From: gmungoc
Date: Mon, 4 Mar 2019 16:44:19 +0000 (+0000)
Subject: Merge remote-tracking branch 'origin/bug/JAL-3082selectRegex' into merge/JAL-3082
X-Git-Tag: Release_2_11_0~17^2~76
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=d8720fc191cba996c440171ef8e07462ef9f7035;p=jalview.git
Merge remote-tracking branch 'origin/bug/JAL-3082selectRegex' into merge/JAL-3082
---
diff --git a/.ant-targets-build.xml b/.ant-targets-build.xml
index 7ef21f1..2a9de83 100644
--- a/.ant-targets-build.xml
+++ b/.ant-targets-build.xml
@@ -1,2 +1,31 @@
+build
+buildPropertiesFile
+buildTests
+buildextclients
+buildindices
+clean
+compileApplet
+distclean
help
+init
+jaxb-bindings
+linkcheck
+makeApplet
+makedist
+makefulldist
+obfuscate
+packageApplet
+prepare
+prepareTests
+preparejnlp
+prepubapplet_1
+pubapplet
+runenv
+signApplet
+sourcedist
+sourcedoc
+sourcescrub
+testclean
+testng
usage
+writejnlpf
diff --git a/.classpath b/.classpath
index d32799b..7d02b37 100644
--- a/.classpath
+++ b/.classpath
@@ -13,7 +13,6 @@
-
@@ -47,7 +46,8 @@
-
+
+
@@ -69,5 +69,6 @@
+
diff --git a/.gitignore b/.gitignore
index 86637df..211ddc9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,11 +1,13 @@
-.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
@@ -14,3 +16,4 @@ TESTNG
/jalviewApplet.jar
/benchmarking/lib
*.class
+/site
diff --git a/.settings/org.eclipse.jdt.ui.prefs b/.settings/org.eclipse.jdt.ui.prefs
index 30e76be..958613b 100644
--- a/.settings/org.eclipse.jdt.ui.prefs
+++ b/.settings/org.eclipse.jdt.ui.prefs
@@ -40,6 +40,7 @@ sp_cleanup.qualify_static_member_accesses_through_subtypes_with_declaring_class=
sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_modifiers=false
sp_cleanup.remove_redundant_type_arguments=true
sp_cleanup.remove_trailing_whitespaces=false
sp_cleanup.remove_trailing_whitespaces_all=true
diff --git a/AUTHORS b/AUTHORS
index 1bfc734..2fe3fce 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -7,15 +7,17 @@ or might otherwise be considered author of Jalview.
The people listed below are 'The Jalview Authors', who collectively
own the copyright to the Jalview source code and permit it to be released under GPL.
-This is the authoritative list. It was correct on 23rd November 2016.
+This is the authoritative list: it was correct on 5th September 2018 (or the last commit date!)
+
If you are releasing a version of Jalview, please make sure any
statement of authorship in the GUI reflects the list shown here.
In particular, check the resources/authors.props file !
Jim Procter
Mungo Carstairs
-Tochukwu 'Charles' Ofoegbu
+Ben Soares
Kira Mourao
+Tochukwu 'Charles' Ofoegbu
Andrew Waterhouse
Jan Engelhardt
Lauren Lui
diff --git a/README b/README
index eaf226b..8172066 100755
--- a/README
+++ b/README
@@ -21,13 +21,18 @@ For more help, read the file doc/building.html
##################
-To run application:
+To run application...
+[ NOTE: when using the -classpath option with the '*' wildcard, the argument must be quoted to avoid shell expansion of the wildcard,
+ ALSO, the wildcard MUST be as DIR/* and not DIR/*.jar etc or it will not be interpreted correctly ]
-java -Djava.ext.dirs=JALVIEW_HOME/lib -cp JALVIEW_HOME/jalview.jar jalview.bin.Jalview
+on Windows use:
+ java -classpath "JALVIEW_HOME/lib/*;JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+and on MacOS or Linux:
+ java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
Replace JALVIEW_HOME with the full path to Jalview Installation Directory. If building from source:
-java -Djava.ext.dirs=JALVIEW_BUILD/dist -cp JALVIEW_BUILD/dist/jalview.jar jalview.bin.Jalview
+ java -classpath "JALVIEW_BUILD/dist/*" jalview.bin.Jalview
##################
diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index a0b8d94..afa99d2 100644
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -49,15 +49,21 @@ jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfre
quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/
-vaqua: v4 (latest stable) by Alan Snyder et al. GPLv2 with Classpathe xception, also includes contributions from Quaqua: ownloaded from http://violetlib.org/vaqua/overview.html
+vaqua5-patch: This is a patched version of VAqua v5 (latest stable) by Alan Snyder et al. GPLv3 with Classpath exception, also includes contributions from Quaqua: http://violetlib.org/vaqua/overview.html - see doc/patching-vaqua.txt for patch details, and http://issues.jalview.org/browse/JAL-2988 for details of the bug that the patch addresses.
-lib/htsjdk-1.120-SNAPSHOT.jar: (currently not required for 2.10) built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
+lib/htsjdk-2.12.jar: built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
lib/biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
lib/biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
+Libraries for Test Suite
+
+utils/classgraph-4.1.6.jar: BSD License - allows recovery of classpath for programmatic construction of a Java command line to launch Jalview
+ version 4.1.6 downloaded from https://mvnrepository.com/artifact/io.github.classgraph/classgraph/4.1.6
+
+
Additional dependencies
examples/javascript/deployJava.js : http://java.com/js/deployJava.js
diff --git a/build.xml b/build.xml
index 454b994..9cd966c 100755
--- a/build.xml
+++ b/build.xml
@@ -356,10 +356,15 @@
-
+
+
+
+
+
+
@@ -369,7 +374,7 @@
-
+
@@ -396,7 +401,7 @@
-->
-
+
@@ -404,7 +409,7 @@
-
+
@@ -694,30 +699,50 @@
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
-
+
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
-
-
+
+
-
-
-
+
+
+
+
+
+
+
+
+
@@ -936,13 +961,13 @@
-
+
-
+
diff --git a/doc/patching-vaqua.txt b/doc/patching-vaqua.txt
new file mode 100644
index 0000000..65c9974
--- /dev/null
+++ b/doc/patching-vaqua.txt
@@ -0,0 +1,27 @@
+VAqua5-patched.jar - how the patch was created
+
+1. Download VAqua5 source from https://violetlib.org/release/vaqua/5/VAqua5Source.zip
+2. Unzip to a directory and apply this patch
+
+diff --git a/src/org/violetlib/aqua/fc/AquaFileChooserUI.java b/src/org/violetlib/aqua/fc/AquaFileChooserUI.java
+index 833366d..61f66e5 100644
+--- a/src/org/violetlib/aqua/fc/AquaFileChooserUI.java
++++ b/src/org/violetlib/aqua/fc/AquaFileChooserUI.java
+@@ -1171,7 +1171,8 @@ public class AquaFileChooserUI extends BasicFileChooserUI {
+ goToFolderCancelButtonText = getString("FileChooser.goToFolderCancelButtonText", l, "Cancel");
+ goToFolderAcceptButtonText = getString("FileChooser.goToFolderAcceptButtonText", l, "Accept");
+ goToFolderErrorText = getString("FileChooser.goToFolderErrorText", l, "The folder can\u2019t be found.");
+- defaultInitialSaveFileName = getString("FileChooser.defaultSaveFileName", l, "Untitled");
++ // Don't set an initial filename for saving (or loading) !
++ // defaultInitialSaveFileName = getString("FileChooser.defaultSaveFileName", l, "Untitled");
+ }
+
+ /**
+
+3. Ensure XCode is installed, along with command line tools and the OSX developer packs
+ - you should have /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk
+
+4. Download the VAqua rendering library from violetlib.org and save to the VAqua source's lib folder as lib/VAquaRendering.jar
+
+5. change to the release directory and execute 'ant' - a few warnings are generated but providing a final jar is created, all is good!
+
diff --git a/examples/backupfilestest.fa b/examples/backupfilestest.fa
new file mode 100644
index 0000000..c536a79
--- /dev/null
+++ b/examples/backupfilestest.fa
@@ -0,0 +1,2 @@
+>BACKUP_FILES/1-6 backupfiles
+AAAARG
diff --git a/examples/rna_ss_test.stk b/examples/rna_ss_test.stk
new file mode 100644
index 0000000..429612e
--- /dev/null
+++ b/examples/rna_ss_test.stk
@@ -0,0 +1,6 @@
+# STOCKHOLM 1.0
+#=GF ID RNA.SS.TEST
+#=GF TP RNA;
+Test.sequence GUACAAAAAAAAAA
+#=GC SS_cons <(EHBheb(E)e)>
+//
diff --git a/examples/testdata/example_annot_file.jva b/examples/testdata/example_annot_file.jva
index 1779247..6b9faa4 100644
--- a/examples/testdata/example_annot_file.jva
+++ b/examples/testdata/example_annot_file.jva
@@ -18,5 +18,5 @@ SEQUENCE_GROUP Group_A 30 50 *
SEQUENCE_GROUP Group_B 1 351 2-5
SEQUENCE_GROUP Group_C 12 14 -1 seq1 seq2 seq3
PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false colourText=false textCol1=black textCol2=black textColThreshold=0
-PROPERTIES Group_B outlineColour=red colour=None
+PROPERTIES Group_B outlineColour=green colour=None
PROPERTIES Group_C colour=Clustal
diff --git a/examples/testdata/projects/manyViews.jvp b/examples/testdata/projects/manyViews.jvp
new file mode 100644
index 0000000..065b29c
Binary files /dev/null and b/examples/testdata/projects/manyViews.jvp differ
diff --git a/examples/testdata/projects/twoViews.jvp b/examples/testdata/projects/twoViews.jvp
new file mode 100644
index 0000000..80333cd
Binary files /dev/null and b/examples/testdata/projects/twoViews.jvp differ
diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 0104078..5b76d10 100755
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -60,15 +60,15 @@
Calculating PCAs for aligned sequences
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 BLOSUM62,
+ eigenvector decomposition of the matrix formed from pairwise similarity
+ scores between each pair of sequences. The similarity score model is
+ selected on the calculations dialog, and
+ may use one of the available score matrices, such as
+ BLOSUM62,
PAM250, or the simple single
- nucleotide substitution matrix. The options available for
- calculation are given in the Change
- Parameters menu.
+ nucleotide substitution matrix, or by sequence percentage identity,
+ or sequence feature similarity.
diff --git a/help/html/features/commandline.html b/help/html/features/commandline.html
index 9cffc51..92d9323 100644
--- a/help/html/features/commandline.html
+++ b/help/html/features/commandline.html
@@ -49,11 +49,11 @@
provided by InstallAnywhere any output from the application will be
sent to output.txt, not standard out.
The Jalview
application also requires a number of additional libraries on the
- class path. The command line below adds the Jalview installation's
- 'lib' directory to the list of directories that are searched for
- jars to be added to the classpath:
+ class path. The command line below adds all the jar files in the
+ Jalview installation's 'lib' directory to the classpath, as well as
+ the Jalview application jar file:
- java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE]
+ java -classpath "$INSTALL_DIR$/lib/*:$INSTALL_DIR$/jalview.jar" jalview.bin.Jalview -open [FILE]
Use '-help' to get more information on the command line arguments that
diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html
index fd6b99f..4d13dcd 100755
--- a/help/html/features/featuresFormat.html
+++ b/help/html/features/featuresFormat.html
@@ -60,7 +60,10 @@
contains tab separated text fields. No comments are
allowed.
- The first set of lines contain type definitions:
+
+ Feature Colours
+
+ The first set of lines contain feature type definitions and their colours:
Feature label Feature Colour
@@ -72,21 +75,37 @@
- A single colour specified as either a red,green,blue 24 bit
triplet in hexadecimal (eg. 00ff00) or as comma separated numbers
- (ranging from 0 to 255))
+ (ranging from 0 to 255))
+ (For help with colour values, see https://www.w3schools.com/colors/colors_converter.asp.)
- A graduated colourscheme
specified as a "|" separated list of fields:
-[label|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]]
+[label or score or attribute|attName|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<novalue>][|<thresholdtype>|[<threshold value>]]
The fields are as follows:
- - label
Indicate that the feature
+ - label
Indicates that the feature
description should be used to create a colour for features of
this type.
Note: if no threshold value is
- needed then the final '|' may be omitted.
This
+ needed then only 'label' is required.
This
keyword was added in Jalview 2.6
+ - score
Indicates that the feature
+ score should be used to create a graduated colour for features of
+ this type, in conjunction with mincolor, maxcolor.
This keyword was added in Jalview 2.11.
+ It may be omitted (score is the default) if mincolor and maxcolor are specified.
+
+
+ - attribute|attName
Indicates that the value of feature
+ attribute 'attName' should be used to create a colour for features of
+ this type.
+
For example, attribute|clinical_significance to colour by clinical_significance.
+
To colour by range of a numeric attribute, include mincolor and maxcolor, or omit to colour by text (category).
+
(Note: the value of the attribute used for colouring will also be shown in the tooltip as you mouse over features.)
+
A sub-attribute should be written as, for example, CSQ:IMPACT.
+
This keyword was added in Jalview 2.11
+
- mincolor and maxcolor
Colour
triplets specified as hexadecimal or comma separated values
(may be left blank for a label style colourscheme,
@@ -99,10 +118,15 @@
- minvalue and maxvalue
Minimum and maximum values defining the range of scores for
- which the colour range will be defined over. If minvalue is
+ which the colour range will be defined over.
If minvalue is
greater than maxvalue then the linear mapping will have
negative gradient.
+ - novalue
+ Specifies the colour to use if colouring by attribute, when the attribute is absent.
+ Valid options are novaluemin, novaluemax, novaluenone, to use mincolor, maxcolor, or no colour.
+
If not specified this will default to novaluemin.
+
- thresholdtype
Either
"none", "below", or "above". below
and above require an additional threshold
@@ -113,12 +137,46 @@
+
+ Feature Filters
+
+ This section is optional, and allows one or more filters to be defined for each feature type.
+
Only features that satisfy the filter conditions will be displayed.
+
Begin with a line which is just STARTFILTERS, and end with a line which is just ENDFILTERS.
+
Each line has the format:
+
featureType <tab> (filtercondition1) [and|or] (filtercondition2) [and|or]...
+ The parentheses are not needed if there is only one condition.
+ Combine multiple conditions with either and or or (but not a mixture).
+
Each condition is written as:
+ Label or Score or AttributeName condition [value]
+ where either the label (description), (numeric) score, or (text or numeric) attribute is tested against the condition.
+
condition is not case sensitive, and should be one of
+
+ - Contains - description (or attribute) should contain the given value (not case sensitive); example clinical_significance contains Pathogenic
+ - NotContains - description (or attribute) should not contain the given value
+ - Matches - description (or attribute) should match the given value (not case sensitive)
+ - NotMatches - description (or attribute) should not match the given value (not case sensitive)
+ - Present - attribute is present on the feature (no value required); example CSQ:SIFT present
+ - NotPresent - attribute is not present on the feature (no value required)
+ - EQ - feature score, or specified attribute, is equal to the (numeric) value
+ - NE, LT, LE, GT, GE - tests for not equal to / less than / less than or equal to / greater than / greater than or equal to the value
+
+ A non-numeric value always fails a numeric test.
If either attribute name, or value to compare, contains spaces, then enclose in single quotes:
+ 'mutagenesis site' contains 'decreased affinity'
+
Tip: some examples of filter syntax are given below; or to see more, first configure colours and filters in Jalview, then File | Export Features to Textbox in Jalview Format.
+
Feature filters were added in Jalview 2.11
+
+
+
+ Feature Instances
+
+
The remaining lines in the file are the sequence annotation
definitions, where the now defined features are attached to regions
on particular sequences. Each feature can optionally include some
descriptive text which is displayed in a tooltip when the mouse is
- near the feature on that sequence (and can also be used to generate
- a colour the feature).
+ near the feature on that sequence (and may also be used to generate
+ a colour for the feature).
If your sequence annotation is already available in GFF2 (http://gmod.org/wiki/GFF2) or
@@ -204,6 +262,13 @@ signal peptide 0,155,165
helix ff0000
strand 00ff00
coil cccccc
+kdHydrophobicity ccffcc|333300|-3.9|4.5|above|-2.0
+
+STARTFILTERS
+metal ion-binding site Label Contains sulfur
+kdHydrophobicity (Score LT 1.5) OR (Score GE 2.8)
+ENDFILTERS
+
Your Own description here FER_CAPAA -1 3 93 domain
Your Own description here FER_CAPAN -1 48 144 chain
Your Own description here FER_CAPAN -1 50 140 domain
@@ -211,10 +276,16 @@ Your Own description here FER_CAPAN -1 136 136 modified residue
Your Own description here FER1_LYCES -1 1 47 transit peptide
Your Own description here Q93XJ9_SOLTU -1 1 48 signal peptide
Your Own description here Q93XJ9_SOLTU -1 49 144 chain
-startgroup secondarystucture
+
+STARTGROUP secondarystucture
PDB secondary structure annotation FER1_SPIOL -1 52 59 strand
PDB secondary structure annotation FER1_SPIOL -1 74 80 helix
-endgroup secondarystructure
+ENDGROUP secondarystructure
+
+STARTGROUP kd
+Hydrophobicity score by kD Q93XJ9_SOLTU -1 48 48 kdHydrophobicity 1.8
+ENDGROUP kd
+
GFF
FER_CAPAA GffGroup domain 3 93 . .
diff --git a/help/html/memory.html b/help/html/memory.html
index 2142f98..9437a60 100755
--- a/help/html/memory.html
+++ b/help/html/memory.html
@@ -115,7 +115,7 @@ lax.nl.java.option.java.heap.size.initial=500m
! <string>-Xms2M</string>
! <string>-Xmx64M</string>
</array>
- Exchange the above two string tags for :
+
Exchange the above two string tags for :
<string>-Xms500M</string>
<string>-Xmx1000M</string>
@@ -125,6 +125,11 @@ lax.nl.java.option.java.heap.size.initial=500m
the file and try to start Jalview in the normal way. If it doesn't
start, see below...
+
+ Please Note: We do modify the default memory settings in
+ Jalview from time to time, so you may find different numbers to
+ those shown in the examples above.
+
Jalview doesn't start... What do the
memory settings mean ?
@@ -140,6 +145,12 @@ lax.nl.java.option.java.heap.size.initial=500m
enlighten us if you know better!). Our experiments found 1000m to be
the biggest setting that could be used on a 1GB machine. Just try
reducing the sizes until Jalview starts up properly!
+
+ We increased the default memory in Jalview 2.10.5 to 1G. To launch
+ Jalview with the pre 2.10.5 default memory allocation, use the Jalview
+ 256MB JNLP.
+