-<applet code="jalview.bin.JalviewLite" width="756" height="560" archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar"> +<applet code="jalview.bin.JalviewLite" width="756" height="560" archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar"> <param name="permissions" value="sandbox" /> <param name="file" value="plantfdx.fa" /> <param name="features" value="plantfdx.features" /> diff --git a/examples/applets.html b/examples/applets.html index 1f65565..d997f14 100644 --- a/examples/applets.html +++ b/examples/applets.html @@ -41,7 +41,7 @@ Try out JalviewLite by pressing one of the buttons below. + archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar"> @@ -64,7 +64,7 @@ Try out JalviewLite by pressing one of the buttons below. + archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar"> @@ -89,7 +89,7 @@ Try out JalviewLite by pressing one of the buttons below. + archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar"> @@ -116,7 +116,7 @@ Try out JalviewLite by pressing one of the buttons below. + archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar"> @@ -147,7 +147,7 @@ Try out JalviewLite by pressing one of the buttons below. + archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar"> @@ -171,7 +171,7 @@ Try out JalviewLite by pressing one of the buttons below. + archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar"> diff --git a/examples/embedded.html b/examples/embedded.html index 0d5ddf3..0cea17d 100644 --- a/examples/embedded.html +++ b/examples/embedded.html @@ -40,7 +40,7 @@ View the source code for this example here (If the link doesn't work on your browser try going to this page and viewing the page source manually). + archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar"> diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html index 501c20e..6fdcc07 100644 --- a/examples/embeddedWJmol.html +++ b/examples/embeddedWJmol.html @@ -211,7 +211,7 @@ jQuery.extend(Drupal.settings, {"basePath":"\/","pathPrefix":"","ajaxPageState": +archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar" width="0" height="0"> diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html index 5890515..8ddfd2f 100644 --- a/examples/linkedapplets_ng.html +++ b/examples/linkedapplets_ng.html @@ -38,7 +38,7 @@ + code="jalview.bin.JalviewLite" width="800" height="300" id="jvapp" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar"> @@ -61,7 +61,7 @@ + code="jalview.bin.JalviewLite" width="800" height="300" id="jvfollower" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar"> diff --git a/help/help.jhm b/help/help.jhm index 407899e..e034fc2 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -22,7 +22,7 @@ - + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index bf1710c..3a6b0b3 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -23,9 +23,6 @@ - - - diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html index cbef2c1..5ae00af 100644 --- a/help/html/features/chimera.html +++ b/help/html/features/chimera.html @@ -73,7 +73,10 @@ When a selection is highlighted in a Jalview window, use the Select→Select Highlighted Region or press B to add the mapped positions to the alignment window's column - selection. + selection. Hint: Use your machine's 'switch + application' key combination (Alt-Tab on Windows and Linux, + Cmd-Tab on OSX) to quickly switch between UCSF Chimera and Jalview + before pressing 'B' to select highlighted regions. Basic screen operations (see Selecting regions from Search Results - Press 'B' or select the Select Highlighted Columns option - from the alignment window's select menu to add columns containing + Press 'B' or use the Select Highlighted Columns option from + the alignment window's select menu to add columns containing highlighted search results to the alignment window's column - selection. + selection. Alt-'B' will add all but the highlighted columns, and + Ctrl (or Cmd) -B will toggle the column selection for the + highlighted region. diff --git a/help/html/keys.html b/help/html/keys.html index b79ce4d..1a5fc18 100755 --- a/help/html/keys.html +++ b/help/html/keys.html @@ -169,16 +169,16 @@ columns are selected, you should use the H B Both - Mark the currently highlighted columns + Add highlighted columns to current column selection Alt 'B' Both - Mark all but the currently highlighted columns + Add all but the currently highlighted columns to current selection Control 'B' Both - Toggle the marks on the currently highlighted - columns (or all others if Alt is pressed) + Toggle the column selection marks for the currently highlighted + columns (or all others if Alt is also pressed) H diff --git a/help/html/releases.html b/help/html/releases.html index 2d0c4e8..6f44b3d 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -48,67 +48,151 @@ 2.10.1 - 24/11/2016 + 29/11/2016 - General - - Improved memory usage: sparse arrays used for all consensus calculations - - - Application - - Sequence ID tool tips have been tamed (databases sorted alphabetically, abridged ID sets) - New replacement token for creating URLs just from database cross references. Users with custom links will receive a warning dialog asking them to update their preferences. - Cancel button and escape listener on dialog warning user about disconnecting Jalview from a Chimera session - Custom URL links for database cross-references are matched to database name regardless of case - - - - - Applet + General + + Improved memory usage: sparse arrays used + for all consensus calculations + + + Jmol updated to version 14.6.4 (released 3rd Oct 2016) + + Updated Jalview's Certum code signing certificate + for 2016-2017 - Build and deployment + Application - + + Sequence ID tool tip presents abridged + set of database cross-references, sorted alphabetically + + + New replacement token for creating URLs just + from database cross references. Users with custom links + will receive a warning + dialog asking them to update their preferences. + + + Cancel button and escape listener on + dialog warning user about disconnecting Jalview from a + Chimera session + + + Jalview's Chimera control window closes if + the Chimera it is connected to is shut down + + + New keystroke (B) and Select highlighted + columns menu item to mark columns containing + highlighted regions (e.g. from structure selections or results + of a Find operation) + + + Command line option for batch-generation + of HTML pages rendering alignment data with the BioJS + MSAviewer + - - + General - Columns with more than one modal residue are not coloured or thresholded according to percent identity (first observed in Jalview 2.8.2) - Threonine incorrectly reported as not hydrophobic - Updates to documentation pages (above PID threshold, amino acid properties) - Lower case residues in sequences are not reported as mapped to residues in a structure file in the View Mapping report + + Columns with more than one modal residue + are not coloured or thresholded according to percent + identity (first observed in Jalview 2.8.2) + + + Threonine incorrectly reported as not + hydrophobic + + + Updates to documentation pages (above PID + threshold, amino acid properties) + + + Lower case residues in sequences are not + reported as mapped to residues in a structure file in the + View Mapping report + + + Identical features with non-numeric scores + could be added multiple times to a sequence + + + Disulphide + bond features shown as two highlighted residues rather + than a range in linked structure views, and treated + correctly when selecting and computing trees from features + + + Custom URL links for database + cross-references are matched to database name regardless + of case + + Application - Custom URL links for specific database names without regular expressions also offer invalid links from Sequence ID - Removing a single configured link in the URL links pane in Connections preferences doesn't actually update Jalview configuration - CTRL-Click on a selected region to open the alignment area popup menu doesn't work on El-Capitan - Jalview doesn't offer to associate mmCIF files with similarly named sequences if dropped onto the alignment - Additional mappings are shown for PDB entries where more chains exist in the PDB accession than are reported in the SIFTS file - Certain structures do not get mapped to the structure view when displayed with Chimera - No chains shown in the Chimera view panel's View->Show Chains submenu - - - - - Applet - - - Build and deployment - - Failing/passing unit tests + + Custom URL links for specific database + names without regular expressions also offer links from + Sequence ID + + + Removing a single configured link in the + URL links pane in Connections preferences doesn't actually + update Jalview configuration + + + CTRL-Click on a selected region to open + the alignment area popup menu doesn't work on El-Capitan + + + Jalview doesn't offer to associate mmCIF + files with similarly named sequences if dropped onto the + alignment + + + Additional mappings are shown for PDB + entries where more chains exist in the PDB accession than + are reported in the SIFTS file + + + Certain structures do not get mapped to + the structure view when displayed with Chimera + + + No chains shown in the Chimera view + panel's View->Show Chains submenu + + + Export as HTML with embedded SVG doesn't + work for wrapped alignment views + + + Rename UI components for running JPred + predictions from 'JNet' to 'JPred' + + + Export as PNG or SVG is + corrupted when annotation panel vertical scroll is not at + first annotation row + + + Attempting to view structure for Hen + lysozyme results in a PDB Client error dialog box + - New Known Issues + diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html index 36c7c6b..088a539 100644 --- a/help/html/webServices/urllinks.html +++ b/help/html/webServices/urllinks.html @@ -66,10 +66,19 @@ the sequence ID for the sequence (since Jalview 2.10.1). - If Jalview opens a project with links which include $SEQUENCE_ID$ tokens, it will present - the user with a warning message, as these links may need to be updated to use $DB_ACCESSION$, if - they were added before Jalview 2.10.1. The message lists the links which should be reviewed. - The warning can be turned off completely via a checkbox in the message dialog. + Warning dialog about updating + your configured URL links In the desktop + prior to Jalview 2.10.1, the only way to configure custom links for + a particular database cross-reference for a sequence was to give it + a name that + exactly matched the database source, and a regular + expression for filtering out any spurious matches generated when the + custom linked was tested against the Sequence's ID string. Since the + introduction of the $DB_ACCESSION$ token, however, $SEQUENCE_ID$ + will not be used for database cross-reference accession strings, and + if you have custom links configured, Jalview will raise a warning + message so let you know that you may need to update your links to + use $DB_ACCESSION$. Regular Expression Substitution A url may diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 448430d..1c20885 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,70 +24,55 @@ - What's new in Jalview 2.10.0b1 ? + What's new in Jalview 2.10.1 ? - Jalview 2.10.0b1 is a patch release for 2.10, the next major release - in the Jalview 2 series. Full details are in the Jalview 2.10b1 Release - Notes, but the highlights are below. + Jalview 2.10.1 was released on 24th November 2016. Full details are + in the Jalview 2.10.1 + Release Notes, but the highlights are below. This is also the + first release to include contributions from Kira Mourão, who + joined Jalview's core development team in October 2016. - Drag and drop reinstated for the Jalview desktop on - Windows, Linux and older OSX systems. - Problems loading local PDB files have been fixed - Conservation shading can be disabled for PID and consensus - based colour scheme - - Major highlights of the 2.10.0 Release - - Ensembl sequence fetcher Annotated - Genes, transcripts and proteins can be retrieved via Jalview's new - Ensembl REST - client. Support for import of Ensembl data allows: - - Aligned locus view Transcripts - retrieved for a gene identifier via the Ensembl or - EnsemblGenomes sequence databases are automatically aligned to - their reference genome, and introns hidden from the view. - Sequence variant data Jalview - propagates variant annotation on genomic regions onto - transcripts and protein products, complete with associated - metadata such as clinical significance. - - Ensembl and ENA 'show cross-references' - support The Calculations menu's 'Show - cross-references' now offers Ensembl as well as EMBLCDS and - Uniprot when CDS/Protein mapping data is available for download or - display. This allows variant annotation to be added directly to an - alignment of UniProt sequences. - Working with structures - - More accurate structure mappings - Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI) - to match structures - to UniProt sequences, even for structures containing - multiple copies of a sequence. - Import structures as mmCIF Jalview - now downloads data from the EMBL-EBI's PDBe site as mmCIF. This allows very large - structures to be imported, such as the HIV virus capsid - assembly. - Chimera users will need to upgrade to - 1.11.1 If you use Chimera to view structures - downloaded by Jalview 2.10, you will need to make sure you are - running the latest version of Chimera. - - UniProt Free Text Search The new - search dialog for UniProt allows you to browse and retrieve - sequences with free-text search, or structured queries. - Reference sequence alignment view - Jalview 2.9 introduced support for reference sequences. In 2.10, - when a reference sequence is defined for the alignment, the - alignment column ruler is now numbered according to the reference - sequence. The reference sequence for alignment views can also be - saved and restored from Jalview projects. + More memory efficient We've slimmed + down the consensus analysis data structures used by Jalview so + even wider alignments can be worked with. + Select highlighted region Press 'B' + or use the new menu option in the alignment window's Select menu + to mark columns containing highlighted regions generated from + structure selections, mouse-overs, or resulting from a Find + operation. + New custom link mechanism for opening URLs + for database cross references. If you have customised URL + links in your Jalview preferences, then you may already have seen + the warning dialog (see below). + New command line export option for BioJS + MSAviewer A number of small bugs with the HTML export + functions from the Jalview desktop were also fixed. + Small but significant changes to the + physicochemical properties and consensus calculations Threonine + is no longer considered a non-hydrophobic residue in the protein + conservation calculation, and minor bugs addressed in PID and + consensus colouring. + Correct display of disulphide bond + features In linked structure views, Jalview would + highlight all residues between in addition to the two linked + cysteines. The 'select columns by feature' function in the feature + settings would also select all intermediate columns. + + Warning dialog about updating + your configured URL links In the desktop prior to Jalview + 2.10.1, the only way to configure custom links for a particular + database cross-reference for a sequence was to give it a name that exactly + matched the database source, and a regular expression for filtering + out any spurious matches generated when the custom linked was tested + against the Sequence's ID string. Since the introduction of the + $DB_ACCESSION$ token, however, $SEQUENCE_ID$ will not be used for + database cross-reference accession strings, and if you have custom + links configured, Jalview will raise a warning message so let you + know that you may need to update your links to use $DB_ACCESSION$. + diff --git a/lib/Jmol-14.2.14_2015.06.11.jar b/lib/Jmol-14.2.14_2015.06.11.jar deleted file mode 100644 index 1470745..0000000 Binary files a/lib/Jmol-14.2.14_2015.06.11.jar and /dev/null differ diff --git a/lib/Jmol-14.6.4_2016.10.26.jar b/lib/Jmol-14.6.4_2016.10.26.jar new file mode 100644 index 0000000..1016c3f Binary files /dev/null and b/lib/Jmol-14.6.4_2016.10.26.jar differ diff --git a/nbproject/project.properties b/nbproject/project.properties index ac1a2e3..b569f55 100644 --- a/nbproject/project.properties +++ b/nbproject/project.properties @@ -59,8 +59,8 @@ file.reference.jalview-src=src file.reference.jaxrpc.jar=lib/jaxrpc.jar file.reference.JGoogleAnalytics_0.3.jar=lib/JGoogleAnalytics_0.3.jar file.reference.jhall.jar=lib/jhall.jar -file.reference.Jmol-14.2.14_2015.06.11.jar=lib/Jmol-14.2.14_2015.06.11.jar -file.reference.JmolApplet-14.2.14_2015.06.11.jar=appletlib/JmolApplet-14.2.14_2015.06.11.jar +file.reference.Jmol-14.6.4_2016.10.26.jar=lib/Jmol-14.6.4_2016.10.26.jar +file.reference.JmolApplet-14.6.4_2016.10.26.jar=appletlib/JmolApplet-14.6.4_2016.10.26.jar file.reference.log4j-1.2.8.jar=lib/log4j-1.2.8.jar file.reference.mail.jar=lib/mail.jar file.reference.min-jaba-client.jar=lib/min-jaba-client-2.0.jar @@ -92,7 +92,7 @@ javac.classpath=\ ${file.reference.jaxrpc.jar}:\ ${file.reference.JGoogleAnalytics_0.3.jar}:\ ${file.reference.jhall.jar}:\ - ${file.reference.Jmol-14.2.14_2015.06.11.jar}:\ + ${file.reference.Jmol-14.6.4_2016.10.26.jar}:\ ${file.reference.miglayout-4.0-swing.jar}:\ ${file.reference.log4j-1.2.8.jar}:\ ${file.reference.mail.jar}:\ @@ -101,7 +101,7 @@ javac.classpath=\ ${file.reference.xml-apis.jar}:\ ${file.reference.xercesImpl.jar}:\ ${file.reference.wsdl4j.jar}:\ - ${file.reference.JmolApplet-14.2.14_2015.06.11.jar} \ + ${file.reference.JmolApplet-14.6.4_2016.10.26.jar} \ ${file.reference.varna-3.9-dev.jar} # Space-separated list of extra javac options javac.compilerargs= diff --git a/resources/authors.props b/resources/authors.props index bcb07cf..3488ac6 100644 --- a/resources/authors.props +++ b/resources/authors.props @@ -1,4 +1,4 @@ YEAR=2016 -AUTHORS=J Procter, M Carstairs, 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, 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 +AUTHORS=J Procter, M Carstairs, TC Ofoegbu, K Mourao, 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, Tochukwu 'Charles' Ofoegbu, Kira Mourao, 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 diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 9a58965..6360dc7 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -126,7 +126,7 @@ action.colour = Colour action.calculate = Calculate action.select_all = Select all action.select_highlighted_columns = Select Highlighted Columns -tooltip.select_highlighted_columns = Press B to mark highlighted columns, Ctrl-B to toggle, and Alt-B to mark all but highlighted columns +tooltip.select_highlighted_columns = Press B to mark highlighted columns, Ctrl-(or Cmd)-B to toggle, and Alt-B to mark all but highlighted columns action.deselect_all = Deselect all action.invert_selection = Invert selection action.using_jmol = Using Jmol diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index 9c2436c..e5b5e27 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -122,6 +122,8 @@ action.change_font_tree_panel = Cambiar fuente (panel del action.colour = Color action.calculate = Calcular action.select_all = Seleccionar Todo +action.select_highlighted_columns = Seleccionar columnas resaltadas +tooltip.select_highlighted_columns = Presione B para marcar las columnas resaltadas, Ctrl (o Cmd)-B para cambiarlas, y Alt-B para marcar todas menos las columnas resaltadas action.deselect_all = Deseleccionar Todo action.invert_selection = Invertir selección action.using_jmol = Usar Jmol diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java index 95221d2..1d57a31 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java @@ -1,3 +1,35 @@ +/* vim: set ts=2: */ +/** + * Copyright (c) 2006 The Regents of the University of California. + * All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions + * are met: + * 1. Redistributions of source code must retain the above copyright + * notice, this list of conditions, and the following disclaimer. + * 2. Redistributions in binary form must reproduce the above + * copyright notice, this list of conditions, and the following + * disclaimer in the documentation and/or other materials provided + * with the distribution. + * 3. Redistributions must acknowledge that this software was + * originally developed by the UCSF Computer Graphics Laboratory + * under support by the NIH National Center for Research Resources, + * grant P41-RR01081. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR + * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE + * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT + * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR + * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, + * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE + * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, + * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ package ext.edu.ucsf.rbvi.strucviz2; import java.awt.Color; diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java index fdcf34f..736e459 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java @@ -1,3 +1,35 @@ +/* vim: set ts=2: */ +/** + * Copyright (c) 2006 The Regents of the University of California. + * All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions + * are met: + * 1. Redistributions of source code must retain the above copyright + * notice, this list of conditions, and the following disclaimer. + * 2. Redistributions in binary form must reproduce the above + * copyright notice, this list of conditions, and the following + * disclaimer in the documentation and/or other materials provided + * with the distribution. + * 3. Redistributions must acknowledge that this software was + * originally developed by the UCSF Computer Graphics Laboratory + * under support by the NIH National Center for Research Resources, + * grant P41-RR01081. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR + * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE + * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT + * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR + * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, + * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE + * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, + * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ package ext.edu.ucsf.rbvi.strucviz2; import jalview.ws.HttpClientUtils; diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java index 7da7a48..d2f4b11 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java @@ -1,3 +1,35 @@ +/* vim: set ts=2: */ +/** + * Copyright (c) 2006 The Regents of the University of California. + * All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions + * are met: + * 1. Redistributions of source code must retain the above copyright + * notice, this list of conditions, and the following disclaimer. + * 2. Redistributions in binary form must reproduce the above + * copyright notice, this list of conditions, and the following + * disclaimer in the documentation and/or other materials provided + * with the distribution. + * 3. Redistributions must acknowledge that this software was + * originally developed by the UCSF Computer Graphics Laboratory + * under support by the NIH National Center for Research Resources, + * grant P41-RR01081. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR + * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE + * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT + * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR + * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, + * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE + * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, + * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ package ext.edu.ucsf.rbvi.strucviz2; import java.awt.Color; diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java index 6fd6340..effe556 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java @@ -1,3 +1,35 @@ +/* vim: set ts=2: */ +/** + * Copyright (c) 2006 The Regents of the University of California. + * All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions + * are met: + * 1. Redistributions of source code must retain the above copyright + * notice, this list of conditions, and the following disclaimer. + * 2. Redistributions in binary form must reproduce the above + * copyright notice, this list of conditions, and the following + * disclaimer in the documentation and/or other materials provided + * with the distribution. + * 3. Redistributions must acknowledge that this software was + * originally developed by the UCSF Computer Graphics Laboratory + * under support by the NIH National Center for Research Resources, + * grant P41-RR01081. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR + * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE + * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT + * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR + * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, + * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE + * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, + * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ package ext.edu.ucsf.rbvi.strucviz2; import jalview.bin.Cache; diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureSettings.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureSettings.java index 08a6cb7..77c1883 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureSettings.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureSettings.java @@ -1,3 +1,35 @@ +/* vim: set ts=2: */ +/** + * Copyright (c) 2006 The Regents of the University of California. + * All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions + * are met: + * 1. Redistributions of source code must retain the above copyright + * notice, this list of conditions, and the following disclaimer. + * 2. Redistributions in binary form must reproduce the above + * copyright notice, this list of conditions, and the following + * disclaimer in the documentation and/or other materials provided + * with the distribution. + * 3. Redistributions must acknowledge that this software was + * originally developed by the UCSF Computer Graphics Laboratory + * under support by the NIH National Center for Research Resources, + * grant P41-RR01081. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR + * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE + * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT + * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR + * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, + * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE + * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, + * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ package ext.edu.ucsf.rbvi.strucviz2; /** diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/port/ListenerThreads.java b/src/ext/edu/ucsf/rbvi/strucviz2/port/ListenerThreads.java index 2b2ce48..379097c 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/port/ListenerThreads.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/port/ListenerThreads.java @@ -1,3 +1,35 @@ +/* vim: set ts=2: */ +/** + * Copyright (c) 2006 The Regents of the University of California. + * All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions + * are met: + * 1. Redistributions of source code must retain the above copyright + * notice, this list of conditions, and the following disclaimer. + * 2. Redistributions in binary form must reproduce the above + * copyright notice, this list of conditions, and the following + * disclaimer in the documentation and/or other materials provided + * with the distribution. + * 3. Redistributions must acknowledge that this software was + * originally developed by the UCSF Computer Graphics Laboratory + * under support by the NIH National Center for Research Resources, + * grant P41-RR01081. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR + * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE + * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT + * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR + * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, + * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE + * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, + * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ package ext.edu.ucsf.rbvi.strucviz2.port; import java.io.BufferedReader; diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 160224b..0c80c37 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -843,9 +843,10 @@ public class APopupMenu extends java.awt.PopupMenu implements void addPDB() { - if (seq.getAllPDBEntries() != null) + Vector pdbs = seq.getAllPDBEntries(); + if (pdbs != null&& !pdbs.isEmpty()) { - PDBEntry entry = seq.getAllPDBEntries().firstElement(); + PDBEntry entry = pdbs.firstElement(); if (ap.av.applet.jmolAvailable) { diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java index 3a36ed5..684d357 100644 --- a/src/jalview/appletgui/AppletJmolBinding.java +++ b/src/jalview/appletgui/AppletJmolBinding.java @@ -29,8 +29,6 @@ import jalview.structure.StructureSelectionManager; import java.awt.Container; import java.util.Map; -import javajs.awt.Dimension; - import org.jmol.api.JmolAppConsoleInterface; import org.jmol.console.AppletConsole; import org.jmol.java.BS; @@ -186,7 +184,7 @@ class AppletJmolBinding extends JalviewJmolBinding } @Override - public Dimension resizeInnerPanel(String data) + public int[] resizeInnerPanel(String data) { // TODO Auto-generated method stub return null; diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index 9451c3b..e9a0dbf 100644 --- a/src/jalview/controller/AlignViewController.java +++ b/src/jalview/controller/AlignViewController.java @@ -243,10 +243,6 @@ public class AlignViewController implements AlignViewControllerI SequenceFeature[] sfs = sq.getSequenceFeatures(); if (sfs != null) { - /* - * check whether the feature start/end (base 1) - * overlaps the selection start/end - */ int ist = sq.findIndex(sq.getStart()); int iend = sq.findIndex(sq.getEnd()); if (iend < startPosition || ist > endPosition) @@ -264,29 +260,54 @@ public class AlignViewController implements AlignViewControllerI // - findIndex wastes time by starting from first character and // counting - int i = sq.findIndex(sf.getBegin()); - int j = sq.findIndex(sf.getEnd()); - if (j < startPosition || i > endPosition) + int sfStartCol = sq.findIndex(sf.getBegin()); + int sfEndCol = sq.findIndex(sf.getEnd()); + + if (sf.isContactFeature()) + { + /* + * 'contact' feature - check for 'start' or 'end' + * position within the selected region + */ + if (sfStartCol >= startPosition + && sfStartCol <= endPosition) + { + bs.set(sfStartCol - 1); + sequenceHasFeature = true; + } + if (sfEndCol >= startPosition && sfEndCol <= endPosition) + { + bs.set(sfEndCol - 1); + sequenceHasFeature = true; + } + continue; + } + + /* + * contiguous feature - select feature positions (if any) + * within the selected region + */ + if (sfStartCol > endPosition || sfEndCol < startPosition) { // feature is outside selected region continue; } sequenceHasFeature = true; - if (i < startPosition) + if (sfStartCol < startPosition) { - i = startPosition; + sfStartCol = startPosition; } - if (i < ist) + if (sfStartCol < ist) { - i = ist; + sfStartCol = ist; } - if (j > endPosition) + if (sfEndCol > endPosition) { - j = endPosition; + sfEndCol = endPosition; } - for (; i <= j; i++) + for (; sfStartCol <= sfEndCol; sfStartCol++) { - bs.set(i - 1); // convert to base 0 + bs.set(sfStartCol - 1); // convert to base 0 } } } diff --git a/src/jalview/datamodel/Profile.java b/src/jalview/datamodel/Profile.java index 5464596..1501808 100644 --- a/src/jalview/datamodel/Profile.java +++ b/src/jalview/datamodel/Profile.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; diff --git a/src/jalview/datamodel/ProfileI.java b/src/jalview/datamodel/ProfileI.java index cf2b394..65a5c0d 100644 --- a/src/jalview/datamodel/ProfileI.java +++ b/src/jalview/datamodel/ProfileI.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; public interface ProfileI diff --git a/src/jalview/datamodel/Profiles.java b/src/jalview/datamodel/Profiles.java index 98a8c6d..f65830a 100644 --- a/src/jalview/datamodel/Profiles.java +++ b/src/jalview/datamodel/Profiles.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; public class Profiles implements ProfilesI diff --git a/src/jalview/datamodel/ProfilesI.java b/src/jalview/datamodel/ProfilesI.java index 6719de6..82398d9 100644 --- a/src/jalview/datamodel/ProfilesI.java +++ b/src/jalview/datamodel/ProfilesI.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; public interface ProfilesI diff --git a/src/jalview/datamodel/ResidueCount.java b/src/jalview/datamodel/ResidueCount.java index 0d0348c..3e3a966 100644 --- a/src/jalview/datamodel/ResidueCount.java +++ b/src/jalview/datamodel/ResidueCount.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; import jalview.util.Comparison; diff --git a/src/jalview/datamodel/SearchResultMatchI.java b/src/jalview/datamodel/SearchResultMatchI.java index 732f1dc..a47ca8b 100644 --- a/src/jalview/datamodel/SearchResultMatchI.java +++ b/src/jalview/datamodel/SearchResultMatchI.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; /** diff --git a/src/jalview/datamodel/SearchResultsI.java b/src/jalview/datamodel/SearchResultsI.java index 93183f2..52a0467 100644 --- a/src/jalview/datamodel/SearchResultsI.java +++ b/src/jalview/datamodel/SearchResultsI.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; import java.util.BitSet; diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index 0baa78e..15f54b9 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -532,4 +532,20 @@ public class SequenceFeature return s.hashCode() + getBegin() + getEnd() + (int) getScore() + getStrand(); } + + /** + * Answers true if the feature's start/end values represent two related + * positions, rather than ends of a range. Such features may be visualised or + * reported differently to features on a range. + */ + public boolean isContactFeature() + { + // TODO abstract one day to a FeatureType class + if ("disulfide bond".equalsIgnoreCase(type) + || "disulphide bond".equalsIgnoreCase(type)) + { + return true; + } + return false; + } } diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 56287a9..7a394f7 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -49,8 +49,6 @@ import java.util.List; import java.util.Map; import java.util.Vector; -import javajs.awt.Dimension; - import org.jmol.adapter.smarter.SmarterJmolAdapter; import org.jmol.api.JmolAppConsoleInterface; import org.jmol.api.JmolSelectionListener; @@ -1411,7 +1409,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } @Override - public Dimension resizeInnerPanel(String data) + public int[] resizeInnerPanel(String data) { // Jalview doesn't honour resize panel requests return null; diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java index b2ba256..180da8f 100644 --- a/src/jalview/ext/jmol/JmolParser.java +++ b/src/jalview/ext/jmol/JmolParser.java @@ -38,8 +38,6 @@ import java.util.List; import java.util.Map; import java.util.Vector; -import javajs.awt.Dimension; - import org.jmol.api.JmolStatusListener; import org.jmol.api.JmolViewer; import org.jmol.c.CBK; @@ -626,7 +624,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener * Not implemented - returns null */ @Override - public Dimension resizeInnerPanel(String data) + public int[] resizeInnerPanel(String data) { return null; } diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index dc1f95b..e61b042 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1299,8 +1299,8 @@ public class AlignmentPanel extends GAlignmentPanel implements if (onscreen || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) { - return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth() - : calculateIdWidth().width + 4); + int w = getIdPanel().getWidth(); + return (w > 0 ? w : calculateIdWidth().width + 4); } return idwidth.intValue() + 4; } @@ -1448,7 +1448,7 @@ public class AlignmentPanel extends GAlignmentPanel implements public void makePNGImageMap(File imgMapFile, String imageName) { - // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS + // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS // //////////////////////////////////////////// int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); @@ -1462,7 +1462,6 @@ public class AlignmentPanel extends GAlignmentPanel implements { int s, sSize = av.getAlignment().getHeight(), res, alwidth = av .getAlignment().getWidth(), g, gSize, f, fSize, sy; - StringBuffer text = new StringBuffer(); PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); out.println(jalview.io.HTMLOutput.getImageMapHTML()); out.println(" res) { - text.append(" " + groups[g].getName() + ""); + text.append(" ").append(groups[g].getName()) + .append(""); } } @@ -1521,12 +1522,13 @@ public class AlignmentPanel extends GAlignmentPanel implements { if (text.length() < 1) { - text.append("= seq.findPosition(res))) { - if (features[f].getType().equals("disulfide bond")) + if (features[f].isContactFeature()) { if (features[f].getBegin() == seq.findPosition(res) || features[f].getEnd() == seq .findPosition(res)) { - text.append(" disulfide bond " - + features[f].getBegin() + ":" - + features[f].getEnd()); + text.append(" ").append(features[f].getType()) + .append(" ").append(features[f].getBegin()) + .append(":").append(features[f].getEnd()); } } else @@ -1554,13 +1556,13 @@ public class AlignmentPanel extends GAlignmentPanel implements && !features[f].getType().equals( features[f].getDescription())) { - text.append(" " + features[f].getDescription()); + text.append(" ").append(features[f].getDescription()); } if (features[f].getValue("status") != null) { - text.append(" (" + features[f].getValue("status") - + ")"); + text.append(" (").append(features[f].getValue("status")) + .append(")"); } } } diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java index d5593e3..3feae5d 100755 --- a/src/jalview/io/JnetAnnotationMaker.java +++ b/src/jalview/io/JnetAnnotationMaker.java @@ -192,13 +192,13 @@ public class JnetAnnotationMaker if (id.equals("JNETCONF")) { annot = new AlignmentAnnotation(preds[i].getName(), - "JNet Output", annotations, 0f, 10f, + "JPred Output", annotations, 0f, 10f, AlignmentAnnotation.BAR_GRAPH); } else { annot = new AlignmentAnnotation(preds[i].getName(), - "JNet Output", annotations); + "JPred Output", annotations); } if (seqRef != null) diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java index 850b1dc..6c8f40f 100644 --- a/src/jalview/io/SequenceAnnotationReport.java +++ b/src/jalview/io/SequenceAnnotationReport.java @@ -141,8 +141,7 @@ public class SequenceAnnotationReport void appendFeature(final StringBuilder sb, int rpos, Map minmax, SequenceFeature feature) { - String tmpString; - if (feature.getType().equals("disulfide bond")) + if (feature.isContactFeature()) { if (feature.getBegin() == rpos || feature.getEnd() == rpos) { @@ -150,7 +149,8 @@ public class SequenceAnnotationReport { sb.append(" "); } - sb.append("disulfide bond ").append(feature.getBegin()).append(":") + sb.append(feature.getType()).append(" ").append(feature.getBegin()) + .append(":") .append(feature.getEnd()); } } @@ -178,7 +178,7 @@ public class SequenceAnnotationReport if (feature.getDescription() != null && !feature.description.equals(feature.getType())) { - tmpString = feature.getDescription(); + String tmpString = feature.getDescription(); String tmp2up = tmpString.toUpperCase(); int startTag = tmp2up.indexOf(""); if (startTag > -1) @@ -223,11 +223,11 @@ public class SequenceAnnotationReport // check score should be shown if (!Float.isNaN(feature.getScore())) { - float[][] rng = (minmax == null) ? null : ((float[][]) minmax - .get(feature.getType())); + float[][] rng = (minmax == null) ? null : minmax.get(feature + .getType()); if (rng != null && rng[0] != null && rng[0][0] != rng[0][1]) { - sb.append(" Score=" + feature.getScore()); + sb.append(" Score=").append(String.valueOf(feature.getScore())); } } String status = (String) feature.getValue("status"); diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index b007365..9e0089f 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -188,15 +188,20 @@ public class FeatureRenderer extends FeatureRendererModel } /** - * This is used by the Molecule Viewer and Overview to get the accurate colour - * of the rendered sequence + * This is used by Structure Viewers and the Overview Window to get the + * feature colour of the rendered sequence, returned as an RGB value + * + * @param defaultColour + * @param seq + * @param column + * @return */ - public synchronized int findFeatureColour(int initialCol, + public synchronized int findFeatureColour(int defaultColour, final SequenceI seq, int column) { if (!av.isShowSequenceFeatures()) { - return initialCol; + return defaultColour; } SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures(); @@ -223,7 +228,7 @@ public class FeatureRenderer extends FeatureRendererModel if (lastSequenceFeatures == null || sfSize == 0) { - return initialCol; + return defaultColour; } if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column))) @@ -244,7 +249,7 @@ public class FeatureRenderer extends FeatureRendererModel if (offscreenImage != null) { - offscreenImage.setRGB(0, 0, initialCol); + offscreenImage.setRGB(0, 0, defaultColour); drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0); return offscreenImage.getRGB(0, 0); @@ -255,7 +260,7 @@ public class FeatureRenderer extends FeatureRendererModel if (currentColour == null) { - return initialCol; + return defaultColour; } else { @@ -275,6 +280,19 @@ public class FeatureRenderer extends FeatureRendererModel int epos; + /** + * Draws the sequence on the graphics context, or just determines the colour + * that would be drawn (if flag offscreenrender is true). + * + * @param g + * @param seq + * @param start + * start column (or sequence position in offscreenrender mode) + * @param end + * end column (not used in offscreenrender mode) + * @param y1 + * vertical offset at which to draw on the graphics + */ public synchronized void drawSequence(Graphics g, final SequenceI seq, int start, int end, int y1) { @@ -312,12 +330,10 @@ public class FeatureRenderer extends FeatureRendererModel } sfSize = lastSequenceFeatures.length; - String type; for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) { - type = renderOrder[renderIndex]; - - if (type == null || !showFeatureOfType(type)) + String type = renderOrder[renderIndex]; + if (!showFeatureOfType(type)) { continue; } @@ -332,16 +348,16 @@ public class FeatureRenderer extends FeatureRendererModel continue; } - if (featureGroups != null - && sequenceFeature.featureGroup != null - && sequenceFeature.featureGroup.length() != 0 - && featureGroups.containsKey(sequenceFeature.featureGroup) - && !featureGroups.get(sequenceFeature.featureGroup) - .booleanValue()) + if (featureGroupNotShown(sequenceFeature)) { continue; } + /* + * check feature overlaps the visible part of the alignment, + * unless doing offscreenRender (to the Overview window or a + * structure viewer) which is not limited + */ if (!offscreenRender && (sequenceFeature.getBegin() > epos || sequenceFeature .getEnd() < spos)) @@ -349,35 +365,43 @@ public class FeatureRenderer extends FeatureRendererModel continue; } + Color featureColour = getColour(sequenceFeature); + boolean isContactFeature = sequenceFeature.isContactFeature(); + if (offscreenRender && offscreenImage == null) { - if (sequenceFeature.begin <= start - && sequenceFeature.end >= start) + /* + * offscreen mode with no image (image is only needed if transparency + * is applied to feature colours) - just check feature is rendered at + * the requested position (start == sequence position in this mode) + */ + boolean featureIsAtPosition = sequenceFeature.begin <= start + && sequenceFeature.end >= start; + if (isContactFeature) + { + featureIsAtPosition = sequenceFeature.begin == start + || sequenceFeature.end == start; + } + if (featureIsAtPosition) { // this is passed out to the overview and other sequence renderers // (e.g. molecule viewer) to get displayed colour for rendered // sequence - currentColour = new Integer(getColour(sequenceFeature).getRGB()); + currentColour = new Integer(featureColour.getRGB()); // used to be retreived from av.featuresDisplayed // currentColour = av.featuresDisplayed // .get(sequenceFeatures[sfindex].type); } } - else if (sequenceFeature.type.equals("disulfide bond")) + else if (isContactFeature) { renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1, - seq.findIndex(sequenceFeature.begin) - 1, - getColour(sequenceFeature) - // new Color(((Integer) av.featuresDisplayed - // .get(sequenceFeatures[sfindex].type)).intValue()) - , start, end, y1); + seq.findIndex(sequenceFeature.begin) - 1, featureColour, + start, end, y1); renderFeature(g, seq, seq.findIndex(sequenceFeature.end) - 1, - seq.findIndex(sequenceFeature.end) - 1, - getColour(sequenceFeature) - // new Color(((Integer) av.featuresDisplayed - // .get(sequenceFeatures[sfindex].type)).intValue()) - , start, end, y1); + seq.findIndex(sequenceFeature.end) - 1, featureColour, + start, end, y1); } else if (showFeature(sequenceFeature)) @@ -388,19 +412,17 @@ public class FeatureRenderer extends FeatureRendererModel renderScoreFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1, seq.findIndex(sequenceFeature.end) - 1, - getColour(sequenceFeature), start, end, y1, + featureColour, start, end, y1, normaliseScore(sequenceFeature)); } else { renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1, seq.findIndex(sequenceFeature.end) - 1, - getColour(sequenceFeature), start, end, y1); + featureColour, start, end, y1); } } - } - } if (transparency != 1.0f && g != null) @@ -412,6 +434,24 @@ public class FeatureRenderer extends FeatureRendererModel } /** + * Answers true if the feature belongs to a feature group which is not + * currently displayed, else false + * + * @param sequenceFeature + * @return + */ + protected boolean featureGroupNotShown( + final SequenceFeature sequenceFeature) + { + return featureGroups != null + && sequenceFeature.featureGroup != null + && sequenceFeature.featureGroup.length() != 0 + && featureGroups.containsKey(sequenceFeature.featureGroup) + && !featureGroups.get(sequenceFeature.featureGroup) + .booleanValue(); + } + + /** * Called when alignment in associated view has new/modified features to * discover and display. * diff --git a/src/jalview/util/SparseCount.java b/src/jalview/util/SparseCount.java index e6b45f2..7fd9792 100644 --- a/src/jalview/util/SparseCount.java +++ b/src/jalview/util/SparseCount.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.util; import jalview.ext.android.SparseIntArray; diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 4ac4804..c1ad465 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -288,8 +288,12 @@ public abstract class FeatureRendererModel implements continue; } - if ((features[i].getBegin() <= res) - && (features[i].getEnd() >= res)) + // check if start/end are at res, and if not a contact feature, that res + // lies between start and end + if ((features[i].getBegin() == res || features[i].getEnd() == res) + || (!features[i].isContactFeature() + && (features[i].getBegin() < res) && (features[i] + .getEnd() >= res))) { tmp.add(features[i]); } @@ -564,9 +568,16 @@ public abstract class FeatureRendererModel implements return fc.isColored(sequenceFeature); } + /** + * Answers true if the feature type is currently selected to be displayed, + * else false + * + * @param type + * @return + */ protected boolean showFeatureOfType(String type) { - return av.getFeaturesDisplayed().isVisible(type); + return type == null ? false : av.getFeaturesDisplayed().isVisible(type); } @Override diff --git a/test/jalview/analysis/ConservationTest.java b/test/jalview/analysis/ConservationTest.java index 5d21672..fb58655 100644 --- a/test/jalview/analysis/ConservationTest.java +++ b/test/jalview/analysis/ConservationTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.analysis; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java index bae98c5..e215b6b 100644 --- a/test/jalview/analysis/FinderTest.java +++ b/test/jalview/analysis/FinderTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.analysis; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java index 2b48032..1da23ea 100644 --- a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java +++ b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java @@ -28,6 +28,8 @@ import jalview.gui.JvOptionPane; import jalview.io.FileLoader; import jalview.io.FormatAdapter; +import java.util.Arrays; + import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; @@ -147,4 +149,45 @@ public class FeatureScoreModelTest + "(" + s + ") should still be distinct from FER1_MAIZE (3)"); } } + + /** + * Check findFeatureAt doesn't return contact features except at contact + * points TODO:move to under the FeatureRendererModel test suite + */ + @Test(groups = { "Functional" }) + public void testFindFeatureAt_PointFeature() throws Exception + { + String alignment = "a CCCCCCGGGGGGCCCCCC\n" + "b CCCCCCGGGGGGCCCCCC\n" + + "c CCCCCCGGGGGGCCCCCC\n"; + AlignFrame af = new jalview.io.FileLoader(false) + .LoadFileWaitTillLoaded(alignment, FormatAdapter.PASTE); + SequenceI aseq = af.getViewport().getAlignment().getSequenceAt(0); + SequenceFeature sf = null; + sf = new SequenceFeature("disulphide bond", "", 2, 5, Float.NaN, ""); + aseq.addSequenceFeature(sf); + Assert.assertTrue(sf.isContactFeature()); + af.refreshFeatureUI(true); + af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond")); + Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes() + .size(), 1, "Should be just one feature type displayed"); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 1) + .size(), 0); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 2) + .size(), 1); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 3) + .size(), 0); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 4) + .size(), 0); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 5) + .size(), 1); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 6) + .size(), 0); + } + } diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java index 7ac1452..f8ea142 100644 --- a/test/jalview/controller/AlignViewControllerTest.java +++ b/test/jalview/controller/AlignViewControllerTest.java @@ -55,10 +55,10 @@ public class AlignViewControllerTest @Test(groups = "Functional") public void testFindColumnsWithFeature() { - SequenceI seq1 = new Sequence("seq1", "aMMMaaaaaaaaaaaaaaaa"); - SequenceI seq2 = new Sequence("seq2", "aaaMMMMMMMaaaaaaaaaa"); - SequenceI seq3 = new Sequence("seq3", "aaaaaaaaaaMMMMMaaaaa"); - SequenceI seq4 = new Sequence("seq3", "aaaaaaaaaaaaaaaaaaaa"); + SequenceI seq1 = new Sequence("seq1", "-a-MMMaaaaaaaaaaaaaaaa"); + SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa"); + SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa"); + SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa"); /* * features start/end are base 1 @@ -71,13 +71,16 @@ public class AlignViewControllerTest null)); seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15, 0f, null)); + // disulfide bond is a 'contact feature' - only select its 'start' and 'end' + seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc", 8, 12, + 0f, null)); /* - * select the first three columns --> Metal in seq1 2-3 + * select the first five columns --> Metal in seq1 cols 4-5 */ SequenceGroup sg = new SequenceGroup(); sg.setStartRes(0); // base 0 - sg.setEndRes(2); + sg.setEndRes(4); sg.addSequence(seq1, false); sg.addSequence(seq2, false); sg.addSequence(seq3, false); @@ -88,36 +91,37 @@ public class AlignViewControllerTest bs); assertEquals(1, seqCount); assertEquals(2, bs.cardinality()); - assertTrue(bs.get(1)); - assertTrue(bs.get(2)); + assertTrue(bs.get(3)); // base 0 + assertTrue(bs.get(4)); /* - * select the first four columns: Metal in seq1 2:4, seq2 4:4 + * select the first seven columns: Metal in seq1 cols 4-6, seq2 cols 6-7 */ - sg.setEndRes(3); + sg.setEndRes(6); bs.clear(); seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs); assertEquals(2, seqCount); - assertEquals(3, bs.cardinality()); - assertTrue(bs.get(1)); - assertTrue(bs.get(2)); + assertEquals(4, bs.cardinality()); assertTrue(bs.get(3)); + assertTrue(bs.get(4)); + assertTrue(bs.get(5)); + assertTrue(bs.get(6)); /* - * select column 11: Metal in seq3 only + * select column 14: Metal in seq3 only */ - sg.setStartRes(10); - sg.setEndRes(10); + sg.setStartRes(13); + sg.setEndRes(13); bs.clear(); seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs); assertEquals(1, seqCount); assertEquals(1, bs.cardinality()); - assertTrue(bs.get(10)); + assertTrue(bs.get(13)); /* - * select columns 16-20: no Metal feature + * select columns 18-20: no Metal feature */ - sg.setStartRes(15); + sg.setStartRes(17); sg.setEndRes(19); bs.clear(); seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs); @@ -125,6 +129,30 @@ public class AlignViewControllerTest assertEquals(0, bs.cardinality()); /* + * columns 11-13 should not match disulfide bond at 8/12 + */ + sg.setStartRes(10); + sg.setEndRes(12); + bs.clear(); + seqCount = AlignViewController.findColumnsWithFeature("disulfide bond", + sg, bs); + assertEquals(0, seqCount); + assertEquals(0, bs.cardinality()); + + /* + * columns 6-18 should match disulfide bond at columns 9, 14 + */ + sg.setStartRes(5); + sg.setEndRes(17); + bs.clear(); + seqCount = AlignViewController.findColumnsWithFeature("disulfide bond", + sg, bs); + assertEquals(1, seqCount); + assertEquals(2, bs.cardinality()); + assertTrue(bs.get(8)); + assertTrue(bs.get(13)); + + /* * look for a feature that isn't there */ sg.setStartRes(0); diff --git a/test/jalview/datamodel/ResidueCountTest.java b/test/jalview/datamodel/ResidueCountTest.java index ac3ee69..4eb6dbf 100644 --- a/test/jalview/datamodel/ResidueCountTest.java +++ b/test/jalview/datamodel/ResidueCountTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java index e87d7e5..2da8918 100644 --- a/test/jalview/datamodel/SequenceFeatureTest.java +++ b/test/jalview/datamodel/SequenceFeatureTest.java @@ -208,4 +208,24 @@ public class SequenceFeatureTest sf1.setStatus("new"); assertTrue(sf1.equals(sf2)); } + + @Test(groups = { "Functional" }) + public void testIsContactFeature() + { + SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f, + "group"); + assertFalse(sf.isContactFeature()); + sf.setType(""); + assertFalse(sf.isContactFeature()); + sf.setType(null); + assertFalse(sf.isContactFeature()); + sf.setType("Disulfide Bond"); + assertTrue(sf.isContactFeature()); + sf.setType("disulfide bond"); + assertTrue(sf.isContactFeature()); + sf.setType("Disulphide Bond"); + assertTrue(sf.isContactFeature()); + sf.setType("disulphide bond"); + assertTrue(sf.isContactFeature()); + } } diff --git a/test/jalview/ext/android/SparseIntArrayTest.java b/test/jalview/ext/android/SparseIntArrayTest.java index 2da45ed..d9ed73d 100644 --- a/test/jalview/ext/android/SparseIntArrayTest.java +++ b/test/jalview/ext/android/SparseIntArrayTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ext.android; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/ext/android/SparseShortArrayTest.java b/test/jalview/ext/android/SparseShortArrayTest.java index 2a89e65..034368f 100644 --- a/test/jalview/ext/android/SparseShortArrayTest.java +++ b/test/jalview/ext/android/SparseShortArrayTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ext.android; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/schemes/ResidueColourSchemeTest.java b/test/jalview/schemes/ResidueColourSchemeTest.java index 12a5491..d3a4fff 100644 --- a/test/jalview/schemes/ResidueColourSchemeTest.java +++ b/test/jalview/schemes/ResidueColourSchemeTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.schemes; import static org.testng.AssertJUnit.assertEquals; diff --git a/test/jalview/util/FormatTest.java b/test/jalview/util/FormatTest.java index 24cb573..1404f0b 100644 --- a/test/jalview/util/FormatTest.java +++ b/test/jalview/util/FormatTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.util; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/util/PlatformTest.java b/test/jalview/util/PlatformTest.java index 1f7db54..307f450 100644 --- a/test/jalview/util/PlatformTest.java +++ b/test/jalview/util/PlatformTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.util; import static org.testng.Assert.assertFalse; diff --git a/test/jalview/util/SparseCountTest.java b/test/jalview/util/SparseCountTest.java index 4c5b55b..c4d67b6 100644 --- a/test/jalview/util/SparseCountTest.java +++ b/test/jalview/util/SparseCountTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.util; import static org.testng.Assert.assertEquals; diff --git a/utils/InstallAnywhere/Jalview.iap_xml b/utils/InstallAnywhere/Jalview.iap_xml index fc799bb..bf6eb0d 100755 --- a/utils/InstallAnywhere/Jalview.iap_xml +++ b/utils/InstallAnywhere/Jalview.iap_xml @@ -1245,7 +1245,7 @@ and any path to a file to save to the file]]> - + false @@ -1263,7 +1263,7 @@ and any path to a file to save to the file]]> true - + 5417196 @@ -3846,7 +3846,7 @@ Press "Done" to quit the installer.]]> true - + 10 @@ -3883,7 +3883,7 @@ Press "Done" to quit the installer.]]> true - + 10 @@ -3954,10 +3954,10 @@ Press "Done" to quit the installer.]]> true - true + false - + 10 @@ -3994,7 +3994,7 @@ Press "Done" to quit the installer.]]> true - + 10 @@ -4102,7 +4102,7 @@ Press "Done" to quit the installer.]]> true - + 10 @@ -4173,7 +4173,7 @@ Press "Done" to quit the installer.]]> true - + 10