold)
+ */
+ fc = new FeatureColour();
+ fc.setColourByLabel(true);
+ assertEquals("By Label", fc.getDescription());
+
+ /*
+ * colour by attribute text (no threshold)
+ */
+ fc = new FeatureColour();
+ fc.setColourByLabel(true);
+ fc.setAttributeName("CLIN_SIG");
+ assertEquals("By CLIN_SIG", fc.getDescription());
+
+ /*
+ * colour by label (above score threshold)
+ */
+ fc = new FeatureColour();
+ fc.setColourByLabel(true);
+ fc.setAutoScaled(false);
+ fc.setThreshold(12.5f);
+ fc.setAboveThreshold(true);
+ assertEquals("By Label (Score > 12.5)",
+ fc.getDescription());
+
+ /*
+ * colour by label (below score threshold)
+ */
+ fc.setBelowThreshold(true);
+ assertEquals("By Label (Score < 12.5)",
+ fc.getDescription());
+
+ /*
+ * colour by attributes text (below score threshold)
+ */
+ fc.setBelowThreshold(true);
+ fc.setAttributeName("CSQ", "Consequence");
+ assertEquals(
+ "By CSQ:Consequence (Score < 12.5)",
+ fc.getDescription());
+
+ /*
+ * graduated colour by score, no threshold
+ */
+ fc = new FeatureColour(null, Color.GREEN, Color.RED, null, 12f, 25f);
+ assertEquals("By Score", fc.getDescription());
+
+ /*
+ * graduated colour by score, below threshold
+ */
+ fc.setThreshold(12.5f);
+ fc.setBelowThreshold(true);
+ assertEquals("By Score (< 12.5)",
+ fc.getDescription());
+
+ /*
+ * graduated colour by score, above threshold
+ */
+ fc.setThreshold(12.5f);
+ fc.setAboveThreshold(true);
+ fc.setAutoScaled(false);
+ assertEquals("By Score (> 12.5)",
+ fc.getDescription());
+
+ /*
+ * graduated colour by attribute, no threshold
+ */
+ fc.setAttributeName("CSQ", "AF");
+ fc.setAboveThreshold(false);
+ fc.setAutoScaled(false);
+ assertEquals("By CSQ:AF", fc.getDescription());
+
+ /*
+ * graduated colour by attribute, above threshold
+ */
+ fc.setAboveThreshold(true);
+ fc.setAutoScaled(false);
+ assertEquals("By CSQ:AF (> 12.5)",
+ fc.getDescription());
+ }
}
assertTrue(JalviewColourScheme.PurinePyrimidine.getSchemeClass() == PurinePyrimidineColourScheme.class);
assertTrue(JalviewColourScheme.TCoffee.getSchemeClass() == TCoffeeColourScheme.class);
assertTrue(JalviewColourScheme.RNAHelices.getSchemeClass() == RNAHelicesColour.class);
+ assertTrue(JalviewColourScheme.IdColour
+ .getSchemeClass() == IdColourScheme.class);
}
@Test(groups = "Functional")
"Purine/Pyrimidine");
assertEquals(JalviewColourScheme.TCoffee.toString(), "T-Coffee Scores");
assertEquals(JalviewColourScheme.RNAHelices.toString(), "RNA Helices");
+ assertEquals(JalviewColourScheme.IdColour.toString(), "Sequence ID");
}
}
}
@Test(groups = { "Functional" })
+ public void testGetDssp3State()
+ {
+ assertNull(ResidueProperties.getDssp3state(null));
+ assertEquals("", ResidueProperties.getDssp3state(""));
+ String foo = "0123 []<>abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ";
+ String bar = " E E HHH ";
+ assertEquals(bar, ResidueProperties.getDssp3state(foo));
+ }
+
+ @Test(groups = { "Functional" })
public void testPhysicoChemicalProperties()
{
checkProperty("aromatic", "FYWH-*");
package jalview.util;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
}
-
- @Test(groups = { "Functional" })
- public void testIsDasCoordinateSystem()
- {
- assertFalse(DBRefUtils.isDasCoordinateSystem(null, null));
- assertFalse(DBRefUtils.isDasCoordinateSystem("pdbresnum", null));
- assertFalse(DBRefUtils.isDasCoordinateSystem(null, new DBRefEntry(
- "PDB", "v1", "a1")));
-
- assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
- new DBRefEntry("PDB", "v1", "a1")));
- assertTrue(DBRefUtils.isDasCoordinateSystem("PDBRESNUM",
- new DBRefEntry("PDB", "v1", "a1")));
- // "pdb" is converted to upper-case in DBRefEntry constructor
- assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
- new DBRefEntry("pdb", "v1", "a1")));
- assertFalse(DBRefUtils.isDasCoordinateSystem("pdb", new DBRefEntry(
- "pdb", "v1", "a1")));
-
- assertTrue(DBRefUtils.isDasCoordinateSystem("UNIPROT", new DBRefEntry(
- "Uniprot", "v1", "a1")));
- assertTrue(DBRefUtils.isDasCoordinateSystem("Uniprot", new DBRefEntry(
- "UNIPROT", "v1", "a1")));
- assertFalse(DBRefUtils.isDasCoordinateSystem("UNIPROTKB",
- new DBRefEntry("pdb", "v1", "a1")));
-
- assertTrue(DBRefUtils.isDasCoordinateSystem("EMBL", new DBRefEntry(
- "EMBL", "v1", "a1")));
- assertTrue(DBRefUtils.isDasCoordinateSystem("embl", new DBRefEntry(
- "embl", "v1", "a1")));
- }
-
/**
* Test 'parsing' a DBRef - non PDB case
*/
--- /dev/null
+package jalview.util;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+
+import org.json.JSONException;
+import org.json.simple.JSONArray;
+import org.testng.annotations.Test;
+
+public class JSONUtilsTest
+{
+ @Test(groups = "Functional")
+ public void testArrayToList() throws JSONException
+ {
+ assertNull(JSONUtils.arrayToList(null));
+
+ JSONArray ja = new JSONArray();
+ assertNull(JSONUtils.arrayToList(null));
+
+ ja.add("hello");
+ assertEquals(JSONUtils.arrayToList(ja), "hello");
+
+ ja.add("world");
+ assertEquals(JSONUtils.arrayToList(ja), "hello,world");
+ }
+}
for (Field field : fields)
{
field.setAccessible(true);
- if (!copyConstructorIgnores(field.getName()))
+ if (!copyConstructorIgnores(field))
{
changeValue(vs1, field);
}
for (Field field1 : fields)
{
- final Object value1 = field1.get(vs1);
- final Object value2 = field1.get(vs2);
- String msg = "Mismatch in " + field1.getName() + "(" + value1 + "/"
+ if (!copyConstructorIgnores(field1))
+ {
+ final Object value1 = field1.get(vs1);
+ final Object value2 = field1.get(vs2);
+ String msg = "Mismatch in " + field1.getName() + "(" + value1 + "/"
+ value2 + ") - not set in copy constructor?";
- assertEquals(msg, value1, value2);
+ assertEquals(msg, value1, value2);
+ }
}
assertEquals("Hashcode not equals", vs1.hashCode(), vs2.hashCode());
}
/**
- * Add any field names in here that we expect to be ignored by the copy
- * constructor
+ * Add tests here for any fields that we expect to be ignored by
+ * the copy constructor
*
- * @param name
+ * @param field
* @return
*/
- private boolean copyConstructorIgnores(String name)
+ private boolean copyConstructorIgnores(Field field)
{
/*
- * currently none!
+ * ignore instrumentation added by jacoco for test coverage
*/
+ if (field.isSynthetic())
+ {
+ return true;
+ }
+ if (field.getType().toString().contains("com_atlassian_clover"))
+ {
+ return true;
+ }
+
return false;
}
-
+
/**
- * Change the value of one field in a ViewStyle object
- *
- * @param vs
- * @param field
- * @throws IllegalAccessException
- */
+ * Change the value of one field in a ViewStyle object
+ *
+ * @param vs
+ * @param field
+ * @throws IllegalAccessException
+ */
protected void changeValue(ViewStyle vs, Field field)
throws IllegalAccessException
{
Field[] fields = ViewStyle.class.getDeclaredFields();
for (Field field : fields)
{
- field.setAccessible(true);
- Object oldValue = field.get(vs2);
- changeValue(vs2, field);
- assertFalse("equals method ignores " + field.getName(),
+ if (!copyConstructorIgnores(field))
+ {
+ field.setAccessible(true);
+ Object oldValue = field.get(vs2);
+ changeValue(vs2, field);
+ assertFalse("equals method ignores " + field.getName(),
vs1.equals(vs2));
- if (vs1.hashCode() == vs2.hashCode())
- {
- // uncomment next line to see which fields hashCode ignores
- // System.out.println("hashCode ignores " + field.getName());
+ if (vs1.hashCode() == vs2.hashCode())
+ {
+ // uncomment next line to see which fields hashCode ignores
+ // System.out.println("hashCode ignores " + field.getName());
+ }
+ // restore original value before testing the next field
+ field.set(vs2, oldValue);
}
- // restore original value before testing the next field
- field.set(vs2, oldValue);
}
}
}
SequenceI seq = new Uniprot().uniprotEntryToSequence(entry);
assertNotNull(seq);
assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
+ assertEquals(seq.getSequenceAsString(),
+ seq.createDatasetSequence().getSequenceAsString());
}
Checkstyle for Jalview
----------------------
+See
+https://issues.jalview.org/browse/JAL-1854
http://checkstyle.sourceforge.net/
GNU LGPL
- Help | Eclipse Marketplace
- search for checkstyle
- install eclipse-cs checkstyle plugin
-The current version is 6.19.1 (August 2016).
+Change Log
+----------
+See http://checkstyle.sourceforge.net/releasenotes.html
+Aug 2016 Initial version used is 6.19.1
+Dec 2018 Updated to 8.12.0 (latest on Eclipse Marketplace, 8.15 is latest release)
+ SuppressionCommentFilter relocated (changed in 8.1)
+ FileContentsHolder removed (changed in 8.2)
+ Updates to import-control.xml for code changes (htsjdk, stackoverflowusers)
+
Config
------
Option 2: on demand on selected code
- right-click on a class or package and Checkstyle | Check code with checkstyle
- (or Clear Checkstyle violations to remove checkstyle warnings)
+ - recommended to use this as a QA step when changing or reviewing code
Checkstyle rules
----------------
Tips
----
Sometimes checkstyle needs a kick before it will refresh its findings.
- A whitespace edit in checkstyle.xml usually does this. There may be better ways.
+ Click the 'refresh' icon at top right in Eclipse | Preferences | Checkstyle.
Invalid configuration files may result in checkstyle failing with an error reported
in the Eclipse log file.
- Help | Installation Details | Configuration takes you to a screen with a
+ Eclipse | About | Installation Details | Configuration takes you to a screen with a
'View Error Log' button.
Sometimes checkstyle can fail silently. Try 'touching' (editing) config files, failing
<suppress checks="[a-zA-Z0-9]*" files="[\\/]ext[\\/]edu*"/>
<suppress checks="[a-zA-Z0-9]*" files="[\\/]ext[\\/]vamsas*"/>
<suppress checks="[a-zA-Z0-9]*" files="[\\/]org[\\/]jibble*"/>
+ <suppress checks="[a-zA-Z0-9]*" files="[\\/]org[\\/]stackoverflowusers*"/>
<suppress checks="[a-zA-Z0-9]*" files="[\\/]uk[\\/]ac*"/>
<!--
</module>
<!--
- Allow suppression of rules by comments, e.g.:
- // CHECKSTYLE.OFF: ParameterNumber
- ..method declaration
- // CHECKSTYLE.ON: ParameterNumber
- -->
- <module name="SuppressionCommentFilter">
- <property name="offCommentFormat" value="CHECKSTYLE.OFF\: ([\w\|]+)"/>
- <property name="onCommentFormat" value="CHECKSTYLE.ON\: ([\w\|]+)"/>
- <property name="checkFormat" value="$1"/>
- </module>
-
- <!--
Check language bundles have the same keys and no duplicates
(ensure Checkstyle is configured to scan non-source files)
-->
<property name="tabWidth" value="4"/>
<!--
- Enables parsing of suppressions comments
- see http://checkstyle.sourceforge.net/config_filters.html#SuppressionCommentFilter
+ Allow suppression of rules by comments, e.g.:
+ // CHECKSTYLE.OFF: ParameterNumber
+ ..method declaration
+ // CHECKSTYLE.ON: ParameterNumber
-->
- <module name="FileContentsHolder"/>
+ <module name="SuppressionCommentFilter">
+ <property name="offCommentFormat" value="CHECKSTYLE.OFF\: ([\w\|]+)"/>
+ <property name="onCommentFormat" value="CHECKSTYLE.ON\: ([\w\|]+)"/>
+ <property name="checkFormat" value="$1"/>
+ </module>
<!-- ****************************** -->
<!-- NAMING STANDARDS -->
<allow pkg="compbio.metadata" class="jalview.gui.WsJobParameters"/>
<allow pkg="fr.orsay.lri.varna" class="jalview.gui.AppVarna"/>
<allow pkg="fr.orsay.lri.varna" class="jalview.gui.AppVarnaBinding"/>
+ <allow pkg="org.stackoverflowusers.file" class="jalview.gui.Desktop"/>
<allow pkg="uk.ac.vamsas" class="jalview.gui.VamsasApplication"/>
</subpackage>
<allow pkg="uk.ac.vamsas"/>
<allow pkg="fr.orsay.lri.varna"/>
<allow pkg="MCview"/>
+ <subpackage name="vcf">
+ <allow pkg="htsjdk\.*" regex="true"/>
+ </subpackage>
</subpackage>
<subpackage name="javascript">
<taskdef resource="net/sf/antcontrib/antcontrib.properties">
<classpath>
- <pathelement location="${basedir}/utils/ant-contrib-0.3.jar"/>
+ <pathelement location="${basedir}/utils/ant-contrib-1.0b3.jar"/>
+ </classpath>
+</taskdef>
+<taskdef resource="net/sf/antcontrib/antlib.xml">
+ <classpath>
+ <pathelement location="${basedir}/utils/ant-contrib-1.0b3.jar"/>
</classpath>
</taskdef>
-<taskdef resource="net/sf/antcontrib/antlib.xml"/>
<target name="checkLang" description="Reports missing entries in language bundles compared to Message.properties">
<!-- adapted from http://stackoverflow.com/questions/14381660/ant-task-to-compare-two-properties-files -->
git://source.jalview.org / jalview.git / commitdiff
