combined new logic for 2.11.2 3d-beacons with original hack to resolve PAE and CIF
Conflicts:
src/jalview/ws/dbsources/EBIAlfaFold.java
httpcore-4.0.1.jar
httpmime-4.0.3.jar
intervalstore-v1.0.jar
-jabaws-min-client-2.2.0.jar
+jabaws-min-client-NO_LOG4J-2.2.0.jar Apache license
java-json.jar
jaxrpc.jar
jersey-client-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
jfreesvg-2.1.jar GPL v3 licensed library from the JFree suite - http://www.jfree.org/jfreesvg/
JGoogleAnalytics_0.3.jar APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
jhall.jar
-Jmol-14.6.4_2016.10.26.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
+Jmol-14.31.53.jar GPL/LGPLv2 built manually from commit https://github.com/BobHanson/Jmol-SwingJS/commit/a6a2fb767e3fc2a73e72d926a11fd93a0e4c9f23 (excluded jspecview/application to compile)
json_simple-1.1.jar Apache 2.0 license - downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)
jsoup-1.8.1.jar
jsr311-api-1.1.1.jar
jswingreader-0.3.jar Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
libquaqua64-8.0.jnilib.jar quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/
libquaqua-8.0.jnilib.jar quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/
-log4j-1.2.8.jar
+log4j-1.2-api-2.16.0.jar Apache license version 2.0
+log4j-api-2.16.0.jar Apache license version 2.0
+log4j-core-2.16.0.jar Apache license version 2.0
+log4j-slf4j18-impl-2.16.0.jar Apache license version 2.0
mail.jar
miglayout-4.0-swing.jar BSD - http://www.migcalendar.com/miglayout/versions/4.0/license.txt
quaqua-filechooser-only-8.0.jar quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/
regex.jar
saaj.jar
servlet-api-3.1.jar
-slf4j-api-1.7.7.jar
-slf4j-log4j12-1.7.7.jar
+slf4j-api-1.7.32.jar MIT license - https://opensource.org/licenses/mit-license.php
+slf4j-log4j12-1.7.32.jar MIT license - https://opensource.org/licenses/mit-license.php
vamsas-client.jar
VAqua5-patch.jar 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.
VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr
jaxb-api-2.3.1.jar CDDL 1.1 + GPL2 w/ CPE - https://oss.oracle.com/licenses/CDDL+GPL-1.1
jaxb-runtime-2.3.2.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
jaxws-api-2.3.1.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md
-Jmol-14.6.4_2016.10.26-no_netscape.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
jsr311-api-1.1.1.jar CDDL License - http://www.opensource.org/licenses/cddl1.php
mimepull-1.9.11.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
policy-2.7.6.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
-slf4j-api-1.7.26.jar MIT License - https://opensource.org/licenses/mit-license.php
-slf4j-log4j12-1.7.26.jar MIT License - https://opensource.org/licenses/mit-license.php
stax-ex-1.8.1.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
stax2-api-4.2.jar The BSD License - http://www.opensource.org/licenses/bsd-license.php
streambuffer-1.5.7.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
}
+
// in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
def string(Object o) {
return o == null ? "" : o.toString()
// Import channel_properties
channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
channelGradleProperties = string("${channelDir}/channel_gradle.properties")
+ channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
overrideProperties(channelGradleProperties, false)
// local build environment properties
// can be "projectDir/local.properties"
'--add-modules', j11modules
]
*/
- } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
- JAVA_INTEGER_VERSION = JAVA_VERSION
- libDir = j11libDir
- libDistDir = j11libDir
- compile_source_compatibility = JAVA_VERSION
- compile_target_compatibility = JAVA_VERSION
+ } else if (JAVA_VERSION.equals("17")) {
+ JAVA_INTEGER_VERSION = string("17")
+ libDir = j17libDir
+ libDistDir = j17libDir
+ compile_source_compatibility = 17
+ compile_target_compatibility = 17
getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
- eclipseJavaRuntimeName = string("JavaSE-11")
+ eclipseJavaRuntimeName = string("JavaSE-17")
/* compile without modules -- using classpath libraries
additional_compiler_args += [
'--module-path', modules_compileClasspath.asPath,
def outputDir = "${jalviewDir}/${package_dir}"
destinationDirectory = file(outputDir)
archiveFileName = rootProject.name+".jar"
+ duplicatesStrategy "EXCLUDE"
+
exclude "cache*/**"
exclude "*.jar"
attributes "Implementation-Version": JALVIEW_VERSION,
"Application-Name": install4jApplicationName
}
+
+ duplicatesStrategy "INCLUDE"
+
mainClassName = shadow_jar_main_class
mergeServiceFiles()
classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
}
getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
+ copy {
+ from channelPropsFile
+ into getdownWebsiteDir
+ }
+ getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
+
// set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
def props = project.properties.sort { it.key }
if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
from launchJvl
from getdownLauncher
from "${getdownWebsiteDir}/${getdown_build_properties}"
+ from "${getdownWebsiteDir}/${channel_props}"
if (file(getdownLauncher).getName() != getdown_launcher) {
rename(file(getdownLauncher).getName(), getdown_launcher)
}
preserve {
include "**"
}
+
+ // should this be exclude really ?
+ duplicatesStrategy "INCLUDE"
+
outputs.files outputFiles
inputs.files inputFiles
}
new org.apache.tools.ant.util.TeeOutputStream(
logErrFOS,
stderr),
- errorOutput)
+ System.err)
} else {
standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
logOutFOS,
-## Creating the .ico (Windows) and .icns (macOS) files from PNG images in linux
+## There is now a script utils/mk_jalview_icons.sh that creates the .icns and .ico icon files, and also the rotatable icon.
+Run it as
+```
+mk_jalview_icons.sh <BASENAME>-512.png
+```
+Having an existing 512x512 PNG image with the above filename format is important.
+It will then create multiple files
+`<BASENAME>-<N>.png`
+for N being 16, 32, 38, 48, 64, 128, 256.
+**NB** You might want to edit these as described below. The `mk_jalview_icons.sh` will not overwrite these files, but it
+will overwrite the `.ico` and `.icns` files, so after editing the `<BASENAME>-<N>.png` files, just run the script again.
+
+As below, the script relies on ImageMagick and icnsutils being installed with `convert` and `png2icns` in the PATH.
+
+The rotatable logo will also be created (and overwritten) as
+`rotatable_<BASENAME>-38.png`
+
+
+## Old text
+### Creating the .ico (Windows) and .icns (macOS) files from PNG images in linux
Create multiple square versions of your icon at the following resolutions:
16x16, 32x32, 48x48, 64x64, 128x128, 256x256, 512x512
This icon is used by the web services progress window, with the rotating Jalview logo.
It requires some small margin of white pixels around the logo to enable antialiasing around the edge of the logo.
-You can make one form a 48x48 transparent logo with
+You can make one form a 38x38 transparent logo with
```
convert jalview_logo-38.png -gravity center -background white -extent 60x60 rotatable_jalview_logo-38.png
```
-1.8.3-1.2.10_FJVL
+1.8.3-1.2.11_FJVL
-1.8.3-1.2.10_JVL
+1.8.3-1.2.11_JVL
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.2.10_FJVL</version>
+ <version>1.8.3-1.2.11_FJVL</version>
</parent>
<artifactId>getdown-ant</artifactId>
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.2.10_FJVL</version>
+ <version>1.8.3-1.2.11_FJVL</version>
</parent>
<artifactId>getdown-core</artifactId>
import jalview.bin.HiDPISetting;
import jalview.bin.MemorySetting;
-//import com.install4j.api.launcher.Variables;
+import jalview.util.LaunchUtils;
import com.threerings.getdown.util.*;
// avoid ambiguity with java.util.Base64 which we can't use as it's 1.8+
continue;
}
}
+
+ // use saved preferences if no cmdline args
+ LaunchUtils.loadChannelProps(getAppDir());
+ if (LaunchUtils.getBooleanUserPreference(MemorySetting.CUSTOMISED_SETTINGS)) {
+ if (jvmmempc == null) {
+ jvmmempc = LaunchUtils.getUserPreference(MemorySetting.MEMORY_JVMMEMPC);
+ }
+ if (jvmmemmax == null) {
+ jvmmemmax = LaunchUtils.getUserPreference(MemorySetting.MEMORY_JVMMEMMAX);
+ }
+ }
// add the memory setting from jvmmempc and jvmmemmax
long maxMemLong = -1;
String[] sargs = args.toArray(new String[args.size()]);
log.info("Running " + StringUtil.join(sargs, "\n "));
- return Runtime.getRuntime().exec(sargs, envp, getAppDir());
+ // don't set the working dir, leave it the same as the working dir of the invocation
+ //return Runtime.getRuntime().exec(sargs, envp, getAppDir());
+ return Runtime.getRuntime().exec(sargs, envp);
}
/**
/*
+
+ private static String ADJUSTMENT_MESSAGE = null;
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* @author bsoares
*
*/
+
public class MemorySetting
{
public static final String MAX_HEAPSIZE_PERCENT_PROPERTY_NAME = "jvmmempc";
private static final long NOMEM_MAX_HEAPSIZE_GB_DEFAULT = 8;
+ public static final String NS = "MEMORY";
+
+ public static final String CUSTOMISED_SETTINGS = NS
+ + "_CUSTOMISED_SETTINGS";
+
+ public static final String MEMORY_JVMMEMPC = NS + "_"
+ + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME.toUpperCase();
+
+ public static final String MEMORY_JVMMEMMAX = NS + "_"
+ + MAX_HEAPSIZE_PROPERTY_NAME.toUpperCase();
+
protected static boolean logToClassChecked = false;
+ public static String memorySuffixes = "bkmgt"; // order of the suffixes is
+ // important!
+
public static long getMemorySetting()
{
return getMemorySetting(null, null);
}
+ public static long getMemorySetting(String jvmmemmaxarg,
+ String jvmmempcarg)
+ {
+ return getMemorySetting(jvmmemmaxarg, jvmmempcarg, true, false);
+ }
+
/**
* Decide on appropriate memory setting for Jalview based on the two arguments
* values: jvmmempc - the maximum percentage of total physical memory to
* @param jvmmempcarg
* Max percentage of physical memory to use. Defaults to "90".
*
+ * @param useProps
+ * boolean to decide whether to look at System properties.
+ *
* @return The amount of memory (in bytes) to allocate to Jalview
*/
public static long getMemorySetting(String jvmmemmaxarg,
- String jvmmempcarg)
+ String jvmmempcarg, boolean useProps, boolean quiet)
{
// actual Xmx value-to-be
long maxMemLong = -1;
+ clearAdjustmentMessage();
// (absolute) jvmmaxmem setting, start with default
long memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
- if (jvmmemmaxarg == null)
+ if (jvmmemmaxarg == null && useProps)
{
jvmmemmaxarg = System.getProperty(MAX_HEAPSIZE_PROPERTY_NAME);
}
String jvmmemmax = jvmmemmaxarg;
if (jvmmemmax != null && jvmmemmax.length() > 0)
{
- long multiplier = 1;
- switch (jvmmemmax.toLowerCase().substring(jvmmemmax.length() - 1))
- {
- case "t":
- multiplier = 1099511627776L; // 2^40
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "g":
- multiplier = 1073741824; // 2^30
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "m":
- multiplier = 1048576; // 2^20
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "k":
- multiplier = 1024; // 2^10
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "b":
- multiplier = 1; // 2^0
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- default:
- break;
- }
-
// parse the arg
try
{
- memmax = Long.parseLong(jvmmemmax);
+ memmax = memoryStringToLong(jvmmemmax);
+ if (memmax == 0)
+ {
+ throw (new NumberFormatException("Not allowing 0"));
+ }
} catch (NumberFormatException e)
{
memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
- + "') badly formatted, using default ("
- + MAX_HEAPSIZE_GB_DEFAULT + "g).");
- }
-
- // apply multiplier if not too big (i.e. bigger than a long)
- if (Long.MAX_VALUE / memmax < multiplier)
- {
- memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
- System.out.println("MemorySetting Property '"
- + MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
- + ") too big, using default (" + MAX_HEAPSIZE_GB_DEFAULT
- + "g).");
- }
- else
- {
- memmax = multiplier * memmax;
+ + "') badly formatted or 0, using default ("
+ + MAX_HEAPSIZE_GB_DEFAULT + "g).", quiet);
}
// check at least minimum value (this accounts for negatives too)
if (memmax < APPLICATION_MIN_MEMORY)
{
memmax = APPLICATION_MIN_MEMORY;
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
+ ") too small, using minimum (" + APPLICATION_MIN_MEMORY
- + ").");
+ + ").", quiet);
}
}
else
{
// no need to warn if no setting
- // System.out.println("MemorySetting Property '" + maxHeapSizeProperty
+ // adjustmentMessage("MemorySetting Property '" + maxHeapSizeProperty
// + "' not
// set.");
}
// get max percent of physical memory, starting with default
float percent = MAX_HEAPSIZE_PERCENT_DEFAULT;
- if (jvmmempcarg == null)
+ if (jvmmempcarg == null && useProps)
{
jvmmempcarg = System.getProperty(MAX_HEAPSIZE_PERCENT_PROPERTY_NAME);
}
{
if (jvmmempc != null)
{
- float trypercent = Float.parseFloat(jvmmempc);
- if (0 < trypercent && trypercent <= 100f)
+ int trypercent = Integer.parseInt(jvmmempc);
+ if (0 <= trypercent && trypercent <= 100)
{
percent = trypercent;
}
else
{
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME
- + "' should be in range 1..100. Using default " + percent
- + "%");
+ + "' should be in range 0..100. Using default " + percent
+ + "%", quiet);
}
}
} catch (NumberFormatException e)
{
- System.out.println("MemorySetting property '"
+ setAdjustmentMessage("MemorySetting property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg
- + ") badly formatted");
+ + ") badly formatted", quiet);
}
// catch everything in case of no com.sun.management.OperatingSystemMXBean
{
mempc = physicalMem - LEAVE_FREE_MIN_MEMORY;
reducedmempc = true;
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg
+ ") too large. Leaving free space for OS and reducing to ("
- + mempc + ").");
+ + mempc + ").", quiet);
}
// check for minimum application memsize
{
if (reducedmempc)
{
- System.out.println("Reduced MemorySetting (" + mempc
+ setAdjustmentMessage("Reduced MemorySetting (" + mempc
+ ") too small. Increasing to application minimum ("
- + APPLICATION_MIN_MEMORY + ").");
+ + APPLICATION_MIN_MEMORY + ").", quiet);
}
else
{
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' ("
+ jvmmempcarg + ") too small. Using minimum ("
- + APPLICATION_MIN_MEMORY + ").");
+ + APPLICATION_MIN_MEMORY + ").", quiet);
}
mempc = APPLICATION_MIN_MEMORY;
}
{
// not enough memory for application, just try and grab what we can!
mempc = physicalMem;
- System.out.println(
+ setAdjustmentMessage(
"Not enough physical memory for application. Ignoring MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' ("
+ jvmmempcarg
+ "). Using maximum memory available ("
- + physicalMem + ").");
+ + physicalMem + ").",
+ quiet);
}
} catch (Throwable t)
{
memoryPercentError = true;
- System.out.println(
- "Problem calling GetMemory.getPhysicalMemory(). Likely to be problem with com.sun.management.OperatingSystemMXBean");
+ setAdjustmentMessage(
+ "Problem calling GetMemory.getPhysicalMemory(). Likely to be problem with com.sun.management.OperatingSystemMXBean",
+ quiet);
t.printStackTrace();
}
// == null))
&& memmax > NOMEM_MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE)
{
- System.out.println(
+ setAdjustmentMessage(
"Capping maximum memory to " + NOMEM_MAX_HEAPSIZE_GB_DEFAULT
- + "g due to failure to read physical memory size.");
+ + "g due to failure to read physical memory size.",
+ quiet);
memmax = NOMEM_MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
}
return maxMemLong;
}
+ public static boolean isValidMemoryString(String text)
+ {
+ if (text.length() > 0)
+ {
+ char lastChar = text.charAt(text.length() - 1);
+ char[] otherChars = text.substring(0, text.length() - 1)
+ .toCharArray();
+ for (char c : otherChars)
+ {
+ if (c < '0' || c > '9')
+ {
+ return false;
+ }
+ }
+ if ((lastChar < '0' || lastChar > '9') && memorySuffixes
+ .indexOf(Character.toLowerCase(lastChar)) == -1)
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ public static long memoryStringToLong(String memString)
+ throws NumberFormatException
+ {
+ if (!isValidMemoryString(memString)) // not valid
+ {
+ throw (new NumberFormatException("Not a valid memory string"));
+ }
+ char suffix = Character
+ .toLowerCase(memString.charAt(memString.length() - 1));
+ if ('0' <= suffix && suffix <= '9') // no suffix
+ {
+ return Long.valueOf(memString);
+ }
+ if (memorySuffixes.indexOf(suffix) == -1) // suffix is unknown
+ {
+ return -1;
+ }
+
+ long multiplier = (long) Math.pow(2,
+ memorySuffixes.indexOf(suffix) * 10); // note order of suffixes in
+ // memorySuffixes important
+ // here!
+ // parse the arg. NumberFormatExceptions passed on to calling method
+ long mem = Long
+ .parseLong(memString.substring(0, memString.length() - 1));
+ if (mem == 0)
+ {
+ return 0;
+ }
+
+ // apply multiplier only if result is not too big (i.e. bigger than a long)
+ if (Long.MAX_VALUE / mem > multiplier)
+ {
+ return multiplier * mem;
+ }
+ else
+ {
+ // number too big for a Long. Limit to Long.MAX_VALUE
+ System.out.println("Memory parsing of '" + memString
+ + "' produces number too big. Limiting to Long.MAX_VALUE="
+ + Long.MAX_VALUE);
+ return Long.MAX_VALUE;
+ }
+ }
+
+ public static String memoryLongToString(long mem)
+ {
+ return memoryLongToString(mem, "%.1f");
+ }
+
+ public static String memoryLongToString(long mem, String format)
+ {
+ int exponent = 0;
+ float num = mem;
+ char suffix = 'b';
+
+ for (int i = 0; i < memorySuffixes.length(); i++)
+ {
+ char s = Character.toUpperCase(memorySuffixes.charAt(i));
+ if (mem < (long) Math.pow(2, exponent + 10)
+ || i == memorySuffixes.length() - 1) // last suffix
+ {
+ suffix = s;
+ num = (float) (mem / Math.pow(2, exponent));
+ break;
+ }
+ exponent += 10;
+ }
+
+ return String.format(format, num) + suffix;
+ }
+
+ private static String ADJUSTMENT_MESSAGE = null;
+
+ private static void setAdjustmentMessage(String reason, boolean quiet)
+ {
+ ADJUSTMENT_MESSAGE = reason;
+ if (!quiet)
+ {
+ System.out.println(reason);
+ }
+ }
+
+ public static void clearAdjustmentMessage()
+ {
+ ADJUSTMENT_MESSAGE = null;
+ }
+
+ public static String getAdjustmentMessage()
+ {
+ return ADJUSTMENT_MESSAGE;
+ }
+
}
\ No newline at end of file
--- /dev/null
+package jalview.util;
+
+import java.awt.Image;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+import javax.swing.ImageIcon;
+
+public class ChannelProperties
+{
+
+ public static final String CHANNEL_PROPERTIES_FILENAME = "channel.props";
+
+ private static Properties channelProps;
+
+ private static final Properties defaultProps;
+
+ private static Map<String, Image> imageMap = new HashMap<String, Image>();
+
+ private static Map<String, URL> urlMap = new HashMap<String, URL>();
+
+ private static final ArrayList<Image> iconList;
+
+ static
+ {
+ defaultProps = new Properties();
+ // these should be kept up to date, but in real life they should never
+ // actually be used anyway.
+ defaultProps.put("app_name", "Jalview");
+ defaultProps.put("banner", "/default_images/jalview_banner.png");
+ defaultProps.put("logo.16", "/default_images/jalview_logo-16.png");
+ defaultProps.put("logo.32", "/default_images/jalview_logo-32.png");
+ defaultProps.put("logo.38", "/default_images/jalview_logo-38.png");
+ defaultProps.put("logo.48", "/default_images/jalview_logo-48.png");
+ defaultProps.put("logo.64", "/default_images/jalview_logo-64.png");
+ defaultProps.put("logo.128", "/default_images/jalview_logo-128.png");
+ defaultProps.put("logo.256", "/default_images/jalview_logo-256.png");
+ defaultProps.put("logo.512", "/default_images/jalview_logo-512.png");
+ defaultProps.put("rotatable_logo.48",
+ "/default_images/rotatable_jalview_logo-38.png");
+ defaultProps.put("bg_logo.28", "/default_images/barton_group-28.png");
+ defaultProps.put("bg_logo.30", "/default_images/barton_group-30.png");
+ defaultProps.put("bg_logo.32", "/default_images/barton_group-32.png");
+ defaultProps.put("uod_banner.28", "/default_images/UoD_banner-28.png");
+ defaultProps.put("uod_banner.30", "/default_images/UoD_banner-30.png");
+ defaultProps.put("uod_banner.32", "/default_images/UoD_banner-32.png");
+ defaultProps.put("default_appbase",
+ "https://www.jalview.org/getdown/release/1.8");
+ defaultProps.put("preferences.filename", ".jalview_properties");
+
+ // load channel_properties
+ Properties tryChannelProps = new Properties();
+ URL channelPropsURL = ChannelProperties.class
+ .getResource("/" + CHANNEL_PROPERTIES_FILENAME);
+ if (channelPropsURL == null)
+ {
+ // complete failure of channel_properties, set all properties to defaults
+ System.err.println("Failed to find '/" + CHANNEL_PROPERTIES_FILENAME
+ + "' file at '"
+ + (channelPropsURL == null ? "null"
+ : channelPropsURL.toString())
+ + "'. Using class defaultProps.");
+ tryChannelProps = defaultProps;
+ }
+ else
+ {
+ try
+ {
+ InputStream channelPropsIS = channelPropsURL.openStream();
+ tryChannelProps.load(channelPropsIS);
+ channelPropsIS.close();
+ } catch (IOException e)
+ {
+ System.err.println(e.getMessage());
+ // return false;
+ }
+ }
+ channelProps = tryChannelProps;
+
+ /*
+ * The following slight palava for caching an icon list is so that all sizes of icons
+ * are the same. i.e. if there are /any/ channel_properties icons to use, then _only_
+ * use those channel_properties icons, don't mix in class default icons for missing
+ * sizes. If there are _no_ (usable) channel icons then we can use the class default icons.
+ */
+ iconList = new ArrayList<Image>();
+ List<String> sizes = Arrays.asList("16", "32", "48", "64", "128", "256",
+ "512");
+ for (String size : sizes)
+ {
+ Image logo = null;
+ // not using defaults or class props first time through
+ logo = ChannelProperties.getImage("logo." + size, null, false);
+ if (logo != null)
+ {
+ iconList.add(logo);
+ }
+ }
+ // now add the class defaults if there were no channel icons defined
+ if (iconList.size() == 0)
+ {
+ for (String size : sizes)
+ {
+ Image logo = null;
+ String path = defaultProps.getProperty("logo." + size);
+ URL imageURL = ChannelProperties.class.getResource(path);
+ ImageIcon imgIcon = imageURL == null ? null
+ : new ImageIcon(imageURL);
+ logo = imgIcon == null ? null : imgIcon.getImage();
+ if (logo != null)
+ {
+ iconList.add(logo);
+ }
+ }
+ }
+ }
+
+ protected static void loadProps(File dir)
+ {
+ File channelPropsFile = new File(dir, CHANNEL_PROPERTIES_FILENAME);
+ if (channelPropsFile.exists())
+ {
+ try
+ {
+ InputStream is = new FileInputStream(channelPropsFile);
+ channelProps.load(is);
+ } catch (FileNotFoundException e)
+ {
+ System.err.println(e.getMessage());
+ } catch (IOException e)
+ {
+ System.err.println(e.getMessage());
+ }
+ }
+ }
+
+ private static Properties channelProps()
+ {
+ return channelProps;
+ }
+
+ private static Map<String, Image> imageMap()
+ {
+ return imageMap;
+ }
+
+ private static Map<String, URL> urlMap()
+ {
+ return urlMap;
+ }
+
+ /*
+ * getProperty(key) will get property value from channel_properties for key.
+ * If no property for key is found, it will fall back to using the defaultProps defined for this class.
+ */
+ public static String getProperty(String key)
+ {
+ return getProperty(key, null, true);
+ }
+
+ /*
+ * getProperty(key, defaultVal) will get property value from channel_properties for key.
+ * If no property for key is found, it will return defaultVal and NOT fall back to the class defaultProps.
+ */
+ public static String getProperty(String key, String defaultVal)
+ {
+ return getProperty(key, defaultVal, false);
+ }
+
+ /*
+ * internal method. note that setting useClassDefaultProps=true will ignore the provided defaultVal
+ */
+ private static String getProperty(String key, String defaultVal,
+ boolean useClassDefaultProps)
+ {
+ if (channelProps() != null)
+ {
+ if (channelProps().containsKey(key))
+ {
+ return channelProps().getProperty(key,
+ useClassDefaultProps ? defaultProps.getProperty(key)
+ : defaultVal);
+ }
+ else
+ {
+ System.err.println("Failed to get channel property '" + key + "'");
+ }
+ }
+ return null;
+ }
+
+ /*
+ * getImage(key) returns the channel defined image for property key. If that is null (e.g. due to
+ * no defined channel image or the image file being corrupt/unusable/missing) it uses the image
+ * defined in defaultChannelProps
+ */
+ public static Image getImage(String key)
+ {
+ return getImage(key, null, true);
+ }
+
+ /*
+ * getImage(key, defaultImg) will get image associated with value from channel_properties for key.
+ * If no property or associated image for key is found (or is usable), it will return defaultImg
+ * and NOT fall back to the class defaultProps.
+ */
+ public static Image getImage(String key, Image defaultImg)
+ {
+ return getImage(key, defaultImg, false);
+ }
+
+ /*
+ * internal method. note that setting useClassDefaultImage=true will ignore the provided defaultImg
+ */
+ private static Image getImage(String key, Image defaultImg,
+ boolean useClassDefaultImage)
+ {
+ Image img = null;
+ if (imageMap().containsKey(key))
+ {
+ img = imageMap().get(key);
+ }
+ // Catch a previously untried or failed load
+ if (img == null)
+ {
+ String path = getProperty(key, null, useClassDefaultImage);
+ if (path == null) // no channel property or class default property (if
+ // requested)
+ {
+ return useClassDefaultImage ? null : defaultImg;
+ }
+
+ URL imageURL = ChannelProperties.class.getResource(path);
+ ImageIcon imgIcon = imageURL == null ? null : new ImageIcon(imageURL);
+ img = imgIcon == null ? null : imgIcon.getImage();
+ if (img == null)
+ {
+ System.err.println(
+ "Failed to load channel image " + key + "=" + path);
+ if (!useClassDefaultImage)
+ {
+ return defaultImg;
+ }
+ }
+ else
+ {
+ imageMap().put(key, img);
+ urlMap.put(key, imageURL);
+ }
+ }
+ return img;
+ }
+
+ /*
+ * Public method to get the URL object pointing to a cached image.
+ */
+ public static URL getImageURL(String key)
+ {
+ if (getImage(key) != null)
+ {
+ if (urlMap().containsKey(key))
+ {
+ return urlMap().getOrDefault(key, null);
+ }
+ System.err.println(
+ "Do not use getImageURL(key) before using getImage(key...)");
+ }
+ return null;
+ }
+
+ /*
+ * Get a List of Icon images of different sizes.
+ */
+ public static ArrayList<Image> getIconList()
+ {
+ return iconList;
+ }
+}
--- /dev/null
+package jalview.util;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.Properties;
+
+public class LaunchUtils
+{
+
+ public static void loadChannelProps(File dir)
+ {
+ ChannelProperties.loadProps(dir);
+ }
+
+ private static Properties userPreferences = null;
+
+ public static String getUserPreference(String key)
+ {
+ if (userPreferences == null)
+ {
+ String channelPrefsFilename = ChannelProperties
+ .getProperty("preferences.filename");
+ if (channelPrefsFilename == null)
+ {
+ return null;
+ }
+ File propertiesFile = new File(System.getProperty("user.home"),
+ channelPrefsFilename);
+ if (!propertiesFile.exists())
+ {
+ return null;
+ }
+ try
+ {
+ userPreferences = new Properties();
+ userPreferences.load(new FileInputStream(propertiesFile));
+ } catch (FileNotFoundException e)
+ {
+ // didn't find user preferences file
+ return null;
+ } catch (IOException e)
+ {
+ System.err.println(e.getMessage());
+ return null;
+ }
+ }
+ return userPreferences.getProperty(key);
+ }
+
+ public static boolean getBooleanUserPreference(String key)
+ {
+ return Boolean.parseBoolean(getUserPreference(key));
+ }
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+import java.io.UnsupportedEncodingException;
+import java.net.URLEncoder;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.regex.Pattern;
+
+public class StringUtils
+{
+ private static final Pattern DELIMITERS_PATTERN = Pattern
+ .compile(".*='[^']*(?!')");
+
+ private static final char PERCENT = '%';
+
+ private static final boolean DEBUG = false;
+
+ /*
+ * URL encoded characters, indexed by char value
+ * e.g. urlEncodings['='] = urlEncodings[61] = "%3D"
+ */
+ private static String[] urlEncodings = new String[255];
+
+ /**
+ * Returns a new character array, after inserting characters into the given
+ * character array.
+ *
+ * @param in
+ * the character array to insert into
+ * @param position
+ * the 0-based position for insertion
+ * @param count
+ * the number of characters to insert
+ * @param ch
+ * the character to insert
+ */
+ public static final char[] insertCharAt(char[] in, int position,
+ int count, char ch)
+ {
+ char[] tmp = new char[in.length + count];
+
+ if (position >= in.length)
+ {
+ System.arraycopy(in, 0, tmp, 0, in.length);
+ position = in.length;
+ }
+ else
+ {
+ System.arraycopy(in, 0, tmp, 0, position);
+ }
+
+ int index = position;
+ while (count > 0)
+ {
+ tmp[index++] = ch;
+ count--;
+ }
+
+ if (position < in.length)
+ {
+ System.arraycopy(in, position, tmp, index, in.length - position);
+ }
+
+ return tmp;
+ }
+
+ /**
+ * Delete
+ *
+ * @param in
+ * @param from
+ * @param to
+ * @return
+ */
+ public static final char[] deleteChars(char[] in, int from, int to)
+ {
+ if (from >= in.length || from < 0)
+ {
+ return in;
+ }
+
+ char[] tmp;
+
+ if (to >= in.length)
+ {
+ tmp = new char[from];
+ System.arraycopy(in, 0, tmp, 0, from);
+ to = in.length;
+ }
+ else
+ {
+ tmp = new char[in.length - to + from];
+ System.arraycopy(in, 0, tmp, 0, from);
+ System.arraycopy(in, to, tmp, from, in.length - to);
+ }
+ return tmp;
+ }
+
+ /**
+ * Returns the last part of 'input' after the last occurrence of 'token'. For
+ * example to extract only the filename from a full path or URL.
+ *
+ * @param input
+ * @param token
+ * a delimiter which must be in regular expression format
+ * @return
+ */
+ public static String getLastToken(String input, String token)
+ {
+ if (input == null)
+ {
+ return null;
+ }
+ if (token == null)
+ {
+ return input;
+ }
+ String[] st = input.split(token);
+ return st[st.length - 1];
+ }
+
+ /**
+ * Parses the input string into components separated by the delimiter. Unlike
+ * String.split(), this method will ignore occurrences of the delimiter which
+ * are nested within single quotes in name-value pair values, e.g. a='b,c'.
+ *
+ * @param input
+ * @param delimiter
+ * @return elements separated by separator
+ */
+ public static String[] separatorListToArray(String input,
+ String delimiter)
+ {
+ int seplen = delimiter.length();
+ if (input == null || input.equals("") || input.equals(delimiter))
+ {
+ return null;
+ }
+ List<String> jv = new ArrayList<>();
+ int cp = 0, pos, escape;
+ boolean wasescaped = false, wasquoted = false;
+ String lstitem = null;
+ while ((pos = input.indexOf(delimiter, cp)) >= cp)
+ {
+ escape = (pos > 0 && input.charAt(pos - 1) == '\\') ? -1 : 0;
+ if (wasescaped || wasquoted)
+ {
+ // append to previous pos
+ jv.set(jv.size() - 1, lstitem = lstitem + delimiter
+ + input.substring(cp, pos + escape));
+ }
+ else
+ {
+ jv.add(lstitem = input.substring(cp, pos + escape));
+ }
+ cp = pos + seplen;
+ wasescaped = escape == -1;
+ // last separator may be in an unmatched quote
+ wasquoted = DELIMITERS_PATTERN.matcher(lstitem).matches();
+ }
+ if (cp < input.length())
+ {
+ String c = input.substring(cp);
+ if (wasescaped || wasquoted)
+ {
+ // append final separator
+ jv.set(jv.size() - 1, lstitem + delimiter + c);
+ }
+ else
+ {
+ if (!c.equals(delimiter))
+ {
+ jv.add(c);
+ }
+ }
+ }
+ if (jv.size() > 0)
+ {
+ String[] v = jv.toArray(new String[jv.size()]);
+ jv.clear();
+ if (DEBUG)
+ {
+ System.err.println("Array from '" + delimiter
+ + "' separated List:\n" + v.length);
+ for (int i = 0; i < v.length; i++)
+ {
+ System.err.println("item " + i + " '" + v[i] + "'");
+ }
+ }
+ return v;
+ }
+ if (DEBUG)
+ {
+ System.err.println(
+ "Empty Array from '" + delimiter + "' separated List");
+ }
+ return null;
+ }
+
+ /**
+ * Returns a string which contains the list elements delimited by the
+ * separator. Null items are ignored. If the input is null or has length zero,
+ * a single delimiter is returned.
+ *
+ * @param list
+ * @param separator
+ * @return concatenated string
+ */
+ public static String arrayToSeparatorList(String[] list, String separator)
+ {
+ StringBuffer v = new StringBuffer();
+ if (list != null && list.length > 0)
+ {
+ for (int i = 0, iSize = list.length; i < iSize; i++)
+ {
+ if (list[i] != null)
+ {
+ if (v.length() > 0)
+ {
+ v.append(separator);
+ }
+ // TODO - escape any separator values in list[i]
+ v.append(list[i]);
+ }
+ }
+ if (DEBUG)
+ {
+ System.err
+ .println("Returning '" + separator + "' separated List:\n");
+ System.err.println(v);
+ }
+ return v.toString();
+ }
+ if (DEBUG)
+ {
+ System.err.println(
+ "Returning empty '" + separator + "' separated List\n");
+ }
+ return "" + separator;
+ }
+
+ /**
+ * Converts a list to a string with a delimiter before each term except the
+ * first. Returns an empty string given a null or zero-length argument. This
+ * can be replaced with StringJoiner in Java 8.
+ *
+ * @param terms
+ * @param delim
+ * @return
+ */
+ public static String listToDelimitedString(List<String> terms,
+ String delim)
+ {
+ StringBuilder sb = new StringBuilder(32);
+ if (terms != null && !terms.isEmpty())
+ {
+ boolean appended = false;
+ for (String term : terms)
+ {
+ if (appended)
+ {
+ sb.append(delim);
+ }
+ appended = true;
+ sb.append(term);
+ }
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Convenience method to parse a string to an integer, returning 0 if the
+ * input is null or not a valid integer
+ *
+ * @param s
+ * @return
+ */
+ public static int parseInt(String s)
+ {
+ int result = 0;
+ if (s != null && s.length() > 0)
+ {
+ try
+ {
+ result = Integer.parseInt(s);
+ } catch (NumberFormatException ex)
+ {
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Compares two versions formatted as e.g. "3.4.5" and returns -1, 0 or 1 as
+ * the first version precedes, is equal to, or follows the second
+ *
+ * @param v1
+ * @param v2
+ * @return
+ */
+ public static int compareVersions(String v1, String v2)
+ {
+ return compareVersions(v1, v2, null);
+ }
+
+ /**
+ * Compares two versions formatted as e.g. "3.4.5b1" and returns -1, 0 or 1 as
+ * the first version precedes, is equal to, or follows the second
+ *
+ * @param v1
+ * @param v2
+ * @param pointSeparator
+ * a string used to delimit point increments in sub-tokens of the
+ * version
+ * @return
+ */
+ public static int compareVersions(String v1, String v2,
+ String pointSeparator)
+ {
+ if (v1 == null || v2 == null)
+ {
+ return 0;
+ }
+ String[] toks1 = v1.split("\\.");
+ String[] toks2 = v2.split("\\.");
+ int i = 0;
+ for (; i < toks1.length; i++)
+ {
+ if (i >= toks2.length)
+ {
+ /*
+ * extra tokens in v1
+ */
+ return 1;
+ }
+ String tok1 = toks1[i];
+ String tok2 = toks2[i];
+ if (pointSeparator != null)
+ {
+ /*
+ * convert e.g. 5b2 into decimal 5.2 for comparison purposes
+ */
+ tok1 = tok1.replace(pointSeparator, ".");
+ tok2 = tok2.replace(pointSeparator, ".");
+ }
+ try
+ {
+ float f1 = Float.valueOf(tok1);
+ float f2 = Float.valueOf(tok2);
+ int comp = Float.compare(f1, f2);
+ if (comp != 0)
+ {
+ return comp;
+ }
+ } catch (NumberFormatException e)
+ {
+ System.err
+ .println("Invalid version format found: " + e.getMessage());
+ return 0;
+ }
+ }
+
+ if (i < toks2.length)
+ {
+ /*
+ * extra tokens in v2
+ */
+ return -1;
+ }
+
+ /*
+ * same length, all tokens match
+ */
+ return 0;
+ }
+
+ /**
+ * Converts the string to all lower-case except the first character which is
+ * upper-cased
+ *
+ * @param s
+ * @return
+ */
+ public static String toSentenceCase(String s)
+ {
+ if (s == null)
+ {
+ return s;
+ }
+ if (s.length() <= 1)
+ {
+ return s.toUpperCase();
+ }
+ return s.substring(0, 1).toUpperCase() + s.substring(1).toLowerCase();
+ }
+
+ /**
+ * A helper method that strips off any leading or trailing html and body tags.
+ * If no html tag is found, then also html-encodes angle bracket characters.
+ *
+ * @param text
+ * @return
+ */
+ public static String stripHtmlTags(String text)
+ {
+ if (text == null)
+ {
+ return null;
+ }
+ String tmp2up = text.toUpperCase();
+ int startTag = tmp2up.indexOf("<HTML>");
+ if (startTag > -1)
+ {
+ text = text.substring(startTag + 6);
+ tmp2up = tmp2up.substring(startTag + 6);
+ }
+ // is omission of "<BODY>" intentional here??
+ int endTag = tmp2up.indexOf("</BODY>");
+ if (endTag > -1)
+ {
+ text = text.substring(0, endTag);
+ tmp2up = tmp2up.substring(0, endTag);
+ }
+ endTag = tmp2up.indexOf("</HTML>");
+ if (endTag > -1)
+ {
+ text = text.substring(0, endTag);
+ }
+
+ if (startTag == -1 && (text.contains("<") || text.contains(">")))
+ {
+ text = text.replaceAll("<", "<");
+ text = text.replaceAll(">", ">");
+ }
+ return text;
+ }
+
+ /**
+ * Answers the input string with any occurrences of the 'encodeable'
+ * characters replaced by their URL encoding
+ *
+ * @param s
+ * @param encodable
+ * @return
+ */
+ public static String urlEncode(String s, String encodable)
+ {
+ if (s == null || s.isEmpty())
+ {
+ return s;
+ }
+
+ /*
+ * do % encoding first, as otherwise it may double-encode!
+ */
+ if (encodable.indexOf(PERCENT) != -1)
+ {
+ s = urlEncode(s, PERCENT);
+ }
+
+ for (char c : encodable.toCharArray())
+ {
+ if (c != PERCENT)
+ {
+ s = urlEncode(s, c);
+ }
+ }
+ return s;
+ }
+
+ /**
+ * Answers the input string with any occurrences of {@code c} replaced with
+ * their url encoding. Answers the input string if it is unchanged.
+ *
+ * @param s
+ * @param c
+ * @return
+ */
+ static String urlEncode(String s, char c)
+ {
+ String decoded = String.valueOf(c);
+ if (s.indexOf(decoded) != -1)
+ {
+ String encoded = getUrlEncoding(c);
+ if (!encoded.equals(decoded))
+ {
+ s = s.replace(decoded, encoded);
+ }
+ }
+ return s;
+ }
+
+ /**
+ * Answers the input string with any occurrences of the specified (unencoded)
+ * characters replaced by their URL decoding.
+ * <p>
+ * Example: {@code urlDecode("a%3Db%3Bc", "-;=,")} should answer
+ * {@code "a=b;c"}.
+ *
+ * @param s
+ * @param encodable
+ * @return
+ */
+ public static String urlDecode(String s, String encodable)
+ {
+ if (s == null || s.isEmpty())
+ {
+ return s;
+ }
+
+ for (char c : encodable.toCharArray())
+ {
+ String encoded = getUrlEncoding(c);
+ if (s.indexOf(encoded) != -1)
+ {
+ String decoded = String.valueOf(c);
+ s = s.replace(encoded, decoded);
+ }
+ }
+ return s;
+ }
+
+ /**
+ * Does a lazy lookup of the url encoding of the given character, saving the
+ * value for repeat lookups
+ *
+ * @param c
+ * @return
+ */
+ private static String getUrlEncoding(char c)
+ {
+ if (c < 0 || c >= urlEncodings.length)
+ {
+ return String.valueOf(c);
+ }
+
+ String enc = urlEncodings[c];
+ if (enc == null)
+ {
+ try
+ {
+ enc = urlEncodings[c] = URLEncoder.encode(String.valueOf(c),
+ "UTF-8");
+ } catch (UnsupportedEncodingException e)
+ {
+ enc = urlEncodings[c] = String.valueOf(c);
+ }
+ }
+ return enc;
+ }
+
+ public static int firstCharPosIgnoreCase(String text, String chars)
+ {
+ int min = text.length() + 1;
+ for (char c : chars.toLowerCase().toCharArray())
+ {
+ int i = text.toLowerCase().indexOf(c);
+ if (0 <= i && i < min)
+ {
+ min = i;
+ }
+ }
+ return min < text.length() + 1 ? min : -1;
+ }
+}
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.2.10_FJVL</version>
+ <version>1.8.3-1.2.11_FJVL</version>
</parent>
<artifactId>getdown-launcher</artifactId>
_getdown = getdown;
_msgs = msgs;
+ String[] hostPortAuthUser = ProxyUtil.jalviewProxyProperties(getdown._app);
+ String host = hostPortAuthUser[0];
+ String port = hostPortAuthUser[1];
+ boolean proxyAuth = Boolean.parseBoolean(hostPortAuthUser[2]);
+ String username = hostPortAuthUser[3];
+
setLayout(new VGroupLayout());
setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
add(new SaneLabelField(get("m.configure_proxy")));
JPanel row = new JPanel(new GridLayout());
row.add(new SaneLabelField(get("m.proxy_host")), BorderLayout.WEST);
row.add(_host = new SaneTextField());
+ _host.setText(host);
add(row);
row = new JPanel(new GridLayout());
row.add(new SaneLabelField(get("m.proxy_port")), BorderLayout.WEST);
row.add(_port = new SaneTextField());
+ _port.setText(port);
add(row);
add(new Spacer(5, 5));
row = new JPanel(new GridLayout());
row.add(new SaneLabelField(get("m.proxy_auth_required")), BorderLayout.WEST);
_useAuth = new JCheckBox();
+ _useAuth.setSelected(proxyAuth);
row.add(_useAuth);
add(row);
row = new JPanel(new GridLayout());
row.add(new SaneLabelField(get("m.proxy_username")), BorderLayout.WEST);
_username = new SaneTextField();
- _username.setEnabled(false);
+ _username.setText(username);
+ _username.setEnabled(_useAuth.isSelected());
row.add(_username);
add(row);
row = new JPanel(new GridLayout());
row.add(new SaneLabelField(get("m.proxy_password")), BorderLayout.WEST);
_password = new SanePasswordField();
- _password.setEnabled(false);
+ _password.setEnabled(_useAuth.isSelected());
row.add(_password);
add(row);
package com.threerings.getdown.launcher;
import java.io.File;
+import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
+import java.io.InputStream;
import java.io.PrintStream;
import java.net.Authenticator;
import java.net.HttpURLConnection;
import java.util.Iterator;
import java.util.ServiceLoader;
+import jalview.util.LaunchUtils;
+
import ca.beq.util.win32.registry.RegistryKey;
import ca.beq.util.win32.registry.RegistryValue;
import ca.beq.util.win32.registry.RootKey;
port = hostPort[1];
}
+ // look in jalview_properties
+ String[] hostPortAuthUser = jalviewProxyProperties(app);
+ host = hostPortAuthUser[0];
+ port = hostPortAuthUser[1];
+ boolean proxyAuth = Boolean.parseBoolean(hostPortAuthUser[2]);
+ String username = hostPortAuthUser[3];
+
if (StringUtil.isBlank(host)) {
return false;
}
// yay, we found a proxy configuration, configure it in the app
- initProxy(app, host, port, null, null);
+ initProxy(app, host, port, username, null);
return true;
}
+ public static String[] jalviewProxyProperties(Application app) {
+ String host = null;
+ String port = null;
+ boolean proxyAuth = false;
+ String username = null;
+ LaunchUtils.loadChannelProps(app.getAppDir());
+ if (LaunchUtils.getBooleanUserPreference("USE_PROXY")) {
+ host = LaunchUtils.getUserPreference("PROXY_SERVER_HTTPS");
+ port = LaunchUtils.getUserPreference("PROXY_PORT_HTTPS");
+ if (StringUtil.isBlank(host)) {
+ host = LaunchUtils.getUserPreference("PROXY_SERVER");
+ port = LaunchUtils.getUserPreference("PROXY_PORT");
+ }
+ proxyAuth = LaunchUtils.getBooleanUserPreference("PROXY_AUTH");
+ if (proxyAuth) {
+ username = LaunchUtils.getUserPreference("PROXY_AUTH_USERNAME");
+ }
+ }
+ return new String[]{ host, port, String.valueOf(proxyAuth), username };
+ }
+
public static boolean canLoadWithoutProxy (URL rurl)
{
log.info("Testing whether proxy is needed, via: " + rurl);
public static void initProxy (Application app, String host, String port,
String username, String password)
{
+System.out.println("**** initProxy(app, '"+host+"', "+port+", '"+username+"', "+(password==null?"null":"*x"+password.length())+")");
// check whether we have saved proxy credentials
String appDir = app.getAppDir().getAbsolutePath();
ServiceLoader<ProxyAuth> loader = ServiceLoader.load(ProxyAuth.class);
if [ x$JVLVERSION != x ]; then
export VERSION=$JVLVERSION
else
- export VERSION=1.8.3-1.2.10_JVL
+ export VERSION=1.8.3-1.2.11_JVL
fi
if [ x${VERSION%_JVL} = x$VERSION ]; then
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
<packaging>pom</packaging>
- <version>1.8.3-1.2.10_FJVL</version>
+ <version>1.8.3-1.2.11_FJVL</version>
<name>getdown</name>
<description>An application installer and updater.</description>
getdown_alt_java8_max_version = 01089999
getdown_alt_java11_min_version = 11000000
getdown_alt_java11_max_version =
-#getdown_alt_java11_txt_multi_java_location = [windows-amd64] /getdown/jre/windows-jre11.jar,[linux-amd64] /getdown/jre/linux-jre11.tgz,[mac os x] /getdown/jre/macos-jre11.tgz
-#getdown_alt_java8_txt_multi_java_location = [windows-amd64] /getdown/jre/windows-jre1.8.tgz,[linux-amd64] /getdown/jre/linux-jre1.8.tgz,[mac os x] /getdown/jre/macos-jre1.8.tgz
+#getdown_alt_java11_txt_multi_java_location = [windows-amd64] /getdown/jre/jre-11-windows-x64.zip,[linux-amd64] /getdown/jre/jre-11-linux-x64.zip,[mac os x] /getdown/jre/jre-11-mac-x64.zip
+#getdown_alt_java8_txt_multi_java_location = [windows-amd64] /getdown/jre/jre-8-windows-x64.zip,[linux-amd64] /getdown/jre/jre-8-linux-x64.zip,[mac os x] /getdown/jre/jre-8-mac-x64.zip
jre_installs_dir = ~/buildtools/jre
j8libDir = j8lib
flexmark_css = utils/doc/github.css
channel_properties_dir = utils/channels
+channel_props = channel.props
install4j_home_dir = ~/buildtools/install4j8
install4j_copyright_message = ...
#j2s.compiler.nonqualified.classes = null
#j2s.compiler.mode = debug
#a semicolon-separated list of package (foo.) or class (foo.bar) replacements to be made
-j2s.class.replacements = org.apache.log4j.->jalview.javascript.log4j.
+#j2s.class.replacements = org.apache.logging.log4j.->jalview.javascript.log4j.
j2s.template.html = utils/jalviewjs/template.html
j2s_coretemplate_html = utils/jalviewjs/coretemplate.html
#output file name for logging methods declared - delete the file to regenerate a listing
<mapID target="pdbmcviewer" url="html/features/pdbviewer.html"/>
<mapID target="pdbjmol" url="html/features/jmol.html"/>
<mapID target="chimera" url="html/features/chimera.html"/>
+ <mapID target="pymol" url="html/features/pymol.html"/>
<mapID target="chimera.annotxfer" url="html/features/chimera.html#annotxfer"/>
<mapID target="varna" url="html/features/varna.html"/>
<mapID target="xsspannotation" url="html/features/xsspannotation.html"/>
<mapID target="importvcf" url="html/features/importvcf.html" />
<mapID target="importvcf.attribs" url="html/features/importvcf.html#attribs" />
+ <mapID target="logging" url="html/logging.html" />
</map>
<tocitem text="Virtual Features in CDS/Protein Views" target="splitframe.virtualfeats"/>
<tocitem text="VCF Variant Attributes" target="importvcf.attribs"/>
<tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
-
+ <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
</tocitem>
<tocitem text="Editing Alignments" target="edit" />
</tocitem>
<tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
- <tocitem text="PDB Structure Chooser" target="pdbchooser" />
+ <tocitem text="PDB & 3D-Beacons Structure Chooser" target="pdbchooser" />
<tocitem text="Jmol Viewer" target="pdbjmol" />
- <tocitem text="Chimera Viewer" target="chimera" />
+ <tocitem text="Chimera Viewer" target="chimera" />
+ <tocitem text="Pymol Viewer" target="pymol" />
</tocitem>
<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
<tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
</tocitem>
</tocitem>
<tocitem text="Preferences" target="preferences" />
+ <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
<tocitem text="Scripting with Groovy" target="groovy">
<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
</tocitem>
available in Jalview applet due to AWT 1.1 limitations</em>)</li>
</ul>
</p>
+ <hr />
<p>
<strong><a name="groupdefs">SEQUENCE_GROUP</a></strong><br />
Groups of sequences and column ranges can be defined using a tab
<p>The sequences can be defined by alignment index and a range of
sequences can be defined in a comma delimited field such as</p>
<p>2-5,8-15,20,22</p>
- <p>Enter * to select all groups.</p>
+ <p>Enter * to select all sequences.</p>
+ <p>Set both <em>Group_Start</em> and <em>Group_End</em> to * to include the full sequence(s) range.
<p>
<strong>Note:</strong> If the alignment indices are not known, enter
-1, followed by a tab and then a tab delimited list of sequence IDs.
</head>
<body>
<p>
- <strong>The Chimera Viewer</strong>
+ <strong>The Chimera and ChimeraX Viewers</strong>
</p>
<p>
Since Jalview 2.8.2, <a href="http://www.cgl.ucsf.edu/chimera/">Chimera</a>
(http://www.cgl.ucsf.edu/chimera/) can be used for viewing
structures opened via the <a href="structurechooser.html"><strong>"View
- Structure Data.."</strong> dialog</a>.
+ Structure Data.."</strong> dialog</a>. In Jalview 2.11.2, support
+ was also added for ChimeraX.
</p>
<p>
You can set a default choice of Jmol or Chimera structure viewer in
parameters, then include it at the beginning of the command line to
ensure they are processed before any remaining arguments.
<br>
+ Typical command line execution follows the following pattern:
+ <pre>
+ jalview -open <Alignment File/URL> [additional import arguments] [export arguments]
+ </pre>
+
<table width="100%" border="1" cellspacing="0" cellpadding="0">
<tr>
<td width="27%"><div align="center">-nodisplay</div></td>
User Interface. (automatically disables questionnaire, version
and usage stats checks)</div></td>
</tr>
-
+ <tr>
+ <td><div align="center">-open FILE/URL</div></td>
+ <td><div align="left">Specify the alignment file to
+ open or process by providing additional arguments.</div></td>
+ </tr>
<tr>
<td><div align="center">-props FILE/URL</div></td>
<td><div align="left">Use the given Jalview properties
<ul>
<li>Standard installation on Linux/Unix:<pre>
- /PATH_TO_JALVIEW/Jalview -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
+ /PATH_TO_JALVIEW/Jalview -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
</li>
<li>Standard installation on Windows:<pre>
\PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa</pre>
</p>
<p>
<strong>Passing JVM Arguments to Jalview</strong><br /> If you need
- to modify parameters for Jalview's Java Virtual Machine, then take a
- look at the instructions for how to <a href="../memory.html#jvm">setting
- the JVM's maximum memory</a>.
+ to modify parameters for Jalview's Java Virtual Machine, or
+ configure system properties, then take a look at the instructions
+ for how to <a href="../memory.html#jvm">setting the JVM's
+ maximum memory</a>.<br />
+ <p>
+ <strong>Changing Jalview's 'Look and Feel'</strong> <br />If you
+ are experiencing issues with the font size or layout of Jalview's
+ GUI, you can try changing Jalview's 'Look and feel' by
+ specifying a custom system property 'laf' on startup (see <a
+ href="../memory.html#jvm">setting the JVM's memory</a> for
+ instructions on how to do this for your platform). <br />For the
+ Jalview standalone executable jar, simply provide one of the
+ property settings before the -jar argument
</p>
+ <ul>
+ <li>-Dlaf=system (default look and feel for the OS)</li>
+ <li>-Dlaf=crossplatform (Java's Metal Look and Feel)</li>
+ <li>-Dlaf=nimbus (Java's alternative Nimbus Look and Feel)</li>
+ <li>-Dlaf=mac (only has an effect on OSX)</li>
+ <li>-Dlaf=gtk (only has an effect on Linux)</li>
+ </ul>
+ The currently configured look and feel is logged to Jalview's console.
+ Once the look and feel has been changed, it will be stored in
+ Jalview's .jalview_properties file for future Jalview sessions.
+
<p> </p>
<p> </p>
</body>
installation of Groovy. Just select <strong>Tools→Groovy
Console...</strong> from the Jalview Desktop's drop-down menu. After a
short pause, you should then see the <a
- href="http://groovy-lang.org/groovyconsole.html">Groovy
+ href="https://groovy-lang.org/groovyconsole.html">Groovy
Console</a> appear. This allows you to interactively execute Groovy
scripts whilst Jalview is running. We've also provided a <strong>Calculations→Execute
Groovy Script</strong> button so you can execute the currently loaded
InstallAnywhere version of Jalview, you can find additional groovy
scripts in the examples/groovy subfolder of the installation
directory. The examples are also available at <a
- href="http://www.jalview.org/examples/groovy">http://www.jalview.org/examples/groovy</a>.
+ href="https://www.jalview.org/examples/groovy">https://www.jalview.org/examples/groovy</a>.
</p>
<p>
<em>Using Groovy to add new Alignment Calculations</em><br />We've
<em>Creating custom colourschemes</em><br/>
You can create your own alignment colourschemes with a groovy script. We've provided two examples:<br/>
<ul>
- <li><a href="http://www.jalview.org/examples/groovy/colourConserved.groovy">colourConserved.groovy</a> creates an 'Conserved' colourscheme - similar to the classic <a href="http://www.nrbsc.org/old/gfx/genedoc/">GeneDOC</a> shading model.</li>
- <li><a href="http://www.jalview.org/examples/groovy/colourUnconserved.groovy">colourUnconserved.groovy</a> creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink.</li>
+ <li><a href="https://www.jalview.org/examples/groovy/colourConserved.groovy">colourConserved.groovy</a> creates an 'Conserved' colourscheme - similar to the classic <a href="http://www.nrbsc.org/old/gfx/genedoc/">GeneDOC</a> shading model.</li>
+ <li><a href="https://www.jalview.org/examples/groovy/colourUnconserved.groovy">colourUnconserved.groovy</a> creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink.</li>
</ul>
</p>
<pre>
# Jalview Launch File
# Please install the Jalview Desktop from
-# http://www.jalview.org/getdown/release
+# https://www.jalview.org/getdown/release
# and then try to open this file again
jalview.apparg=-open
-jalview.apparg=http://www.jalview.org/examples/jpred_msa.fasta
+jalview.apparg=https://www.jalview.org/examples/jpred_msa.fasta
jalview.apparg=-annotations
-jalview.apparg=http://www.jalview.org/examples/jpred_msa.seq.concise
+jalview.apparg=https://www.jalview.org/examples/jpred_msa.seq.concise
jalview.apparg=-colour
jalview.apparg=Clustal
</pre>
# Please install the Jalview Desktop from
# http://www.jalview.org/getdown/release
# and then try to open this file again
-appbase=http://www.jalview.org/getdown/archive/2_10_5/
+appbase=https://www.jalview.org/getdown/archive/2_10_5/
</pre>
For security, the Jalview application will only allow
<em>appbase</em> URLs from www.jalview.org.
<em>Add Temperature Factor annotation to alignment</em> - if
selected, values extracted from the Temperature Factor column for
the backbone atoms in the PDB file will be extracted as annotation
- lines shown on the alignment.
+ lines shown on the alignment.<br/><em>Since 2.11.2, scores from the Temperature Column for structures imported via the 3D-Beacons network may be shown instead as model quality or reliability scores.</em>
<p>
- <em>Default structure viewer</em> - choose Jmol or CHIMERA for
+ <em>Default structure viewer</em> - choose Jmol, CHIMERA, CHIMERAX or PYMOL for
viewing 3D structures.
<p>
- <em>Path to Chimera program</em> - Optional, as Jalview will search
- standard installation paths for Windows, Linux or MacOS. If you have
- installed Chimera in a non-standard location, you can specify it
- here, by entering the full path to the Chimera executable program.
- Double-click this field to open a file chooser dialog.
- <p>
+ <em>Path to Chimera/X/Pymol program</em> - Optional, as Jalview will search
+ standard installation paths for Windows, Linux or MacOS. If Jalview cannot locate the installation for your selected structure viewer, a dialog will be shown. If you have
+ installed the chosen viewer in a non-standard location, you can specify it
+ here, by entering the full path to its executable.<br/>For Chimera, locate the path to the chimera program, similarly for ChimeraX and Pymol. Rather than typing in the path, you can also <em>double-click this field</em> to open a file chooser dialog.</p>
<p>
<em>PDB Fields shown in Search and Structure Summaries</em> - ticks
in this table indicate fields shown by default when browsing results
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>The Pymol PDB Viewer</title>
+</head>
+<body>
+ <p>
+ <strong>The Pymol Viewer</strong>
+ </p>
+ <p>
+ In Jalview 2.11.2, support was added for viewing structures opened
+ via the <a href="structurechooser.html"><strong>"View
+ Structure Data.."</strong> dialog</a> with <a
+ href="https://pymol.org/2/">Pymol</a> (https://pymol.org/2/). Like
+ with <a href="chimera.html">Chimera and ChimeraX</a>, Pymol views
+ can be saved and restored from Jalview Project files on any machine
+ with it installed, and structures can be coloured and superimposed
+ according to the alignment.
+ </p>
+ <p>
+ <em>Configuring Jalview to use Pymol</em><br /> You can configure
+ Pymol as your preferred structure viewer in <a
+ href="preferences.html#structure"> Preferences</a>. Jalview will
+ look for an existing installation, and will ask you to specify the
+ installation's path if it cannot be found. You can also optionally
+ specify the path to the Pymol program here if you want Jalview to
+ use a specific installation.
+ </p>
+ <p>
+ <strong>Jalview requires Pymol V 2.5.0 (community edition)
+ or later</strong> <br />Jalview requires Pymol's RPC interface, which is
+ not available in older versions of the Pymol community edition.
+ </p>
+ <p>
+ <strong>Known Limitations</strong><br />
+ </p>
+ <ul>
+ <li>Pymol does not support some forms of legacy structural data
+ (e.g. the 1A70 C-alpha only PDB file included in the Jalview
+ example project).</li>
+ <li>Pymol to Jalview communication does not support transfer of
+ properties or highlighting sequence regions corresponding to
+ structure selections or mouse-overs in Pymol.</li>
+ <li>Jalview to Pymol communication currently doesn't highlight
+ the positions on structures corresponging to moused over residues
+ in Jalview.</li>
+ </ul>
+ <p>
+ Basic screen operations (see <a
+ href="https://pymol.org/dokuwiki/doku.php?id=mouse">Pymol Wiki</a>
+ at https://pymol.org/dokuwiki/doku.php?id=mouse for full details).
+ <table border="1">
+ <tr>
+ <td><strong>Action</strong></td>
+ <td><strong>Windows</strong></td>
+ <td><strong>Unix</strong></td>
+ <td><strong>Mac/OSX</strong></td>
+ </tr>
+ <tr>
+ <td>Rotate View</td>
+ <td>Left Click and Drag</td>
+ <td>Left Click and Drag</td>
+ <td>Left Click and Drag</td>
+ </tr>
+ <tr>
+ <td>Zoom</td>
+ <td>Right Click<br> drag mouse up or down
+ </td>
+ <td>Right Click<br>drag mouse up or down
+ </td>
+ <td>cmd or Right + Click and drag mouse up or down, <br>or
+ use mouse scroll button
+ </td>
+ </tr>
+ <tr>
+ <td>Move Origin</td>
+ <td>Middle Button + Drag</td>
+ <td>Middle Button and drag</td>
+ <td>alt + Click<br> and drag
+ </td>
+ </tr>
+ <tr>
+ <td>Select Residues</td>
+ <td>Ctrl + Click (and drag to select a region)</td>
+ <td>Ctrl + Click (and drag)</td>
+ <td>Ctrl + Click (and drag)</td>
+ </tr>
+ </table>
+ </p>
+ <p>
+ <strong>Jalview Controls</strong>
+ <p>The Jalview Pymol View window has up to five menus:</p>
+ <ul>
+ <li><Strong>File<br>
+ </strong>
+ <ul>
+ <li><strong>View Mapping<br>
+ </strong><em> Opens a text window showing the alignment between the
+ residues corresponding to alpha-carbon atoms in the PDB
+ structure and the residues in the associated sequence.</em></li>
+ </ul></li>
+ <li><strong>View</strong>
+ <ul>
+ <li><strong>Show Chains<br>
+ </strong><em>Select which of the PDB file's chains (if more than
+ one) are to be displayed.</em></li>
+ <li><strong>Colour by ..<br></strong><em>Submenu
+ allowing specific alignment views to be selected for
+ colouring associated chains in the structure display. This
+ menu contains all the alignment views associated with the
+ structure view, with those used to colour the view indicated
+ by ticks. Addditionally, it contains the following menu
+ entries:</em>
+ <ul>
+ <li><strong>Select many views<br></strong><em>When
+ this option is enabled, selecting an alignment view adds
+ it to the set used to colour the structures. Use this
+ when colouring structures related to a number of
+ alignments involving different domains or chains which
+ are shown in the same structure view.</em></li>
+ <li><strong>Select all views<br></strong><em>This
+ is only enabled when </em><strong>Select many views</strong><em>
+ is also enabled, and will add all associated views to
+ the set used to colour the structure display.</em></li>
+ <li><strong>Invert selection<br></strong><em>This
+ is only enabled when </em><strong>Select many views</strong><em>
+ is also enabled, and will replace the current set of
+ views with any remaining views not currently used to
+ colour the structure display.</em></li>
+ </ul></li>
+ </ul>
+ <li><strong>Colours<br>
+ </strong>
+ <ul>
+ <li><strong>By Sequence<br>
+ </strong><em> Colours each residue in the structure with the colour
+ of its corresponding residue in the associated sequence as
+ rendered in the associated alignment views, including any
+ UniProt sequence features or region colourings.<br />Pick
+ which of the associated alignment views are used to colour
+ the structures using the <strong>View→Colour
+ by ..</strong> sub menu.
+ </em><br> Residues which only exist in the PDB structure are
+ coloured white if they are insertions (relative to the
+ associated sequence in the alignment) and grey if they are N
+ or C terminal flanks outside the region mapped to the
+ alignment window's sequence.</em></li>
+ <li><strong>By Chain<br>
+ </strong><em>Uses Pymol's 'spectrum(chain)' command to apply a
+ different colour to each chain.</em></li>
+ <li><strong>Charge & Cysteine<br>
+ </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid
+ or Glutamic Acid) residues in red, and cationic (Lysine or
+ Arginine) residues in blue.</em></li>
+ <li><strong>Colour with Pymol<br></strong><em>Defers
+ any colouring operations to Pymol. Select this if you want
+ to use the Pymol scripting interface or menu to modify the
+ view directly.</em></li>
+ <li><strong>Standard and User Defined Jalview
+ colourschemes.<br>
+ </strong><em>The remaining entries apply the colourschemes available
+ from the standard and user defined <a
+ href="../colourSchemes/index.html">amino acid colours</a>.
+ </em></li>
+ </ul></li>
+ <li><strong>Pymol<br>
+ </strong><em>This pulldown menu provides access to Pymol's capabilities
+ from Jalview.</em>
+ <ul>
+ <li><strong><a name="sAlign">Align</a> <br> </strong><em>
+ When selected, the associated alignment will be used to
+ superimpose all the structures in the view onto the first
+ structure in the alignment via the pair_fit command. The regions used to calculate
+ the superposition will be highlighted using the 'Cartoon'
+ rendering style, and the remaining data shown as a chain
+ trace. RMSD values are output in the Pymol log.<br /> <br />
+ </em></li>
+ <li><a name="annotxfer"><strong>Write Jalview
+ features</strong></a><br /> <em>Selecting this option will create
+ new atom properties for any features currently visible in
+ the associated alignment views. This allows those atoms to
+ be selected and analysed in Pymol directly. </em><br>
+ <ul>
+ <li>Feature transfer in Pymol is experimental.</li>
+ <li>To select by a particular feature use the string
+ matching syntax:<br> select foo,p.jv_helix in helix
+ </li>
+ <li>To view transferred properties use Pymol's
+ Properties Inspector</li>
+ <li>For more information see <a
+ href="https://pymol.org/dokuwiki/doku.php?id=properties#selection_language">Property
+ based selection in Pymol's Documentation</a>.
+ </li>
+ </ul></li>
+ </ul></li>
+ <li><strong>Help<br>
+ </strong>
+ <ul>
+ <li><strong>Pymol Help<br>
+ </strong><em>Access the Pymol Help documentation in a new browser
+ window. window.</em></li>
+ </ul></li>
+ </ul>
+ <p>
+ <strong>Pymol and Windows Firewall</strong>
+ </p>
+ Jalview and Pymol communicate using the
+ <a href="https://pymolwiki.org/index.php/RPC">Pymol's XML-RPC over
+ HTTP interface</a>(https://pymolwiki.org/index.php/RPC).
+
+ <br> Technically this requires both Pymol and Jalview to open
+ ports on the local network, and this may be blocked by Windows
+ Firewall with a warning message such as
+ <br /> "Windows Firewall has blocked some features of this program"
+ (where the program may be java.exe or javaw.exe).
+ <br /> To allow Jalview and Pymol to interact, you may need to add
+ permission for the program to communicate over the network. This can
+ be done from the warning dialogue, or in Control Panel, Firewall
+ settings.
+</body>
+</html>
</p>
<p>The search box is displayed by pressing Control and F or
selecting "Find..." from the "Search" menu.</p>
- <img src="search.png" width="398" height="124">
+ <img src="search.png" width="400" height="152">
<p>"Find next" will find the next occurrence of the
specified and adjust the alignment window view to show it, and
"Find all" highlights all matches for a pattern. The
of posix and perl style regex - see below for a summary)</li>
<li>Gaps are ignored when matching the query to the sequences
in the alignment.</li>
+ <li>Hidden columns can optionally be ignored (<em>since Jalview 2.11</em>)</li>
<li>The search is applied to both sequences and their IDs, and
optionally also to the description string (<em>since Jalview
2.10</em>)
</li>
<li>If a region is selected, then search will <strong>only</strong>
- be performed on that region.
+ be performed on that region.<br />
+ <em>Tip: to quickly clear the current selection, click the
+ alignment view you wish to search, then press 'Escape'.</em>
</li>
- <li>To quickly clear the current selection, press the
- "Escape" key.</li>
<li>Tick the "Match Case" box to perform a case
sensitive search.</li>
- <li>To access a <a ref="#queryhistory">previously used
+ <li>To access a <a href="#queryhistory">previously used
query</a> press the down arrow or click on the button on the right
of the text field.
</ul>
stored along with your Jalview user preferences. To open the search
history, click on the button to the right of the query field, or
press the down arrow key.</p>
- <img src="searchhist.png" width="404" height="185" align="left" />
- <p>The search history keeps up to 99 queries by default. To clear
+ <p><img src="searchhist.png" width="404" height="185" />
+ </p><p>The search history keeps up to 99 queries by default. To clear
the history, or modify the size of the history, right-click the text
box.</p>
- <img src="searchclearhist.png" width="402" height="127" align="left" />
- <p>
+ <p><img src="searchclearhist.png" width="402" height="127"/>
+ </p>
+<p width="100%">
<strong>Other dialogs that provide a query history</strong>
</p>
<p>
the database you want to retrieve sequences</strong> from the database
chooser.
</p>
- <img src="selectfetchdb.gif" align="left" width="480" height="204"
+ <img src="selectfetchdb.gif" align="left"
alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
<p>
The databases are shown as a tree, and ordered alphabetically;
accession ids</strong> (as a semi-colon separated list), or press the
"Example" button to paste the example accession for the
currently selected database into the retrieval box. Finally, press
- "OK" to initiate the retrieval.</li>
+ "OK" to initiate the retrieval.
+ <br />
+ For the PDB and UniProt sequence fetchers, choose the "Retrieve IDs" tab
+ to search for accession ids.</li>
</ol>
- <p>If you use the WSDBFetch sequence fetcher services (EMBL,
- UniProt, PFAM, and RFAM) in work for publication, please cite:</p>
- <p>
- Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
- J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
- R. <br> SOAP-based services provided by the European
- Bioinformatics Institute.<br> Nucleic Acids Res. 33(1):W25-W28
- (2005) <br> <br>
- </p>
+ <p>If you use the Sequence Fetcher, please remember to cite the
+ corresponding services (linked to below):</p>
+ <ul>
+ <li>Ensembl - <a
+ href="https://github.com/Ensembl/ensembl-rest/wiki#citing">The
+ Ensembl REST API</a></li>
+ <li>EMBL/EMBLCDS - Provided by the <a
+ href="https://www.ebi.ac.uk/ena/browser/api/#/ENA_Browser_Data_API/getFlatFileUsingGET">European
+ Nucleotide Archive's ENA Data API</a><br />
+ <em>Note: Versions of Jalview prior to 2.11.1.1 employed the
+ XML endpoint of the ENA browser, which was retired in August
+ 2020.</em></li>
+ <li>Uniprot - Free Text Search and Retrieval via the <a
+ href="https://www.uniprot.org/help/api">Uniprot REST API</a></li>
+ <li>PDB - Free Text Search via the <a
+ href="https://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
+ REST API</a> and retrieval via <a
+ href="https://www.ebi.ac.uk/Tools/dbfetch/">WSDbFetch</a><br />
+ Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
+ J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
+ R. <br> SOAP-based services provided by the European
+ Bioinformatics Institute.<br> Nucleic Acids Res.
+ 33(1):W25-W28 (2005) <br> <br>
+ </li>
+ </ul>
</body>
</html>
The Structure Chooser allows you to select
3D structures to view for the currently selected set of
sequences. It is opened by selecting the <strong>"3D
- Structure Data..."</strong> option from the Sequence ID panel's <a
- href="../menus/popupMenu.html">pop-up menu</a>. The dialog
+ Structure Data..."</strong> option from the Sequence ID panel's
+ <a href="../menus/popupMenu.html">pop-up menu</a>. <br/>
+ <img src="3dstructuredata_popupmenu.png" alt="pop-up menu"/>
+ <br/>
+ The dialog
provides:
</p>
<ul>
associated with the sequence. It does this based on the sequence's
ID string, and any other associated database IDs. <br />
<br />
+ Since Jalview 2.11.2, you can also <a href="#3dbeaconssearch">initiate a search
+ of the 3D-Beacons Network</a>.
+ </p>
<p>
<strong><a name="cachedstructview">Viewing existing
structures for your sequences</a></strong>
</p>
<p>Jalview can automatically select the best structures according
to meta-data provided by the PDB. For alignments with no existing
- structure data, the 'Best Quality' structure for each sequence will
+ structure data, the 'PDBe Best Quality' structure for each sequence will
by default be selected, but clicking on the drop down menu allows
other criteria to be chosen, including Resolution (only defined for
X-Ray structures), Highest Protein Chain etc. When 'Invert' is
<br>The screenshot above shows the Structure Chooser displayed after
selecting all the sequences in the Jalview example project. If no
structures were auto-discovered, options for manually associating
- PDB records will be shown (see below).<p>
+ PDB records will be shown (see below).
+
+ <p>
+ <strong><a name="3dbeaconssearch">3D-Beacons Network Search</a></strong>
+ </p>
+ <p>
+ To initiate a search of the 3D-Beacons Network—which searches
+ across experimentally determined and predicted structure models from
+ several resources including PDBe, AlphaFold DB, SWISS-MODEL, PED, SASDB, Genome3D and
+ PDBe-KB—click on the <strong>3D-Beacons Search</strong> button at the top of the
+ Structure Chooser window.
+ <br/>
+ <img src="3dbeacons_button.png"/>
+ <br/>
+ The 3D-Beacons Network search requires UniProt references and Jalview will ask
+ to attempt to fetch these references for the selected sequences.
+ UniProt references might not always be found in which case you can revert to the PDB
+ search.
+ <br/>
+ <img src="3dbeacons_structurechooser.png"/>
+ <br/>
+ If structures are found through the 3D-Beacons network you can filter which structures
+ are shown using the drop-down filter at the top of the Structure Chooser window.
+ <br/>
+ You can view information about each related model, such as the resource providing
+ each model, in the columns displayed. You can sort the list of models by clicking on
+ column headings.
+ <br/>
+ Select and view the structures in the usual way using the <a href="viewingpdbs.html#afterviewbutton">open structure options</a> at
+ the bottom of the Structure Chooser window.
+ </p>
+
+ <p>
<strong>Exploration of meta-data for available structures</strong>
</p>
<p>Information on each structure available is displayed in columns
2.9. </em>
</p>
</body>
-</html>
\ No newline at end of file
+</html>
</head>
<body>
<p>
- <strong>Discovering and Viewing PDB Structures</strong>
+ <strong>Discovering and Viewing PDB and 3D-Beacons structures</strong>
</p>
Jalview can be used to explore the 3D structures of sequences in an
alignment by following the steps below:
menu</a> to open the <a href="structurechooser.html">Structure
Chooser</a> dialog box.
<ul>
- <li>If one or more structures exists for the given
+ <li>If one or more structures exist in the PDB for the given
sequence, the <a href="structurechooser.html">Structure
Chooser</a> dialog will open with them listed in the results
pane.
href="structurechooser.html">Structure Chooser</a> interface
will present options for manual association of PDB structures.
</li>
+ <li>
+ Since Jalview 2.11.2 you can also search the 3D-Beacons Network
+ for structures. The 3D-Beacons Network acts as a one-stop shop for protein
+ structures by combining and standardising data from several providers.
+ See <a href="structurechooser.html#3dbeaconssearch">3D-Beacons Search</a> for
+ instructions.
+ </li>
</ul>
</li>
- <li><strong>Selecting Structures</strong><br />You can select
+ <li><strong>Selecting PDB Structures</strong><br />
+ If one or more structures have been found from the PDB, you can select
the structures that you want to open and view by selecting them
with the mouse and keyboard.<br />By default, if structures were
discovered, then some will already be selected according to the
<strong>Structure Viewers in the Jalview Desktop</strong><br /> The
<a href="jmol.html">Jmol viewer</a> has been included since Jalview
2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>,
- provided it is installed and can be launched by Jalview. The default
+ provided it is installed and can be launched by Jalview. ChimeraX and PyMOL
+ support is included from Jalview 2.11.2. The default
viewer can be configured in the <a href="preferences.html#structure">Structure
tab</a> in the <strong>Tools→Preferences</strong> dialog box.
for more information.
</p>
<p>
- <img src="schooser_viewbutton.png"
- style="width: 465px; height: 81px" /><br/> <strong><a
+ <strong><a
name="afterviewbutton">Controlling where the new structures
will be shown</a></strong>
+ <br/>
+ <img src="schooser_viewbutton.png" />
<br />The Structure Chooser offers several options
- for viewing a structure. <br/><strong>New View</strong> will open a new
+ for viewing a structure. <br/>
+ The <strong>Open new structure view</strong> button will open a new
structure viewer for the selected structures, but if there are views
already open, you can select which one to use, and press the <strong>Add</strong>
button. Jalview can automatically superimpose new structures based
</ol>
<strong>Please note: The 2.10.2 feature counting interface is not compatible with earlier versions.</strong><br/><br/>
<em><a
- href="http://www.jalview.org/examples/groovy/featuresCounter.groovy">http://www.jalview.org/examples/groovy/featuresCounter.groovy</a>
+ href="https://www.jalview.org/examples/groovy/featuresCounter.groovy">https://www.jalview.org/examples/groovy/featuresCounter.groovy</a>
- rendered with <a href="http://hilite.me">hilite.me</a></em>
<!-- HTML generated using hilite.me --><div style="background: #f8f8f8; overflow:auto;width:auto;border:solid gray;border-width:.1em .1em .1em .8em;padding:.2em .6em;"><pre style="margin: 0; line-height: 125%"><span style="color: #408080; font-style: italic">/*</span>
<span style="color: #408080; font-style: italic"> * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)</span>
<p>
For more information, you might also want to take a look at the
documentation section of the Jalview website (<a
- href="http://www.jalview.org/about/documentation">http://www.jalview.org/about/documentation</a>).
+ href="https://www.jalview.org/about/documentation">https://www.jalview.org/about/documentation</a>).
</p>
<p>
If you are using the Jalview Desktop application and are looking for
google the online version of these pages. If you don't find what you
are looking for, or want to report a bug or make a feature request,
then get in contact over at <a
- href="http://www.jalview.org/community">http://www.jalview.org/community</a>
+ href="https://www.jalview.org/community">https://www.jalview.org/community</a>
+ </p>
+ <p>
+ <strong>Logging, troubleshooting and reporting bugs</strong><br />If
+ something seems to be wrong with your Jalview installation, or you
+ think you've found a problem, take a look at <a href="logging.html">Jalview's
+ logging and bug reporting</a> documentation.
</p>
-
<p>
<strong>Citing Jalview</strong><br />If you use Jalview in your
work, please cite the Jalview 2 paper in Bioinformatics:
<td><strong>Cursor Keys<br> (Arrow Keys)
</strong></td>
<td>Cursor</td>
- <td>Move cursor around alignment</td>
+ <td>Move cursor around alignment.<br /> Press SHIFT to move
+ cursor from an aligned region to next gap, or to the next
+ aligned region when at a gap.
+ </td>
</tr>
<tr>
<td><strong>Cursor Keys<br> (Arrow Keys)
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>The Java Console, Logging and Reporting Bugs</title>
+</head>
+<body>
+ <p>
+ <strong>The Java Console, Logging and Reporting Bugs<br /></strong>
+ </p>
+ <p>
+ Like most programs, Jalview contains bugs, despite our best efforts.
+ However, Jalview also produces a series of messages during its
+ operation, often referred to as 'logs'. These logs provide a record
+ of Jalview's operation. They can also be extremely useful when <a
+ href="#reportingbugs">reporting bugs</a>, since they help the
+ Jalview developers diagnose and find a workaround for specific
+ problems that you might encounter.
+ </p>
+ <p>
+ The primary place to look for logs is in the <a href="#java_console">Java
+ Console</a> which you can open from within Jalview by going to the <em>Tools</em>
+ menu and checking the box next to <em>Show Java Console</em>. This
+ option is stored in your Jalview preferences file and so is
+ remembered across Jalview sessions.
+ </p>
+ <p>The Java Console will show you information about what the
+ Jalview application is doing (often in the background) whilst it is
+ running.</p>
+ <p>However, when tracking down problems preventing Jalview from
+ starting up properly, you need to look at the startup logs - which
+ are not shown in the Jalview Console. The location of these depends
+ on how you launched Jalview:</p>
+ <p>
+ <strong>Jalview Desktop Installation Launch Logs</strong><br />If you are using
+ a standard desktop version of Jalview installed from one of our
+ install4j installers, then messages about Jalview's initial launch
+ can be found in
+ <pre>JALVIEW_APP_DIR/launcher.log</pre>
+ where
+ <em>JALVIEW_APP_DIR</em> is the directory that Jalview's application
+ was installed into.
+ <br /> For Jalview 2.11.0 onwards:
+ <ul>
+ <li>In Windows this is <em>%APPDATA%\Local\Jalview</em> by
+ default
+ </li>
+ <li>In macOS this is <em>/Applications/Jalview.app/Contents/Resources/app</em>
+ by default
+ </li>
+ <li>In Linux and other Unix OSes this is <em>~/opt/jalview</em>
+ by default
+ </li>
+ </ul>
+ <p><strong>Jalview Executable Jar Launch Logs</strong><br/>If you are using the Jalview executable jar file (also
+ used by bioconda and OSX homebrew installations) then the default run class (
+ <em>jalview.bin.Launcher</em> -- a minimised launcher that will set
+ memory and linux dpi settings before re-launching
+ <em>jalview.bin.Jalview</em>), will output logging information to
+ STDOUT and STDERR.
+ </p>
+
+ <p><strong>
+ <a name="java_console">Java Console and Log Level</a>
+ </strong></p>
+ <p>
+ The Java Console is opened by selecting <strong>Tools
+ → Show Java Console</strong>. The visibility of the console is stored
+ in your preferences, so if you quit Jalview with the console open,
+ it will be shown the next time you start Jalview. You can close the
+ console by selecting the same menu option again, or just closing the
+ console window.
+ </p>
+ <p>The Java Console's text display always shows information about
+ your system and Jalview installation details. The rest are the most
+ recent messages output during your Jalview session. Some messages
+ are only captured by the console when it is open, so to get a full
+ log for debugging a problem, enable the console and then restart
+ Jalview.</p>
+
+ <p>
+ Jalview logging will automatically scroll the text in the Java Console
+ but if you want to examine a particular part of the logs whilst logging
+ is still going on you can click on any part of the text area to
+ stop this behaviour. A border should appear arround the
+ text area to signify that autoscroll has been turned off. You can
+ toggle the autoscroll behaviour on and off by clicking again on the
+ text area.
+ </p>
+ <p>
+ You can temporarily control the detail of what appears as output by
+ selecting a <em>Log level</em> using the drop-down list at the
+ bottom left of the console. There are several levels to choose from:
+ The most verbose is TRACE, followed by DEBUG, INFO, WARN. When the
+ Console is opened, the default level will be chosen (INFO).
+ </p>
+ <p>
+ <strong>Note! If you change the log level in the Java
+ Console, this change will only persist for as long as the console
+ is open. Once you close the console the log level will revert back
+ to what it had been when you opened the console (usually INFO).</strong>
+ </p>
+ <p><strong>Permanently changing Jalview's default log level</strong><br/>
+ You can change the default log level by editing the Jalview
+ preferences file, <em>.jalview_properties</em>, found in your home
+ directory (on Windows: %HOMEPATH%, or the folder above 'My
+ Documents'; on macOS: ~ or /Users/<em>username</em>; on linux/unix:
+ ~ or /home/<em>username</em>), and setting the property <em>logs.Jalview.level</em>
+ to the log level you prefer, e.g.
+ <pre>
+ logs.Jalview.level=DEBUG
+ </pre>
+ You can also set the property
+ <pre>
+ logs.Axis.level=DEBUG
+ </pre>
+ <p>to get debug information for Jalview's JPred service. The Axis log
+ level cannot be set from within the Java Console.
+ </p>
+ <p>
+ You can also set the <em>logs.jalview.level</em> property to a log level
+ not usually presented in the Java Console (though restricted to log
+ levels used by Apache Log4j -- see <a
+ href="https://logging.apache.org/log4j/2.x/manual/customloglevels.html">Log4j
+ Custom Log Levels</a> for details of the standard log levels
+ available). Jalview does not currently define any custom log levels.
+ If you do set the property with a log level that is normally not
+ visible in the Java Console this should be respected and visibly
+ selected when you open the console.
+ </p>
+ <p>
+ The <em>Clear</em> button at the bottom of the console will clear
+ all logging messages except for the initial system information which
+ is rewritten to the console.
+ </p>
+ <p>
+ The <em>Copy to clipboard</em> button at the bottom right of the
+ console will copy all of the text in the console to your system
+ clipboard, ready to paste into another application (e.g. email
+ composer or issue tracker).
+ </p>
+
+ <p><strong><a name="reportingbugs">Reporting Bugs</a></strong></p>
+
+ <p>
+ If you come across a problem in Jalview where something is not
+ working as described, or how you think it should, you should first
+ check the <a href="https://www.jalview.org/faq">Jalview FAQ</a> to
+ see if this is a known problem and if there is a suggested
+ workaround.
+ </p>
+ <p>
+ If there is no FAQ answer covering your problem then you can submit
+ a bug report on the <a href="https://issues.jalview.org/">Jalview
+ Issue Tracker</a>. It is good practice to search the issue tracker
+ first to see if the issue has already been reported. If an issue
+ already exists please continue to add your own comments to the issue
+ which may well help narrow down the problem, if not then you can
+ create an account and submit a new bug report:
+ </p>
+ <p>
+ Make sure that you set Project to <em>Jalview (JAL)</em>, and Issue
+ Type to <em>Bug</em> or <em>New Feature</em> or <em>Improvement</em>
+ appropriately.<br /> Give a one line summary of the issue in the <em>Summary</em>.
+ <br /> In the <em>Environment</em> text box you can describe the
+ system you are using. This is usually most easily done by opening
+ the Java Console, clicking the <em>Clear</em> button, and then
+ immediately on the <em>Copy to clipboard</em> button, and then
+ pasting the clipboard into the text box.
+ </p>
+ <p>
+ You can then give more detailed information about how to recreate
+ the problem in the <em>Description</em> text box. If you want to
+ attach any screenshots or example alignment files that demonstrate
+ the problem then you can drag them to the Create Issue dialog in
+ your browser, or use the <em>Attachment</em> browse facility to
+ locate them on your computer.
+ </p>
+
+ <p>
+ To help the Jalview team with diagnosing a particular issue, it is
+ really helpful if you can also add more detailed logs output whilst
+ re-creating the problem. To do this, open the Java Console, click
+ the <em>Clear</em> button and select TRACE in the <em>Log level</em>
+ drop down list. <br /> Whilst leaving the console open, perform the
+ task in Jalview that re-creates the problem. <br /> Then you can
+ copy the debug information in the Java Console by clicking on the <em>Copy
+ to clipboard</em> button and then paste that into the Description, or a
+ Comment of your issue.
+ </p>
+
+ <p>
+ For other queries or comments about Jalview, remember you can
+ contact the Jalview team using email via the
+ <a href="https://www.jalview.org/mailman/listinfo/jalview-discuss">Jalview
+ discussion list</a>, on Twitter <a
+ href="https://twitter.com/Jalview/">@Jalview</a>, or for technical
+ discussions, via the Jalview developer's chatroom at
+ <a href="https://gitter.im/jalview/developers">https://gitter.im/jalview/developers</a>.
+ </p>
+
+</body>
+</html>
arguments, but you must put the <em>jvl</em> file first, e.g. <pre>
/PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa</pre> Alternatively, you can use the standard Jalview command line
arguments with or without the jvl file (first), e.g. <pre>
- /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre> You can use command line arguments to control memory
+ /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre> You can use command line arguments to control memory
settings in Windows and macOS too: <br /> In Windows you must
use, e.g. <pre>
\PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa</pre> In macOS you can use the macOS <em>open</em> command like this: <pre>
+
<html>
<!--
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
</p>
<table border="1">
<tr>
- <th nowrap><em>Release</em></th>
+ <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
<th><em>New Features</em></th>
<th><em>Issues Resolved</em></th>
</tr>
<tr>
<td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
+ <em>24/02/2022</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- -->
+ </li>
+ </ul> <!-- <em>Development</em>
+ <ul>
+ <li>Updated building instructions</li>
+ </ul> -->
+
+ </td>
+ <td>
+ <ul>
+ <li>
+ TO DOCUMENT: JAL-3700,JAL-3751,JAL-3763
+ </li>
+ <li>
+ <!-- JAL-3915 -->Removed RNAview checkbox and logic from
+ Structure Preferences
+ </li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>Fixed non-fatal gradle errors during build</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
+ <em>18/01/2022</em></strong></td>
+ <td></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
+ updated by Jalview or other applications (Windows, other non
+ Unix/BSD OSs)
+ </li>
+ </ul> <em>Security</em>
+ <ul>
+ <li>
+ <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
+ certificates.
+ </li>
+ </ul>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
+ <em>6/01/2022</em></strong></td>
+
+ <td align="left" valign="top"><em>Security</em>
+ <ul>
+ <li>
+ <!-- JAL-3934 -->Version bump library dependency: Log4j 2.16.0 to 2.17.0.
+ </li>
+ </ul></td>
+ <td>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
+ <em>20/12/2021</em></strong></td>
+
+ <td align="left" valign="top"><em>Security</em>
+ <ul>
+ <li>
+ <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
+ (was log4j 1.2.x).
+ </ul> <em>Development</em>
+ <ul>
+ <li>Updated building instructions</li>
+ </ul></td>
+ <td>
+ <ul>
+ <li>
+ <!-- JAL-3840 -->Occupancy calculation is incorrect for
+ alignment columns with over -1+2^32 gaps (breaking filtering
+ and display)
+ </li>
+ <li>
+ <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
+ scale factors being set with buggy window-managers (linux
+ only)
+ </li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>Fixed non-fatal gradle errors during build</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
+ <em>09/03/2021</em></strong></td>
+ <td align="left" valign="top"><em>Improved control of
+ Jalview's use of network services via jalview_properties</em>
+ <ul>
+ <li>
+ <!-- JAL-3814 -->New .jalview_properties token controlling
+ launch of the news browser (like -nonews argument)
+ </li>
+ <li>
+ <!-- JAL-3813 -->New .jalview_properties token controlling
+ download of linkout URLs from
+ www.jalview.org/services/identifiers
+ </li>
+ <li>
+ <!-- JAL-3812 -->New .jalview_properties token controlling
+ download of BIOJSHTML templates
+ </li>
+ <li>
+ <!-- JAL-3811 -->New 'Discover Web Services' option to
+ trigger a one off JABAWS discovery if autodiscovery was
+ disabled
+ </li>
+ </ul></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3818 -->Intermittent deadlock opening structure in
+ Jmol
+ </li>
+ </ul> <em>New Known defects</em>
+ <ul>
+ <li>
+ <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
+ always restored from project (since 2.10.3)
+ </li>
+ <li>
+ <!-- JAL-3806 -->Selections from tree built from CDS aren't
+ propagated to Protein alignment (since 2.11.1.3)
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
+ <em>29/10/2020</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3765 -->Find doesn't always highlight all matching
+ positions in a sequence (bug introduced in 2.11.1.2)
+ </li>
+ <li>
+ <!-- JAL-3760 -->Alignments containing one or more protein
+ sequences can be classed as nucleotide
+ </li>
+ <li>
+ <!-- JAL-3748 -->CDS alignment doesn't match original CDS
+ sequences after alignment of protein products (known defect
+ first reported for 2.11.1.0)
+ </li>
+ <li>
+ <!-- JAL-3725 -->No tooltip or popup menu for genomic
+ features outwith CDS shown overlaid on protein
+ </li>
+ <li>
+ <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
+ correctly mapped by Jalview (e.g. affects viral CDS with
+ ribosomal slippage, since 2.9.0)
+ </li>
+ <li>
+ <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
+ CDS features
+ </li>
+ <li>
+ <!-- JAL-3700 -->Selections in CDS sequence panel don't
+ always select corresponding protein sequences
+ </li>
+ <li>
+ <!-- JAL-3759 --> <em>Make groups from selection</em> for a
+ column selection doesn't always ignore hidden columns
+ </li>
+ </ul> <em>Installer</em>
+ <ul>
+ <li>
+ <!-- JAL-3611 -->Space character in Jalview install path on
+ Windows prevents install4j launching getdown
+ </li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>
+ <!-- JAL-3248 -->Fixed typos and specified compatible gradle
+ version numbers in doc/building.md
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
+ <em>25/09/2020</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
+ "Encountered problems opening
+ https://www.jalview.org/examples/exampleFile_2_7.jvp"
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
- <em>13/07/2020</em></strong></td>
+ <em>17/09/2020</em></strong></td>
<td align="left" valign="top">
<ul>
- <!-- -->
- </ul>
+ <li>
+ <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
+ residue in cursor mode
+ </li>
+ <li>
+ <!-- JAL-3695 -->Support import of VCF 4.3 by updating
+ HTSJDK from 2.12 to 2.23
+ </li>
+ <li>
+ <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
+ optimisations and improvements suggested by Bob Hanson and
+ improved compatibility with JalviewJS
+ </li>
+ <li>
+ <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
+ alignments from Pfam and Rfam
+ </li>
+ <li>
+ <!-- JAL-2656 -->Recognise GZipped content for URLs and File
+ import (no longer based on .gz extension)
+ </li>
+ <li>
+ <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
+ </li>
+ <li>
+ <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
+ ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
+ EMBL flat file
+ </li>
+ <li>
+ <!-- JAL-3667 -->Improved warning messages, debug logging
+ and fixed Retry action when Jalview encounters errors when
+ saving or making backup files.
+ </li>
+ <li>
+ <!-- JAL-3676 -->Enhanced Jalview Java Console:
+ <ul>
+ <li>Jalview's logging level can be configured</li>
+ <li>Copy to Clipboard Buttion</li>
+ </ul>
+ </li>
+ <li>
+ <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
+ when running on Linux (Requires Java 11+)
+ </li>
+ </ul> <em>Launching Jalview</em>
+ <ul>
+ <li>
+ <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
+ through a system property
+ </li>
+ <li>
+ <!-- JAL-3477 -->Improved built-in documentation and command
+ line help for configuring Jalview's memory
+ </li>
+ </ul>
</td>
<td align="left" valign="top">
<ul>
- <li><!-- JAL-3493 -->Escape does not clear highlights on the alignment (Since Jalview 2.10.3)</li>
- </ul>
+ <li>
+ <!-- JAL-3691 -->Conservation and Quality tracks are shown
+ but not calculated and no protein or DNA score models are
+ available for tree/PCA calculation when launched with
+ Turkish language locale
+ </li>
+ <li>
+ <!-- JAL-3493 -->Escape does not clear highlights on the
+ alignment (Since Jalview 2.10.3)
+ </li>
+ <li>
+ <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
+ doesn't slide selected sequences, just sequence under cursor
+ </li>
+ <li>
+ <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
+ sequence under the cursor
+ </li>
+ <li>
+ <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
+ multiple EMBL gene products shown for a single contig
+ </li>
+ <li>
+ <!-- JAL-3696 -->Errors encountered when processing variants
+ from VCF files yield "Error processing VCF: Format specifier
+ '%s'" on the console
+ </li>
+ <li>
+ <!-- JAL-3697 -->Count of features not shown can be wrong
+ when there are both local and complementary features mapped
+ to the position under the cursor
+ </li>
+ <li>
+ <!-- JAL-3673 -->Sequence ID for reference sequence is
+ clipped when Right align Sequence IDs enabled
+ </li>
+ <li>
+ <!-- JAL-2983 -->Slider with negative range values not
+ rendered correctly in VAqua4 (Since 2.10.4)
+ </li>
+ <li>
+ <!-- JAL-3685 -->Single quotes not displayed correctly in
+ internationalised text for some messages and log output
+ </li>
+ <li>
+ <!-- JAL-3490 -->Find doesn't report matches that span
+ hidden gapped columns
+ </li>
+ <li>
+ <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
+ panels, Alignment viewport and annotation renderer.
+ </li>
+ <li>
+ <!-- JAL-3561 -->Jalview ignores file format parameter
+ specifying output format when exporting an alignment via the
+ command line
+ </li>
+ <li>
+ <!-- JAL-3667 -->Windows 10: For a minority of users, if
+ backups are not enabled, Jalview sometimes fails to
+ overwrite an existing file and raises a warning dialog. (in
+ 2.11.0, and 2.11.1.0, the workaround is to try to save the
+ file again, and if that fails, delete the original file and
+ save in place.)
+ </li>
+ <li>
+ <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
+ via command line
+ </li>
+ <li>
+ <!-- JAL-3741 -->References to http://www.jalview.org in
+ program and documentation
+ </li>
+ </ul> <em>Launching Jalview</em>
+ <ul>
+ <li>
+ <!-- JAL-3718 -->Jalview application fails when launched the
+ first time for a version that has different jars to the
+ previous launched version.
+ </li>
+ </ul> <em>Developing Jalview</em>
+ <ul>
+ <li>
+ <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
+ data, causing cloverReport gradle task to fail with an
+ OutOfMemory error.
+ </li>
+ <li>
+ <!-- JAL-3280 -->Migrated the Jalview Version Checker to
+ monitor the release channel
+ </li>
+ </ul> <em>New Known defects</em>
+ <ul>
+ <li>
+ <!-- JAL-3748 -->CDS shown in result of submitting proteins
+ in a CDS/Protein alignment to a web service is wrong when
+ proteins share a common transcript sequence (e.g.
+ genome of RNA viruses)
+ </li>
+ <li>
+ <!-- JAL-3576 -->Co-located features exported and re-imported
+ are ordered differently when shown on alignment and in
+ tooltips. (Also affects v2.11.1.0)
+ </li>
+ <li>
+ <!-- JAL-3702 -->Drag and drop of alignment file onto
+ alignment window when in a HiDPI scaled mode in Linux only
+ works for the top left quadrant of the alignment window
+ </li>
+ <li>
+ <!-- JAL-3701 -->Stale build data in jalview standalone jar
+ builds (only affects 2.11.1.1 branch)
+ </li>
+ <li>
+ <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
+ when alignment view restored from project (since Jalview 2.11.0)
+ </li>
+ <li>
+ <!-- JAL-3749 -->Duplicate CDS sequences are generated when
+ protein products for certain ENA records are repeatedly
+ shown via Calculate->Show Cross Refs
+ </li>
+ </ul>
</td>
</tr>
<tr>
<p>
<strong>The Jalview Desktop RSS News Reader</strong><br /> The
Jalview Desktop includes a built in news reader for the <a
- href="http://www.jalview.org/feeds/desktop/rss">Jalview
+ href="https://www.jalview.org/feeds/desktop/rss">Jalview
Desktop News Channel</a>.
</p>
<br />
<p>
The <em>Jalview news reader</em> was introduced in <a
- href="http://www.jalview.org/releaseHistory.html#Jalview2.7">Jalview
+ href="https://www.jalview.org/releaseHistory.html#Jalview2.7">Jalview
version 2.7</a>. Its implementation is based on <a
- href="http://jswingreader.sourceforge.net/">JSwingReader</a>.
+ href="https://jswingreader.sourceforge.net/">JSwingReader</a>.
</p>
<br />
<em>If you need to prevent the news-reader opening, then add the
</head>
<body>
<p>
- <strong>Jalview 2.11.1.0</strong>
+ <strong>Welcome to Jalview Version $$Version-Rel$$ !!</strong>
+ <br />Please take a
+ look at the <a href="releases.html#Jalview.$$Version-Rel$$">release
+ notes</a> for this build. Read on for the highlights.
</p>
<p>
- Jalview 2.11.1.0 is the first minor release for the 2.11 series.
- Along with a number of critical bug fixes and improvements it brings
- new functionality for mapping sequence features between CDS and
- Protein alignments. It is also the first release made under a new <em>four</em>
- number versioning scheme, which will allow us to keep track of
- patches and bug fixes.
+ <strong>Highlights in 2.11.2</strong>
+ </p>
+ <p><strong>New features for working with 3D Structure</strong><br/>
+ Jalview 2.11.2 features a number of new capabilities:<ul><li><strong>Linked viewing with <em>ChimeraX</em> and <em>PyMol</em></strong><br/>Simply configure your prefered viewer for 3D molecular data in <a href="features/preferences.html#structure">Jalview's structure preferences</a>, make sure that Jalview can locate the viewer's installation, and open a new view via the 3D Structure Chooser!</li>
+ <li><strong>View predicted protein structures via 3D-Beacons</strong><br/>
+ Jalview 2.11.2's <a href="features/structurechooser.html">Structure Chooser includes a client for the 3D-Beacons Network</a>, a new service that allows predicted and observed 3D models for proteins in Uniprot from a range of resources, including AlphaFold DB, SWISS-MODEL and a growing number of other resources.
+ </li>
+ <p><strong>Retrieval
</p>
- <ul>
- <li><strong>Virtual Features</strong><br />In previous
- versions of Jalview, specific nucleotide sequence features such as
- genomic variants and exons were transferred to protein products on
- import. Jalview 2.11.1 instead provides 'virtual features' that
- can be enabled and overlaid on linked CDS/Protein views via their
- <a href="features/splitView.html#virtualfeats">Sequence
- Features dialog</a>. This allows more analyses of nucleotide and
- peptide sequence features on alignments in a more flexible and
- memory efficient way than in earlier versions.<br />
- <em>Note: Virtual features work best when variants are
- annotated with CSQ fields. Please <a
- href="features/importvcf.html#computepepvariants">see this
- Groovy script workaround</a> if you are working with VCF files
- without CSQ fields.
- </em></li>
- <li><strong>Improved VCF data import</strong><br /> <a
- href="features/importvcf.html#attribs">Standard attributes for
- filtering variants</a> (e.g. position, QUAL field etc) are now
- extracted from VCF files. This new feature was suggested by a user
- at the Jalview booth during ISMB 2019.</li>
- <li><strong>Extended feature attributes are exported
- in GFF3</strong><br />Complex attributes from VCF files can be exported
- and imported via GFF3</li>
- <li><strong>Updated Jalview Installer and Launcher</strong><br />Jalview's
- installation packages are now built with Install4j 8, which brings
- better support for Linux and improved control of file
- associations. New <a href="memory.html#jvm">parameters on the
- Jalview launcher</a> allow an upper memory limit to be specified <em>via</em>
- a Jalview launch file, to prevent it from hogging your system.</li>
- </ul>
<p>
- See the <a href="releases.html#Jalview.2.11.1.0">2.11.1.0
- release notes</a> for full details of bugs fixed and new known issues.
+ For the full release notes, see <a
+ href="releases.html#Jalview.2.11.1.4">the Jalview 2.11.1.4
+ release notes</a>.
</p>
<p>
- <em>JalviewJS News</em><br />With the release of Jalview 2.11.1.0,
- the team are now focused on bringing JalviewJS to full production.
- To follow our progress take a look at <em>http://www.jalview.org/jalview-js/</em>
- and follow updates on our new <a
- href="https://github.com/jalview/jalview-js/">JalviewJS
- Releases github repository</a>.
+ <strong>Known Issues</strong>
</p>
+ <p>New known issues in this release affect recovery of CDS/Protein
+ relationships from project files, and interactive selection of
+ protein sequences from a tree built on linked nucleotide sequences.
+ We will provide patches for these issues as soon as possible.</p>
+ </ul>
</body>
</html>
Cath Code;cath_code;String;g2;50;400;95;false;false
Tax Id;tax_id;String;g2;50;400;95;false;false
Tax Query;tax_query;String;g2;50;400;95;false;false
-Interacting Entity Id;interacting_entity_id;String;g2;50;400;95;false;false
Interacting Molecules;interacting_molecules;String;g6;50;400;95;false;false
Pubmed Id;pubmed_id;int;g2;50;400;95;false;false
Status;status;String;g6;50;400;95;false;false
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+tdbeacons_data_columns
+#
+_group.id
+_group.name
+_group.sort_order
+g1;ModelInfo;1
+g2;Quality;2
+g3;Miscellaneous;3
+
+#
+_data_column.primary_key;model_url
+_data_column.default_response_page_size;100
+#
+_data_column.name
+_data_column.code
+_data_column.group_id
+_data_column.data_type | _data_column.isFormated | _data_column.significantDigit
+_data_column.min_col_width
+_data_column.max_col_width
+_data_column.preferred_col_width
+_data_column.is_shown_by_default
+_data_column.is_searchable
+Uniprot Id;id;String;g1;80;150;85;false;false
+Uniprot Start;uniprot_start;Integer;g1;80;150;85;true;false
+Uniprot End;uniprot_end;Integer;g1;80;150;85;true;false
+Provider;provider;String;g1;80;150;85;true;false
+Model id;model_identifier;String;g3;80;150;85;true;false
+Model Category;model_category;String;g1;80;150;85;true;false
+Model Type;model_type;String;g1;80;150;85;false;false
+Title;model_title;String;g1;100;150;105;true;false
+Resolution;resolution;double|T|3;g2;80;150;85;true;false
+Confidence;confidence_avg_local_score;double|T|2;g2;100;150;105;true;false
+Confidence Score Type;confidence_type;String;g2;100;150;105;true;false
+Confidence Score Version;confidence_version;String;g2;100;150;105;true;false
+Coverage;coverage;double|T|2;g2;80;150;85;true;false
+Sequence Identity;sequence_identity;double|T|1;g2;80;150;85;false;false
+Created Date;created;string;g3;80;150;85;true;false
+UniProt Accession;uniprot_accession;String;g1;50;400;95;false;true
+Url;model_url;String;g3;100;150;105;true;false
+Model Format;model_format;String;g3;20;60;20;true;false
+Page URL;model_page_url;String;g3;100;150;105;true;false
+Ensemble Sample Url;ensembl_sample_url;String;g3;100;150;105;false;false
action.format = Format
action.select = Select
action.new_view = New View
+action.new_structure_view_with = Open new structure view with {0}
action.close = Close
action.add = Add
action.save_as = Save as...
label.paste_your_alignment_file = Paste your alignment file here
label.paste_your = Paste your
label.finished_searching = Finished searching
+label.subsequence_matches_found = {0} subsequence matches found
label.search_results= Search results {0} : {1}
label.found_match_for = Found match for {0}
label.font = Font:
label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences = Retrieve and parse sequence database records for the alignment or the currently selected sequences
label.standard_databases = Standard Databases
label.fetch_embl_uniprot = Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources
+label.fetch_uniprot_references = Fetch Uniprot references
+label.search_3dbeacons = 3D-Beacons Search
+label.find_models_from_3dbeacons = Search 3D-Beacons for 3D structures and models
+label.3dbeacons = 3D-Beacons
+label.fetch_references_for = Fetch database references for {0} sequences ?
+label.fetch_references_for_3dbeacons = 3D Beacons needs Uniprot References. Fetch database references for {0} sequences ?
label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults from user preferences.
label.align_structures_using_linked_alignment_views = Superpose structures using {0} selected alignment view(s)
label.threshold_feature_display_by_score = Threshold the feature display by score.
label.web_services = Web Services
label.right_click_to_edit_currently_selected_parameter = Right click to edit currently selected parameter.
label.let_jmol_manage_structure_colours = Let Jmol manage structure colours
-label.fetch_chimera_attributes = Fetch Chimera attributes
-label.fetch_chimera_attributes_tip = Copy Chimera attribute to Jalview feature
+label.fetch_viewer_attributes = Fetch {0} attributes
+label.fetch_viewer_attributes_tip = Copy {0} attribute to Jalview feature
label.marks_leaves_tree_not_associated_with_sequence = Marks leaves of tree not associated with a sequence
label.index_web_services_menu_by_host_site = Index web services in menu by the host site
label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up = Check this option if you want to be informed<br>when a web service URL cannot be accessed by Jalview<br>when it starts up
label.insufficient_residues = Not enough aligned residues ({0}) to perform superposition
label.create_viewer_attributes = Write Jalview features
label.create_viewer_attributes_tip = Set structure residue attributes for Jalview features
-label.attributes_set = {0} attribute values set on Chimera
+label.attributes_set = {0} attribute values set on {1}
label.sort_alignment_by_tree = Sort Alignment By Tree
label.mark_unlinked_leaves = Mark Unlinked Leaves
label.associate_leaves_with = Associate Leaves With
label.couldnt_create_groovy_shell = Couldn't create the groovy Shell. Check the error log for the details of what went wrong.
error.unsupported_version_calcIdparam = Unsupported Version for calcIdparam {0}
error.implementation_error_cant_reorder_tree = Implementation Error: Can't reorder this tree. Not DefaultMutableTreeNode.
-error.invalid_value_for_option = Invalid value {0} for option {1}
+error.invalid_value_for_option = Invalid value ''{0}'' for option ''{1}''
error.implementation_error_cannot_import_vamsas_doc = Implementation Error - cannot import existing vamsas document into an existing session, Yet!
label.vamsas_doc_couldnt_be_opened_as_new_session = VAMSAS Document could not be opened as a new session - please choose another
error.setstatus_called_non_existent_job_pane = setStatus called for non-existent job pane {0}
error.implementation_error_msawbjob_called = Implementation error - StartJob(MsaWSJob) called on a WSJobInstance {0}
error.implementation_error_cannot_attach_ws_menu_entry = IMPLEMENTATION ERROR: cannot attach WS Menu Entry without service handle reference!
error.parameter_migration_not_implemented_yet = Parameter migration not implemented yet
-error.implementation_error_cannot_set_jaba_option = Implementation error: cannot set Jaba Option to a value outside its allowed value range!
error.implementation_error_valuetype_doesnt_support_jabaws_type = IMPLEMENTATION ERROR: jalview.ws.params.ValueConstrainI.ValueType does not support the JABAWS type : {0}
error.cannot_create_jabaws_param_set = Cannot create a JabaWSParamSet from non-JabaWS parameters
error.cannot_set_arguments_to_jabaws_param_set = Cannot set arguments to a JabaWSParamSet that are not JabaWS arguments
exception.invocation_target_calling_url = InvocationTargetException while calling openURL: {0}
exception.illegal_access_calling_url = IllegalAccessException while calling openURL: {0}
exception.interrupted_launching_browser = InterruptedException while launching browser: {0}
-exception.ebiembl_retrieval_failed_on = EBI EMBL XML retrieval failed on {0}:{1}
exception.no_pdb_records_for_chain = No PDB Records for {0} chain {1}
exception.unexpected_handling_rnaml_translation_for_pdb = Unexpected exception when handling RNAML translation of PDB data
exception.couldnt_recover_sequence_properties_for_alignment = Couldn't recover sequence properties for alignment
status.fetching_db_refs = Fetching db refs
status.loading_cached_pdb_entries = Loading Cached PDB Entries
status.searching_for_pdb_structures = Searching for PDB Structures
+status.searching_3d_beacons = Searching 3D Beacons
+status.no_structures_discovered_from_3d_beacons = No models discovered from 3D Beacons
status.opening_file_for = opening file for
status.colouring_structures = Colouring structures
label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data
action.choose_annotations = Choose Annotations...
label.choose_annotations = Choose Annotations
label.find = Find
+label.in = in
label.invalid_search = Search string invalid
error.invalid_regex = Invalid regular expression
label.ignore_gaps_consensus = Ignore Gaps In Consensus
label.log_level_tooltip = Temporarily set the log level for this console. The log level will revert to {0} when this Java console is closed.
label.copy_to_clipboard = Copy to clipboard
label.copy_to_clipboard_tooltip = Copy all of the log text in this console to the system clipboard
+label.startup = Startup
+label.memory = Memory
+label.customise_memory_settings = Customise maximum memory settings
+label.memory_setting_text = New memory settings will only come into effect the next time you start Jalview
+label.maximum_memory_used = Maximum memory limited to both
+label.percent_of_physical_memory = Maximum percent of physical memory
+label.maximum_memory = Maximum absolute memory
+label.maximum_memory_tooltip = Enter memory as an integer number optionally followed by 'b', 'k', 'm', 'g' or 't'
+label.adjustments_for_this_computer = Adjustments for this computer
+label.memory_example_text = Maximum memory that would be used with these settings on this computer
+label.memory_example_tooltip = The memory allocated to Jalview is the smaller of the percentage of physical memory (default 90%) and the maximum absolute memory (default 32GB). If your computer's memory cannot be ascertained then the maximum absolute memory defaults to 8GB (if not customised).<br>Jalview will always try and reserve 512MB for the OS and at least 512MB for itself.
label.no_value = Sin valor
label.colour_by_label = Color por etiquetas
label.new_feature = Nueva función
-label.match_case = Hacer corresponder mayúsculas y minúsculas
+label.match_case = Distinguir min/mayúsculas
label.view_alignment_editor = Ver en el editor de alineamientos
label.labels = Etiquetas
label.output_values = Valores de salida...
label.paste_your_alignment_file = Pegar su fichero de alineamiento aquÃ
label.paste_your = Pegar su
label.finished_searching = Búsqueda finalizada
+label.subsequence_matches_found = {0} resultados encontrados en subsequencias
label.search_results= Buscar Resultados {0} : {1}
label.found_match_for = Buscar coincidencia para {0}
label.font = Fuente:
label.couldnt_create_groovy_shell = No es posible crear el shell de Groovy. Compruebe el fichero de log para conocer los detalles.
error.unsupported_version_calcIdparam = Versión no soportada de {0}
error.implementation_error_cant_reorder_tree = Error de implementación: no es posible reordenar este árbol. No DefaultMutableTreeNode.
-error.invalid_value_for_option = Valor no válido de {0} para la opción {1}
+error.invalid_value_for_option = Valor no válido de ''{0}'' para la opción ''{1}''
error.implementation_error_cannot_import_vamsas_doc = Error de implementación - todavÃa no es posible importar el documento VAMSAS existente en una sesión existente.
label.vamsas_doc_couldnt_be_opened_as_new_session = El documento VAMSAS no ha podido abrirse como una nueva sesión. Por favor, escoja otra.
error.setstatus_called_non_existent_job_pane = se lllamado a setStatus para el panel de trabajo {0} no existente
error.implementation_error_msawbjob_called = Error de implementación - StartJob(MsaWSJob) invocado en un WSJobInstance {0}
error.implementation_error_cannot_attach_ws_menu_entry = Error de implementación: ¡no es posible adjunto una WS Menu Entry sin una referencia a un manejador del servicio!
error.parameter_migration_not_implemented_yet = La migración de parámetros no se ha implementado todavÃa
-error.implementation_error_cannot_set_jaba_option = Error de implementación: no es posible establecer el valor de Jaba Option a un valor fuera de su rango permitido
error.implementation_error_valuetype_doesnt_support_jabaws_type = Error de implementación: jalview.ws.params.ValueConstrainI.ValueType no soporta el tipo JABAWS: {0}
error.cannot_create_jabaws_param_set = No es posible crear un JabaWSParamSet con parámetros no JabaWS
error.cannot_set_arguments_to_jabaws_param_set = No es posible establecer argumentos en JabaWSParamSet que no sean argumentos JabaWS
exception.invocation_target_calling_url = InvocationTargetException mientras se invocaba openURL: {0}
exception.illegal_access_calling_url = IllegalAccessException mientras se invocaba openURL: {0}
exception.interrupted_launching_browser = InterruptedException mientras se lanzaba el navegador: {0}
-exception.ebiembl_retrieval_failed_on = La recuperación de datos EBI EMBL XML ha fallado en {0}:{1}
exception.no_pdb_records_for_chain = No se han encontrado registros {0} para la cadena {1}
exception.unexpected_handling_rnaml_translation_for_pdb = Excepcion inesperada cuando se traducÃan a RNAML los datos PDB
exception.couldnt_recover_sequence_properties_for_alignment = No es posible recuperar las propiedades de la secuencia para el alineamiento
action.unmark_as_reference=Desmarcar como Referencia
label.open_viewer_failed=Error al abrir {0} - está instalado?\nCompruebe ruta en Preferencias, Estructura
label.find=Buscar
+label.in = en
label.select_pdb_file=Seleccionar Fichero PDB
label.structures_filter=Filtro de Estructuras
label.scale_protein_to_cdna=Adaptar proteÃna a cDNA
label.log_level_tooltip = Establezca temporalmente el nivel de registro para esta consola. El nivel de registro volverá a {0} cuando se cierre esta consola de Java.
label.copy_to_clipboard = Copiar en el portapapeles
label.copy_to_clipboard_tooltip = Copie todo el texto de registro en esta consola al portapapeles del sistema
+label.startup = Inicio
+label.memory = Memoria
+label.customise_memory_settings = Personalizar la configuración de memoria máxima
+label.memory_setting_text = La nueva configuración de memoria solo entrará en vigor la próxima vez que inicie Jalview
+label.maximum_memory_used = Memoria máxima limitada a ambos
+label.percent_of_physical_memory = Porcentaje máximo de memoria fÃsica
+label.maximum_memory = Memoria absoluta máxima
+label.maximum_memory_tooltip = Ingrese la memoria como un número entero seguido opcionalmente por 'b', 'k', 'm', 'g' o 't'
+label.adjustments_for_this_computer = Ajustes para esta computadora
+label.memory_example_text = Memoria máxima que se usarÃa con esta configuración en esta computadora
+label.memory_example_tooltip = La memoria asignada a Jalview es el menor entre el porcentaje de memoria fÃsica (predeterminado 90%) y la memoria absoluta máxima (predeterminado 32 GB). Si no se puede determinar la memoria de su computadora, la memoria absoluta máxima predeterminada es de 8 GB (si no está personalizada).<br>Jalview siempre intentará reservar 512 MB para el sistema operativo y al menos 512 MB para sà mismo.
</xs:documentation>
</xs:annotation>
</xs:attribute>
+ <xs:attribute name="canonical" type="xs:boolean" default="false">
+ <xs:annotation>
+ <xs:documentation>
+ true for the representative accession for databases where multiple accessions map to the same entry (eg. Uniprot)
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
</xs:sequence>
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.io.UnsupportedEncodingException;
+import java.net.URLEncoder;
+import java.nio.charset.StandardCharsets;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Collection;
* Select something in Chimera
*
* @param command
- * the selection command to pass to Chimera
+ * the selection command to pass to Chimera
*/
public void select(String command)
{
/**
* Return the list of depiction presets available from within Chimera. Chimera
- * will return the list as a series of lines with the format: Preset type
- * number "description"
+ * will return the list as a series of lines with the format: Preset type number
+ * "description"
*
* @return list of presets
*/
}
/**
- * Launch Chimera, unless an instance linked to this object is already
- * running. Returns true if chimera is successfully launched, or already
- * running, else false.
+ * Launch Chimera, unless an instance linked to this object is already running.
+ * Returns true if chimera is successfully launched, or already running, else
+ * false.
*
* @param chimeraPaths
* @return
* Determine the color that Chimera is using for this model.
*
* @param model
- * the ChimeraModel we want to get the Color for
+ * the ChimeraModel we want to get the Color for
* @return the default model Color for this model in Chimera
*/
public Color getModelColor(ChimeraModel model)
/**
*
* Get information about the residues associated with a model. This uses the
- * Chimera listr command. We don't return the resulting residues, but we add
- * the residues to the model.
+ * Chimera listr command. We don't return the resulting residues, but we add the
+ * residues to the model.
*
* @param model
- * the ChimeraModel to get residue information for
+ * the ChimeraModel to get residue information for
*
*/
public void addResidues(ChimeraModel model)
* Send a command to Chimera.
*
* @param command
- * Command string to be send.
+ * Command string to be send.
* @param reply
- * Flag indicating whether the method should return the reply from
- * Chimera or not.
+ * Flag indicating whether the method should return the reply
+ * from Chimera or not.
* @return List of Strings corresponding to the lines in the Chimera reply or
* <code>null</code>.
*/
*/
int waited = 0;
int pause = 25;
- while (busy && waited < 1001)
+ while (busy && waited < 1001)
{
try
{
String method = getHttpRequestMethod();
if ("GET".equals(method))
{
- command = command.replace(" ", "+").replace("#", "%23")
- .replace("|", "%7C").replace(";", "%3B");
+ try
+ {
+ command = URLEncoder.encode(command, StandardCharsets.UTF_8.name());
+ } catch (UnsupportedEncodingException e)
+ {
+ command = command.replace(" ", "+").replace("#", "%23")
+ .replace("|", "%7C").replace(";", "%3B")
+ .replace(":", "%3A");
+ }
}
commands.add(new BasicNameValuePair("command", command));
* 0.93 is ChimeraX latest, 1.0 expected soon
*/
private static String[] CHIMERA_VERSIONS = new String[] { "1.16.2",
- "1.16.1", "1.16",
- "1.15.2", "1.15.1", "1.15", "1.14.2", "1.14.1", "1.14",
- "1.13.1", "1.13", "1.12.2", "1.12.1", "1.12", "1.11.2",
+ "1.16.1", "1.16", "1.15.2", "1.15.1", "1.15", "1.14.2", "1.14.1",
+ "1.14", "1.13.1", "1.13", "1.12.2", "1.12.1", "1.12", "1.11.2",
"1.11.2", "1.11.1", "1.11" };
- private static String[] CHIMERAX_VERSIONS = new String[] { "1.0", "0.93",
- "0.92", "0.91", "0.9" };
+ // Missing 1.1 as this has known bug see JAL-2422
+ private static String[] CHIMERAX_VERSIONS = new String[] { "1.2.5", "1.0",
+ "0.93", "0.92", "0.91", "0.9" };
static final String[] defaultStructureKeys = { "Structure", "pdb",
"pdbFileName", "PDB ID", "structure", "biopax.xref.PDB", "pdb_ids",
/**
* This is called by the selectionListener to let us know that the user has
- * changed their selection in Chimera. We need to go back to Chimera to find
- * out what is currently selected and update our list.
+ * changed their selection in Chimera. We need to go back to Chimera to find out
+ * what is currently selected and update our list.
*/
public void chimeraSelectionChanged()
{
}
/**
- * Add a selection to the selection list. This is called primarily by the
- * Model Navigator Dialog to keep the selections in sync
+ * Add a selection to the selection list. This is called primarily by the Model
+ * Navigator Dialog to keep the selections in sync
*
* @param selectionToAdd
- * the selection to add to our list
+ * the selection to add to our list
*/
public void addChimSelection(ChimeraStructuralObject selectionToAdd)
{
* Model Navigator Dialog to keep the selections in sync
*
* @param selectionToRemove
- * the selection to remove from our list
+ * the selection to remove from our list
*/
public void removeChimSelection(ChimeraStructuralObject selectionToRemove)
{
// }
// }
- /*
- * Jalview addition: check if path set in user preferences
- */
+ String os = System.getProperty("os.name");
String userPath = Cache
.getDefault(isChimeraX ? Preferences.CHIMERAX_PATH
: Preferences.CHIMERA_PATH, null);
- if (userPath != null)
- {
- pathList.add(userPath);
- }
/*
* paths are based on getChimeraPaths() in
String chimera = isChimeraX ? "ChimeraX" : "Chimera";
String chimeraExe = isChimeraX ? "ChimeraX" : "chimera";
+ /*
+ * Jalview addition: check if path set in user preferences
+ */
+ if (userPath != null)
+ {
+ // in macos, deal with the user selecting the .app folder
+ boolean adjusted = false;
+ if (os.startsWith("Mac") && userPath.endsWith((".app")))
+ {
+ String possiblePath = String.format("%s/Contents/MacOS/%s",
+ userPath, chimeraExe);
+ if (new File(possiblePath).exists())
+ {
+ pathList.add(possiblePath);
+ adjusted = true;
+ }
+ }
+ if (!adjusted)
+ {
+ pathList.add(userPath);
+ }
+ }
+
// Add default installation paths
- String os = System.getProperty("os.name");
if (os.startsWith("Linux"))
{
- // todo should this be /chimeraX/ for ChimeraX? not in structureVizX code
- pathList.add("/usr/local/chimera/bin/" + chimeraExe);
- pathList.add("/usr/local/bin/" + chimeraExe);
- pathList.add("/usr/bin/" + chimeraExe);
- pathList.add(System.getProperty("user.home") + "/opt/bin/" + chimeraExe);
+ // ChimeraX .deb and .rpm packages put symbolic link from /usr/bin/chimerax
+ pathList.add(String.format("/usr/bin/%s", chimeraExe.toLowerCase()));
+ pathList.add(String.format("/usr/bin/%s", chimeraExe));
+
+ pathList.add(
+ String.format("/usr/local/bin/%s", chimeraExe.toLowerCase()));
+ pathList.add(String.format("/usr/local/bin/%s", chimeraExe));
+
+ // these paths also used by .deb and .rpm
+ pathList.add(String.format("/usr/lib/ucsf-%s/bin/%s",
+ chimera.toLowerCase(), chimeraExe));
+ pathList.add(String.format("/usr/libexec/UCSF-%s/bin/%s", chimera,
+ chimeraExe));
+
+ pathList.add(String.format("/usr/local/chimera/bin/%s", chimeraExe));
+
+ // user home paths
+ pathList.add(String.format("%s/bin/%s",
+ System.getProperty("user.home"), chimeraExe.toLowerCase()));
+ pathList.add(String.format("%s/bin/%s",
+ System.getProperty("user.home"), chimeraExe));
+ pathList.add(String.format("%s/opt/bin/%s",
+ System.getProperty("user.home"), chimeraExe.toLowerCase()));
+ pathList.add(String.format("%s/opt/bin/%s",
+ System.getProperty("user.home"), chimeraExe));
+ pathList.add(String.format("%s/local/bin/%s",
+ System.getProperty("user.home"), chimeraExe.toLowerCase()));
+ pathList.add(String.format("%s/local/bin/%s",
+ System.getProperty("user.home"), chimeraExe));
}
else if (os.startsWith("Windows"))
{
pathList.add(path);
pathList.add(path + ".exe");
}
+ // try without a version number too
+ String path = String.format("%s\\%s\\bin\\%s", root, chimera,
+ chimeraExe);
+ pathList.add(path);
+ pathList.add(path + ".exe");
}
}
else if (os.startsWith("Mac"))
{
+ // check for installations with version numbers first
+ String[] candidates = isChimeraX ? CHIMERAX_VERSIONS
+ : CHIMERA_VERSIONS;
+ for (String version : candidates)
+ {
+ pathList.add(
+ String.format("/Applications/%s-%s.app/Contents/MacOS/%s",
+ chimera, version, chimeraExe));
+ pathList.add(
+ String.format("%s/Applications/%s-%s.app/Contents/MacOS/%s",
+ System.getProperty("user.home"), chimera, version,
+ chimeraExe));
+ }
pathList.add(String.format("/Applications/%s.app/Contents/MacOS/%s",
chimera, chimeraExe));
+ pathList.add(String.format("%s/Applications/%s.app/Contents/MacOS/%s",
+ System.getProperty("user.home"), chimera, chimeraExe));
}
return pathList;
}
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.analysis.scoremodels.PIDModel;
import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.analysis.scoremodels.ScoreModels;
public AlignSeq(SequenceI s1, String string1, SequenceI s2,
String string2, String type)
{
- seqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type);
+ seqInit(s1, string1.toUpperCase(Locale.ROOT), s2, string2.toUpperCase(Locale.ROOT), type);
}
/**
*/
package jalview.analysis;
+import java.util.Locale;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.NoSuchElementException;
+import java.util.Set;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import jalview.bin.Console;
import jalview.commands.RemoveGapColCommand;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
import jalview.util.MapList;
import jalview.util.MappingUtils;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.NoSuchElementException;
-import java.util.Set;
-import java.util.SortedMap;
-import java.util.TreeMap;
-
/**
* grab bag of useful alignment manipulation operations Expect these to be
* refactored elsewhere at some point.
// TODO use Character.toLowerCase to avoid creating String objects?
char[] upstream = new String(ds
.getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1))
- .toLowerCase().toCharArray();
+ .toLowerCase(Locale.ROOT).toCharArray();
char[] downstream = new String(
- ds.getSequence(s_end - 1, s_end + dstream_ds)).toLowerCase()
+ ds.getSequence(s_end - 1, s_end + dstream_ds)).toLowerCase(Locale.ROOT)
.toCharArray();
char[] coreseq = s.getSequence();
char[] nseq = new char[offset + upstream.length + downstream.length
if (cdnaLength != mappedLength && cdnaLength > 2)
{
String lastCodon = String.valueOf(cdnaSeqChars,
- cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase();
+ cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase(Locale.ROOT);
for (String stop : ResidueProperties.STOP_CODONS)
{
if (lastCodon.equals(stop))
*/
int startOffset = 0;
if (cdnaLength != mappedLength && cdnaLength > 2
- && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase()
+ && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase(Locale.ROOT)
.equals(ResidueProperties.START))
{
startOffset += CODON_LENGTH;
SequenceI newSeq = null;
- final MapList maplist = mapping.getMap();
- if (maplist.isContiguous() && maplist.isFromForwardStrand())
- {
- /*
- * just a subsequence, keep same dataset sequence
- */
- int start = maplist.getFromLowest();
- int end = maplist.getFromHighest();
- newSeq = seq.getSubSequence(start - 1, end);
- newSeq.setName(seqId);
- }
- else
- {
- /*
- * construct by splicing mapped from ranges
- */
- char[] seqChars = seq.getSequence();
- List<int[]> fromRanges = maplist.getFromRanges();
- int cdsWidth = MappingUtils.getLength(fromRanges);
- char[] newSeqChars = new char[cdsWidth];
+ /*
+ * construct CDS sequence by splicing mapped from ranges
+ */
+ char[] seqChars = seq.getSequence();
+ List<int[]> fromRanges = mapping.getMap().getFromRanges();
+ int cdsWidth = MappingUtils.getLength(fromRanges);
+ char[] newSeqChars = new char[cdsWidth];
- int newPos = 0;
- for (int[] range : fromRanges)
+ int newPos = 0;
+ for (int[] range : fromRanges)
+ {
+ if (range[0] <= range[1])
{
- if (range[0] <= range[1])
- {
- // forward strand mapping - just copy the range
- int length = range[1] - range[0] + 1;
- System.arraycopy(seqChars, range[0] - 1, newSeqChars, newPos,
- length);
- newPos += length;
- }
- else
+ // forward strand mapping - just copy the range
+ int length = range[1] - range[0] + 1;
+ System.arraycopy(seqChars, range[0] - 1, newSeqChars, newPos,
+ length);
+ newPos += length;
+ }
+ else
+ {
+ // reverse strand mapping - copy and complement one by one
+ for (int i = range[0]; i >= range[1]; i--)
{
- // reverse strand mapping - copy and complement one by one
- for (int i = range[0]; i >= range[1]; i--)
- {
- newSeqChars[newPos++] = Dna.getComplement(seqChars[i - 1]);
- }
+ newSeqChars[newPos++] = Dna.getComplement(seqChars[i - 1]);
}
}
}
else
{
- System.err.println(
- "JAL-2154 regression: warning - found (and ignnored a duplicate CDS sequence):"
- + mtch.toString());
+ Console.error(
+ "JAL-2154 regression: warning - found (and ignored) a duplicate CDS sequence:" + mtch.toString());
}
}
}
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
{
return 1;
}
- return label1.toUpperCase().compareTo(label2.toUpperCase());
+ return label1.toUpperCase(Locale.ROOT).compareTo(label2.toUpperCase(Locale.ROOT));
}
/**
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.datamodel.AlignmentAnnotation;
protected static void recordConservation(Map<String, Integer> resultMap,
String res)
{
- res = res.toUpperCase();
+ res = res.toUpperCase(Locale.ROOT);
for (Entry<String, Map<String, Integer>> property : ResidueProperties.propHash
.entrySet())
{
addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss,
retrievedDss);
}
+ // JBPNote: What assumptions are made for dbref structures on
+ // retrieved sequences ?
+ // addedXref will be true means importCrossRefSeq found
+ // sequences with dbrefs with mappings to sequences congruent with dss
+
if (!addedXref)
{
// try again, after looking for matching IDs
/**
* process sequence retrieved via a dbref on source sequence to resolve and
- * transfer data
+ * transfer data JBPNote: as of 2022-02-03 - this assumes retrievedSequence
+ * has dbRefs with Mapping references to a sequence congruent with
+ * sourceSequence
*
* @param cf
* @param sourceSequence
List<DBRefEntry> dbr = retrievedSequence.getDBRefs();
if (dbr != null)
{
- for (int ib = 0, nb = dbr.size(); ib < nb; ib++)
+ for (int ib = 0, nb = dbr.size(); ib < nb; ib++)
{
- DBRefEntry dbref = dbr.get(ib);
+ DBRefEntry dbref = dbr.get(ib);
+ // matched will return null if the dbref has no map
SequenceI matched = findInDataset(dbref);
if (matched == sourceSequence)
{
Mapping map = dbref.getMap();
if (map != null)
{
- SequenceI ms = map.getTo();
+ SequenceI ms = map.getTo();
if (ms != null && map.getMap() != null)
{
if (ms == sourceSequence)
* Returns null or the first sequence in the dataset which is identical to
* xref.mapTo, and has a) a primary dbref matching xref, or if none found, the
* first one with an ID source|xrefacc
- *
+ * JBPNote: Could refactor this to AlignmentI/DatasetI
* @param xref
* with map and mapped-to sequence
* @return
* Updates any empty mappings in the cross-references with one to a compatible
* retrieved sequence if found, and adds any new mappings to the
* AlignedCodonFrame
- *
+ * JBPNote: TODO: this relies on sequence IDs like UNIPROT|ACCESSION - which do not always happen.
* @param mapFrom
* @param xrefs
* @param retrieved
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.api.AlignViewportI;
import jalview.api.FinderI;
import jalview.datamodel.AlignmentI;
idMatches = new ArrayList<>();
String searchString = matchCase ? theSearchString
- : theSearchString.toUpperCase();
+ : theSearchString.toUpperCase(Locale.ROOT);
Regex searchPattern = new Regex(searchString);
searchPattern.setIgnoreCase(!matchCase);
*/
package jalview.analysis;
-import jalview.bin.Cache;
-
+import java.util.Locale;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.util.Map;
import java.util.StringTokenizer;
+import jalview.bin.Console;
+
/**
* A singleton that provides instances of genetic code translation tables
*
}
} catch (IOException | NullPointerException e)
{
- Cache.log.error(
+ Console.error(
"Error reading genetic codes data file " + fileName + ": "
+ e.getMessage());
}
while (line != null)
{
line = readLine(dataIn);
- if (line != null && !"DNA".equals(line.toUpperCase()))
+ if (line != null && !"DNA".equals(line.toUpperCase(Locale.ROOT)))
{
String[] tokens = line.split("\\t");
if (tokens.length == 2)
{
- ambiguityCodes.put(tokens[0].toUpperCase(),
- tokens[1].toUpperCase());
+ ambiguityCodes.put(tokens[0].toUpperCase(Locale.ROOT),
+ tokens[1].toUpperCase(Locale.ROOT));
}
else
{
}
} catch (IOException e)
{
- Cache.log.error(
+ Console.error(
"Error reading nucleotide ambiguity codes data file: "
+ e.getMessage());
}
line.lastIndexOf(QUOTE));
if (aminos.length() != NUCS_COUNT_CUBED) // 4 * 4 * 4 combinations
{
- Cache.log.error("wrong data length in code table: " + line);
+ Console.error("wrong data length in code table: " + line);
}
else
{
@Override
public String translateCanonical(String codon)
{
- return codons.get(codon.toUpperCase());
+ return codons.get(codon.toUpperCase(Locale.ROOT));
}
@Override
public String translate(String codon)
{
- String upper = codon.toUpperCase();
+ String upper = codon.toUpperCase(Locale.ROOT);
String peptide = translateCanonical(upper);
/*
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Point;
import jalview.math.MatrixI;
eigenMatrix.tqli();
} catch (Exception q)
{
- Cache.log.error("Error computing PCA: " + q.getMessage());
+ Console.error("Error computing PCA: " + q.getMessage());
q.printStackTrace();
}
}
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
{
if (s != null)
{
- id = s.toLowerCase();
+ id = s.toLowerCase(Locale.ROOT);
}
else
{
{
if (s instanceof String)
{
- return this.stringequals(((String) s).toLowerCase());
+ return this.stringequals(((String) s).toLowerCase(Locale.ROOT));
}
}
*/
package jalview.analysis;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.NodeTransformI;
if (one2many.contains(nam))
{
// countOne2Many++;
- // if (jalview.bin.Cache.log.isDebugEnabled())
- // jalview.bin.Cache.log.debug("One 2 many relationship for
+ // if (Cache.isDebugEnabled())
+ // Cache.debug("One 2 many relationship for
// "+nam.getName());
}
else
j.setPlaceholder(true);
}
}
- // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
- // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment
+ // if (Cache.isDebugEnabled() && countOne2Many>0) {
+ // Cache.debug("There were "+countOne2Many+" alignment
// sequence ids (out of "+one2many.size()+" unique ids) linked to two or
// more leaves.");
// }
* associated sequence object
*/
public boolean isPrimaryCandidate();
+
+ public boolean isCanonical();
}
* @return
*/
MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence, int pos);
+
+ /**
+ * Sends a message to let any registered parties know that something about
+ * feature rendering has changed
+ */
+ void notifyFeaturesChanged();
+
}
// interface, simplifying instantiating classes
/**
- * Answers true if the specified feature type is displayed
+ * Answers true if the specified feature type is to be displayed, false if no
+ * preference
*
* @param type
* @return
boolean isFeatureDisplayed(String type);
/**
+ * Answers true if the specified feature type is to be hidden, false if no
+ * preference
+ *
+ * @param type
+ * @return
+ */
+ boolean isFeatureHidden(String type);
+
+ /**
* Answers true if the specified feature group is displayed
*
* @param group
void setVisible(String featureType);
+ void setHidden(String featureType);
+
/**
* Sets all the specified feature types to visible. Visibility of other
* feature types is not changed.
*/
void stopProgressBar(String msg, long handle);
+ /**
+ *
+ * @return true if the actions menu is shown for this viewer
+ */
+ boolean hasViewerActionsMenu();
+
}
import javax.swing.LookAndFeel;
import javax.swing.UIManager;
-import org.apache.log4j.ConsoleAppender;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
-import org.apache.log4j.SimpleLayout;
-
import jalview.datamodel.PDBEntry;
import jalview.gui.Preferences;
import jalview.gui.UserDefinedColours;
+import jalview.log.JLoggerLog4j;
import jalview.schemes.ColourSchemeLoader;
import jalview.schemes.ColourSchemes;
import jalview.schemes.UserColourScheme;
* when shading by annotation</li>
* <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
* when shading by annotation</li>
- * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
- * requests to be redirected to a mirror of http://www.jalview.org</li>
+ * <li>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of https://www.jalview.org</li>
* <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
* alignment figure to accommodate even the longest sequence ID or annotation
* label.</li>
/**
* Initialises the Jalview Application Log
*/
- public static Logger log;
+
+ public final static String JALVIEW_LOGGER_NAME = "JalviewLogger";
// save the proxy properties set at startup
public final static String[] startupProxyProperties = {
private final static String JS_PROPERTY_PREFIX = "jalview_";
- public static void initLogger()
- {
- if (log != null)
- {
- return;
- }
- try
- {
- // TODO: redirect stdout and stderr here in order to grab the output of
- // the log
-
- ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
- "System.err");
- ap.setName("JalviewLogger");
- org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
- // log output
- Logger laxis = Logger.getLogger("org.apache.axis");
- Logger lcastor = Logger.getLogger("org.exolab.castor");
- jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
-
- laxis.setLevel(Level.toLevel(
- Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
- lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
- Level.INFO.toString())));
- lcastor = Logger.getLogger("org.exolab.castor.xml");
- lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
- Level.INFO.toString())));
- // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
- // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
- // Level.INFO.toString())));
- // we shouldn't need to do this
- org.apache.log4j.Logger.getRootLogger()
- .setLevel(org.apache.log4j.Level.INFO);
-
- jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
- .getDefault("logs.Jalview.level", Level.INFO.toString())));
- // laxis.addAppender(ap);
- // lcastor.addAppender(ap);
- // jalview.bin.Cache.log.addAppender(ap);
- // Tell the user that debug is enabled
- jalview.bin.Cache.log.debug(ChannelProperties.getProperty("app_name")
- + " Debugging Output Follows.");
- } catch (Exception ex)
- {
- System.err.println("Problems initializing the log4j system\n");
- ex.printStackTrace(System.err);
- }
- }
-
/**
* Loads properties from the given properties file. Any existing properties
* are first cleared.
default:
String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
+ proxyType;
- Cache.warn(message);
+ Console.warn(message);
}
// LOAD THE AUTHORS FROM THE authors.props file
SiftsSettings
.setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
- SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
+ SiftsSettings.setSiftDownloadDirectory(Cache
.getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
SiftsSettings.setFailSafePIDThreshold(
- jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
+ Cache.getDefault("sifts_fail_safe_pid_threshold",
DEFAULT_FAIL_SAFE_PID_THRESHOLD));
SiftsSettings.setCacheThresholdInDays(
- jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
+ Cache.getDefault("sifts_cache_threshold_in_days",
DEFAULT_CACHE_THRESHOLD_IN_DAYS));
IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
- "http://www.jalview.org/services/identifiers"));
+ "https://www.jalview.org/services/identifiers"));
IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
- StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
- .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+ StructureImportSettings.setDefaultStructureFileFormat(
+ Cache.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
StructureImportSettings
.setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
// StructureImportSettings
- // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+ // .setDefaultPDBFileParser(Cache.getDefault(
// "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
String jnlpVersion = System.getProperty("jalview.version");
if (jalview.jbgui.GDesktop.class.getClassLoader()
.loadClass("uk.ac.vamsas.client.VorbaId") != null)
{
- jalview.bin.Cache.log.debug(
- "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+ Console.debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
vamsasJarsArePresent = 1;
- Logger lvclient = Logger.getLogger("uk.ac.vamsas");
- lvclient.setLevel(Level.toLevel(Cache
- .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
-
- lvclient.addAppender(log.getAppender("JalviewLogger"));
+ JLoggerLog4j lvclient = JLoggerLog4j.getLogger("uk.ac.vamsas",
+ Console.getCachedLogLevel("logs.Vamsas.Level"));
+ JLoggerLog4j.addAppender(lvclient, Console.log, JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
lvclient.debug(ChannelProperties.getProperty("app_name")
+ " Vamsas Client Debugging Output Follows.");
} catch (Exception e)
{
vamsasJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Vamsas Classes are not present");
+ Console.debug("Vamsas Classes are not present");
}
}
return (vamsasJarsArePresent > 0);
if (Cache.class.getClassLoader()
.loadClass("groovy.lang.GroovyObject") != null)
{
- jalview.bin.Cache.log.debug(
- "Found Groovy (groovy.lang.GroovyObject can be loaded)");
+ Console.debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
groovyJarsArePresent = 1;
- Logger lgclient = Logger.getLogger("groovy");
- lgclient.setLevel(Level.toLevel(Cache
- .getDefault("logs.Groovy.Level", Level.INFO.toString())));
-
- lgclient.addAppender(log.getAppender("JalviewLogger"));
+ JLoggerLog4j lgclient = JLoggerLog4j.getLogger("groovy",
+ Console.getCachedLogLevel("logs.Groovy.Level"));
+ JLoggerLog4j.addAppender(lgclient, Console.log, JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
lgclient.debug(ChannelProperties.getProperty("app_name")
+ " Groovy Client Debugging Output Follows.");
} catch (Error e)
{
groovyJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
+ Console.debug("Groovy Classes are not present", e);
} catch (Exception e)
{
groovyJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Groovy Classes are not present");
+ Console.debug("Groovy Classes are not present");
}
}
return (groovyJarsArePresent > 0);
.loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
} catch (Exception e)
{
- log.debug(
- "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+ Console.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
tracker = null;
jgoogleanalyticstracker = null;
trackerfocus = null;
{ String.class, String.class, String.class })
.newInstance(new Object[]
{ ChannelProperties.getProperty("app_name") + " Desktop",
- (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
- + jalview.bin.Cache.getDefault("BUILD_DATE",
- "unknown")),
+ (vrs = Cache.getProperty("VERSION") + "_"
+ + Cache.getDefault("BUILD_DATE", "unknown")),
"UA-9060947-1" });
jgoogleanalyticstracker
.getMethod("trackAsynchronously", new Class[]
}
if (re != null || ex != null || err != null)
{
- if (log != null)
+ if (re != null)
{
- if (re != null)
- {
- log.debug("Caught runtime exception in googletracker init:",
- re);
- }
- if (ex != null)
- {
- log.warn(
- "Failed to initialise GoogleTracker for Jalview Desktop with version "
- + vrs,
- ex);
- }
- if (err != null)
- {
- log.error(
- "Whilst initing GoogleTracker for Jalview Desktop version "
- + vrs,
- err);
- }
+ Console.debug("Caught runtime exception in googletracker init:", re);
}
- else
+ if (ex != null)
{
- if (re != null)
- {
- System.err.println(
- "Debug: Caught runtime exception in googletracker init:"
- + vrs);
- re.printStackTrace();
- }
- if (ex != null)
- {
- System.err.println(
- "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
- + vrs);
- ex.printStackTrace();
- }
-
- if (err != null)
- {
- System.err.println(
- "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
- + vrs);
- err.printStackTrace();
- }
+ Console.warn("Failed to initialise GoogleTracker for Jalview Desktop with version "
+ + vrs, ex);
+ }
+ if (err != null)
+ {
+ Console.error("Whilst initing GoogleTracker for Jalview Desktop version "
+ + vrs, err);
}
}
else
{
- log.debug("Successfully initialised tracker.");
+ Console.debug("Successfully initialised tracker.");
}
}
}
Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
- log.warn("Couldn't parse '" + colprop + "' as a colour for "
- + property);
+ Console.warn("Couldn't parse '" + colprop + "' as a colour for " + property);
}
return (col == null) ? defcolour : col;
}
StringBuilder sb = new StringBuilder();
sb.append(ChannelProperties.getProperty("app_name"))
.append(" Version: ");
- sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
+ sb.append(Cache.getDefault("VERSION", "TEST"));
sb.append("\n");
sb.append(ChannelProperties.getProperty("app_name"))
.append(" Installation: ");
- sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+ sb.append(Cache.getDefault("INSTALLATION", "unknown"));
sb.append("\n");
sb.append("Build Date: ");
- sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+ sb.append(Cache.getDefault("BUILD_DATE", "unknown"));
sb.append("\n");
sb.append("Java version: ");
sb.append(System.getProperty("java.version"));
// Not displayed in release version ( determined by possible version number
// regex 9[9.]*9[.-_a9]* )
if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
- jalview.bin.Cache.getDefault("VERSION", "TEST")))
+ Cache.getDefault("VERSION", "TEST")))
{
appendIfNotNull(sb, "Getdown appdir: ",
System.getProperty("getdownappdir"), "\n", null);
{
// consider returning more human friendly info
// eg 'built from Source' or update channel
- return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
+ return Cache.getDefault("INSTALLATION", "unknown");
}
public static String getStackTraceString(Throwable t)
? " [" + startupProxyProperties[6] + "]"
: "");
- Cache.debug(sb.toString());
+ Console.debug(sb.toString());
}
public static void setProxyPropertiesFromPreferences()
case Cache.PROXYTYPE_NONE:
if (!previousProxyType.equals(proxyType))
{
- Cache.log.info("Setting no proxy settings");
+ Console.info("Setting no proxy settings");
Cache.setProxyProperties(null, null, null, null, null, null, null,
null, null);
}
case Cache.PROXYTYPE_CUSTOM:
// always re-set a custom proxy -- it might have changed, particularly
// password
- Cache.log.info("Setting custom proxy settings");
+ Console.info("Setting custom proxy settings");
boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false);
Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null),
Cache.getDefault("PROXY_PORT", null),
proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
break;
default: // system proxy settings by default
- Cache.log.info("Setting system proxy settings");
+ Console.info("Setting system proxy settings");
Cache.resetProxyProperties();
}
}
char[] displayHttpPw = new char[httpPassword == null ? 0
: httpPassword.length];
Arrays.fill(displayHttpPw, '*');
- Cache.debug("CACHE Proxy: setting new Authenticator with httpUser='"
+ Console.debug("CACHE Proxy: setting new Authenticator with httpUser='"
+ httpUser + "' httpPassword='" + displayHttpPw + "'");
if (!Platform.isJS())
/* *
// open Preferences -> Connections
String message = MessageManager
.getString("label.proxy_password_required");
- Preferences.openPreferences(Preferences.CONNECTIONS_TAB,
- message);
+ Preferences.openPreferences(
+ Preferences.TabRef.CONNECTIONS_TAB, message);
Preferences.getInstance()
.proxyAuthPasswordCheckHighlight(true, true);
}
&& getRequestingPort() == Integer
.valueOf(httpPort))
{
- Cache.debug(
+ Console.debug(
"AUTHENTICATOR returning PasswordAuthentication(\""
+ httpUser + "\", '"
+ new String(displayHttpPw) + "')");
{
char[] displayHttpsPw = new char[httpPassword.length];
Arrays.fill(displayHttpsPw, '*');
- Cache.debug(
+ Console.debug(
"AUTHENTICATOR returning PasswordAuthentication(\""
+ httpsUser + "\", '" + displayHttpsPw
+ "'");
}
} catch (NumberFormatException e)
{
- Cache.error("Problem with proxy port values [http:"
+ Console.error("Problem with proxy port values [http:"
+ httpPort + ", https:" + httpsPort + "]");
}
- Cache.debug(
+ Console.debug(
"AUTHENTICATOR after trying to get PasswordAuthentication");
}
}
// non proxy request
- Cache.debug("AUTHENTICATOR returning null");
+ Console.debug("AUTHENTICATOR returning null");
return null;
}
});
// required to re-enable basic authentication (should be okay for a
// local proxy)
- Cache.debug(
+ Console.debug(
"AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\"");
System.setProperty("jdk.http.auth.tunneling.disabledSchemes", "");
} catch (SecurityException e)
{
- Cache.error("Could not set default Authenticator");
- Cache.debug(getStackTraceString(e));
+ Console.error("Could not set default Authenticator");
+ Console.debug(getStackTraceString(e));
}
}
else
*
*/
{
- Cache.debug("AUTHENTICATOR setting default Authenticator to null");
+ Console.debug("AUTHENTICATOR setting default Authenticator to null");
Authenticator.setDefault(null);
}
}
// nonProxyHosts not currently configurable in Preferences
- Cache.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
+ Console.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
+ nonProxyHosts + "\"");
setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
}
}
}
- public final static int TRACE = 10;
-
- public final static int DEBUG = 20;
-
- public final static int INFO = 30;
-
- public final static int WARN = 40;
-
- public final static int ERROR = 50;
-
- public static boolean println(int level, String message)
- {
- if (Cache.log == null)
- {
- if (level >= WARN)
- System.err.println(message);
- else if (level >= INFO)
- System.out.println(message);
- // not printing debug or trace messages
- return false;
- }
- if (level >= ERROR)
- {
- Cache.log.error(message);
- }
- else if (level >= WARN)
- {
- Cache.log.warn(message);
- }
- else if (level >= INFO)
- {
- Cache.log.info(message);
- }
- else if (level >= DEBUG)
- {
- Cache.log.debug(message);
- }
- else
- {
- Cache.log.trace(message);
- }
- return true;
- }
-
- public static void trace(String message)
- {
- println(TRACE, message);
- }
-
- public static void debug(String message)
- {
- println(DEBUG, message);
- }
-
- public static void info(String message)
- {
- println(INFO, message);
- }
-
- public static void warn(String message)
- {
- println(WARN, message);
- }
-
- public static void error(String message)
- {
- println(ERROR, message);
- }
-
/**
* Getdown appbase methods
*/
--- /dev/null
+package jalview.bin;
+
+import jalview.log.JLogger;
+import jalview.log.JLoggerI.LogLevel;
+import jalview.log.JLoggerLog4j;
+import jalview.util.ChannelProperties;
+import jalview.util.Log4j;
+import jalview.util.Platform;
+
+public class Console
+{
+
+ public static JLoggerLog4j log;
+
+ public static void debug(String message, Throwable t)
+ {
+ if (Console.initLogger())
+ {
+ log.debug(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
+
+ }
+
+ public static void info(String message)
+ {
+ if (Console.initLogger())
+ {
+ log.info(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
+
+ }
+
+ public static void trace(String message, Throwable t)
+ {
+ if (Console.initLogger())
+ {
+ log.trace(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
+ }
+
+ public static void debug(String message)
+ {
+ if (Console.initLogger())
+ {
+ log.debug(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
+
+ }
+
+ public static void info(String message, Throwable t)
+ {
+ if (Console.initLogger())
+ {
+ log.info(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
+
+ }
+
+ public static void warn(String message)
+ {
+ if (Console.initLogger())
+ {
+ log.warn(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
+
+ }
+
+ public static void trace(String message)
+ {
+ if (Console.initLogger())
+ {
+ log.trace(message, null);
+ }
+ else
+ {
+ System.out.println(message);
+ }
+ }
+
+ public static void warn(String message, Throwable t)
+ {
+ if (Console.initLogger())
+ {
+ log.warn(message, t);
+ }
+ else
+ {
+ System.out.println(message);
+ t.printStackTrace();
+ }
+
+ }
+
+ public static void error(String message)
+ {
+ if (Console.initLogger())
+ {
+ log.error(message, null);
+ }
+ else
+ {
+ System.err.println(message);
+ }
+
+ }
+
+ public static void error(String message, Throwable t)
+ {
+ if (Console.initLogger())
+ {
+ log.error(message, t);
+ }
+ else
+ {
+ System.err.println(message);
+ t.printStackTrace(System.err);
+ }
+
+ }
+
+ public static void fatal(String message)
+ {
+ if (Console.initLogger())
+ {
+ log.fatal(message, null);
+ }
+ else
+ {
+ System.err.println(message);
+ }
+
+ }
+
+ public static void fatal(String message, Throwable t)
+ {
+ if (Console.initLogger())
+ {
+ log.fatal(message, t);
+ }
+ else
+ {
+ System.err.println(message);
+ t.printStackTrace(System.err);
+ }
+
+ }
+
+ public static boolean isDebugEnabled()
+ {
+ return log == null ? false : log.isDebugEnabled();
+ }
+
+ public static boolean isTraceEnabled()
+ {
+ return log == null ? false : log.isTraceEnabled();
+ }
+
+ public static JLogger.LogLevel getCachedLogLevel()
+ {
+ return Console.getCachedLogLevel(Cache.JALVIEWLOGLEVEL);
+ }
+
+ public static JLogger.LogLevel getCachedLogLevel(String key)
+ {
+ return JLogger.toLevel(Cache.getDefault(key, "INFO"));
+ }
+
+ public static boolean initLogger()
+ {
+ if (log != null)
+ {
+ return true;
+ }
+ try
+ {
+ JLogger.LogLevel cachedLevel = getCachedLogLevel();
+ if (!Platform.isJS())
+ {
+ Log4j.init(cachedLevel);
+ }
+ // log output
+ // is laxis used? Does getLogger do anything without a Logger object?
+ // Logger laxis = Log4j.getLogger("org.apache.axis", myLevel);
+ JLoggerLog4j.getLogger("org.apache.axis", cachedLevel);
+
+ // The main application logger
+ log = JLoggerLog4j.getLogger(Cache.JALVIEW_LOGGER_NAME, cachedLevel);
+ } catch (NoClassDefFoundError e)
+ {
+ System.err.println("Could not initialise the logger framework");
+ e.printStackTrace();
+ }
+
+ // Test message
+ if (log != null)
+ {
+ // Logging test message should got through the logger object
+ if (log.loggerExists())
+ log.debug(Console.LOGGING_TEST_MESSAGE);
+ // Tell the user that debug is enabled
+ debug(ChannelProperties.getProperty("app_name")
+ + " Debugging Output Follows.");
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ public final static String LOGGING_TEST_MESSAGE = "Logging to STDERR";
+
+}
package jalview.bin;
+import java.util.Locale;
+
import java.awt.HeadlessException;
public class HiDPISetting
static
{
String system = System.getProperty("os.name") == null ? null
- : System.getProperty("os.name").toLowerCase();
+ : System.getProperty("os.name").toLowerCase(Locale.ROOT);
if (system != null)
{
isLinux = system.indexOf("linux") > -1;
import java.security.Permissions;
import java.security.Policy;
import java.util.HashMap;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
import java.util.logging.ConsoleHandler;
}
// anything else!
+ // allow https handshakes to download intermediate certs if necessary
+ System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
+
final String jabawsUrl = aparser.getValue("jabaws");
if (jabawsUrl != null)
{
}
System.setProperty("http.agent",
"Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
+
try
{
- Cache.initLogger();
+ Console.initLogger();
} catch (NoClassDefFoundError error)
{
error.printStackTrace();
JalviewTaskbar.setTaskbar(this);
} catch (Exception e)
{
- Cache.log.info("Cannot set Taskbar");
- Cache.log.error(e.getMessage());
+ Console.info("Cannot set Taskbar");
+ Console.error(e.getMessage());
// e.printStackTrace();
} catch (Throwable t)
{
- Cache.log.info("Cannot set Taskbar");
- Cache.log.error(t.getMessage());
+ Console.info("Cannot set Taskbar");
+ Console.error(t.getMessage());
// t.printStackTrace();
}
{
// Start the desktop questionnaire prompter with the specified
// questionnaire
- Cache.log.debug("Starting questionnaire url at " + url);
+ Console.debug("Starting questionnaire url at " + url);
desktop.checkForQuestionnaire(url);
System.out.println("CMD questionnaire[-" + url
+ "] executed successfully!");
// String defurl =
// "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
// //
- String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
- Cache.log.debug(
+ String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
+ Console.debug(
"Starting questionnaire with default url: " + defurl);
desktop.checkForQuestionnaire(defurl);
}
*/
{
file = Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org", "http://www.jalview.org")
- + "/examples/exampleFile_2_7.jar");
- if (file.equals(
- "http://www.jalview.org/examples/exampleFile_2_3.jar"))
+ Cache.getDefault("www.jalview.org", "https://www.jalview.org")
+ + "/examples/exampleFile_2_7.jvp");
+ if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
+ || file.equals(
+ "http://www.jalview.org/examples/exampleFile_2_7.jar"))
{
+ file.replace("http:", "https:");
// hardwire upgrade of the startup file
- file.replace("_2_3.jar", "_2_7.jar");
+ file.replace("_2_3", "_2_7");
+ file.replace("2_7.jar", "2_7.jvp");
// and remove the stale setting
Cache.removeProperty("STARTUP_FILE");
}
lafSet = setCrossPlatformLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "system":
lafSet = setSystemLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "gtk":
lafSet = setGtkLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "metal":
lafSet = setMetalLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "nimbus":
lafSet = setNimbusLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "quaqua":
lafSet = setQuaquaLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "vaqua":
lafSet = setVaquaLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "mac":
lafSet = setMacLookAndFeel();
if (!lafSet)
{
- Cache.log.error("Could not set requested laf=" + laf);
+ Console.error("Could not set requested laf=" + laf);
}
break;
case "none":
break;
default:
- Cache.log.error("Requested laf=" + laf + " not implemented");
+ Console.error("Requested laf=" + laf + " not implemented");
}
if (!lafSet)
{
set = true;
} catch (Exception ex)
{
- Cache.log.error("Unexpected Look and Feel Exception");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Console.error("Unexpected Look and Feel Exception");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
return set;
}
set = true;
} catch (Exception ex)
{
- Cache.log.error("Unexpected Look and Feel Exception");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Console.error("Unexpected Look and Feel Exception");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
return set;
}
for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
{
if (info.getName() != null && nameStartsWith
- ? info.getName().toLowerCase()
- .startsWith(name.toLowerCase())
- : info.getName().toLowerCase().equals(name.toLowerCase()))
+ ? info.getName().toLowerCase(Locale.ROOT)
+ .startsWith(name.toLowerCase(Locale.ROOT))
+ : info.getName().toLowerCase(Locale.ROOT)
+ .equals(name.toLowerCase(Locale.ROOT)))
{
className = info.getClassName();
break;
set = true;
} catch (Exception ex)
{
- Cache.log.error("Unexpected Look and Feel Exception");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Console.error("Unexpected Look and Feel Exception");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
return set;
}
System.setProperty("apple.laf.useScreenMenuBar", "true");
set = setQuaquaLookAndFeel();
if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
- .toLowerCase().contains("quaqua"))
+ .toLowerCase(Locale.ROOT).contains("quaqua"))
{
set = setVaquaLookAndFeel();
}
+ "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+ "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
+ "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
- + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+ + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
}
private static void startUsageStats(final Desktop desktop)
@Override
public void run()
{
- Cache.log.debug(
- "Initialising googletracker for usage stats.");
+ Console.debug("Initialising googletracker for usage stats.");
Cache.initGoogleTracker();
- Cache.log.debug("Tracking enabled.");
+ Console.debug("Tracking enabled.");
}
}, new Runnable()
{
@Override
public void run()
{
- Cache.log.debug("Not enabling Google Tracking.");
+ Console.debug("Not enabling Google Tracking.");
}
}, null, true);
desktop.addDialogThread(prompter);
*/
package jalview.bin;
+import java.util.Locale;
+
import jalview.analysis.AlignmentUtils;
import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
final int pos = apos;
// use vamsas listener to broadcast to all listeners in scope
if (alignedPosition != null && (alignedPosition.trim().length() == 0
- || alignedPosition.toLowerCase().indexOf("false") > -1))
+ || alignedPosition.toLowerCase(Locale.ROOT).indexOf("false") > -1))
{
java.awt.EventQueue.invokeLater(new Runnable()
{
r--;
} catch (NumberFormatException ex)
{
- if (cl.toLowerCase().equals("sequence"))
+ if (cl.toLowerCase(Locale.ROOT).equals("sequence"))
{
// we are in the dataset sequence's coordinate frame.
inseqpos = true;
String externalsviewer = getParameter("externalstructureviewer");
if (externalsviewer != null)
{
- useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE);
+ useXtrnalSviewer = externalsviewer.trim().toLowerCase(Locale.ROOT).equals(TRUE);
}
/**
* if true disable the check for jmol
final String groups, boolean state)
{
final boolean st = state;// !(state==null || state.equals("") ||
- // state.toLowerCase().equals("false"));
+ // state.toLowerCase(Locale.ROOT).equals("false"));
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
*/
package jalview.bin;
+import java.util.Locale;
+
import java.io.File;
import java.io.IOException;
import java.lang.management.ManagementFactory;
import java.util.List;
import jalview.util.ChannelProperties;
+import jalview.util.LaunchUtils;
/**
* A Launcher class for Jalview. This class is used to launch Jalview from the
}
}
+ // use saved preferences if no cmdline args
+ boolean useCustomisedSettings = LaunchUtils
+ .getBooleanUserPreference(MemorySetting.CUSTOMISED_SETTINGS);
+ if (useCustomisedSettings)
+ {
+ if (jvmmempc == null)
+ {
+ jvmmempc = LaunchUtils
+ .getUserPreference(MemorySetting.MEMORY_JVMMEMPC);
+ }
+ if (jvmmemmax == null)
+ {
+ jvmmemmax = LaunchUtils
+ .getUserPreference(MemorySetting.MEMORY_JVMMEMMAX);
+ }
+ }
+
// add memory setting if not specified
boolean memSet = false;
boolean dockIcon = false;
process.waitFor();
} catch (IOException e)
{
- if (e.getMessage().toLowerCase().contains("memory"))
+ if (e.getMessage().toLowerCase(Locale.ROOT).contains("memory"))
{
System.out.println("Caught a memory exception: " + e.getMessage());
// Probably the "Cannot allocate memory" error, try without the memory
e.printStackTrace();
}
// System.exit(0);
-
}
}
/*
+
+ private static String ADJUSTMENT_MESSAGE = null;
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
private static final long NOMEM_MAX_HEAPSIZE_GB_DEFAULT = 8;
+ public static final String NS = "MEMORY";
+
+ public static final String CUSTOMISED_SETTINGS = NS
+ + "_CUSTOMISED_SETTINGS";
+
+ public static final String MEMORY_JVMMEMPC = NS + "_"
+ + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME.toUpperCase();
+
+ public static final String MEMORY_JVMMEMMAX = NS + "_"
+ + MAX_HEAPSIZE_PROPERTY_NAME.toUpperCase();
+
protected static boolean logToClassChecked = false;
+ public static String memorySuffixes = "bkmgt"; // order of the suffixes is
+ // important!
+
public static long getMemorySetting()
{
return getMemorySetting(null, null);
}
+ public static long getMemorySetting(String jvmmemmaxarg,
+ String jvmmempcarg)
+ {
+ return getMemorySetting(jvmmemmaxarg, jvmmempcarg, true, false);
+ }
+
/**
* Decide on appropriate memory setting for Jalview based on the two arguments
* values: jvmmempc - the maximum percentage of total physical memory to
* @param jvmmempcarg
* Max percentage of physical memory to use. Defaults to "90".
*
+ * @param useProps
+ * boolean to decide whether to look at System properties.
+ *
* @return The amount of memory (in bytes) to allocate to Jalview
*/
public static long getMemorySetting(String jvmmemmaxarg,
- String jvmmempcarg)
+ String jvmmempcarg, boolean useProps, boolean quiet)
{
// actual Xmx value-to-be
long maxMemLong = -1;
+ clearAdjustmentMessage();
// (absolute) jvmmaxmem setting, start with default
long memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
- if (jvmmemmaxarg == null)
+ if (jvmmemmaxarg == null && useProps)
{
jvmmemmaxarg = System.getProperty(MAX_HEAPSIZE_PROPERTY_NAME);
}
String jvmmemmax = jvmmemmaxarg;
if (jvmmemmax != null && jvmmemmax.length() > 0)
{
- long multiplier = 1;
- switch (jvmmemmax.toLowerCase().substring(jvmmemmax.length() - 1))
- {
- case "t":
- multiplier = 1099511627776L; // 2^40
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "g":
- multiplier = 1073741824; // 2^30
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "m":
- multiplier = 1048576; // 2^20
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "k":
- multiplier = 1024; // 2^10
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "b":
- multiplier = 1; // 2^0
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- default:
- break;
- }
-
// parse the arg
try
{
- memmax = Long.parseLong(jvmmemmax);
+ memmax = memoryStringToLong(jvmmemmax);
+ if (memmax == 0)
+ {
+ throw (new NumberFormatException("Not allowing 0"));
+ }
} catch (NumberFormatException e)
{
memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
- + "') badly formatted, using default ("
- + MAX_HEAPSIZE_GB_DEFAULT + "g).");
- }
-
- // apply multiplier if not too big (i.e. bigger than a long)
- if (Long.MAX_VALUE / memmax < multiplier)
- {
- memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
- System.out.println("MemorySetting Property '"
- + MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
- + ") too big, using default (" + MAX_HEAPSIZE_GB_DEFAULT
- + "g).");
- }
- else
- {
- memmax = multiplier * memmax;
+ + "') badly formatted or 0, using default ("
+ + MAX_HEAPSIZE_GB_DEFAULT + "g).", quiet);
}
// check at least minimum value (this accounts for negatives too)
if (memmax < APPLICATION_MIN_MEMORY)
{
memmax = APPLICATION_MIN_MEMORY;
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
+ ") too small, using minimum (" + APPLICATION_MIN_MEMORY
- + ").");
+ + ").", quiet);
}
}
else
{
// no need to warn if no setting
- // System.out.println("MemorySetting Property '" + maxHeapSizeProperty
+ // adjustmentMessage("MemorySetting Property '" + maxHeapSizeProperty
// + "' not
// set.");
}
// get max percent of physical memory, starting with default
float percent = MAX_HEAPSIZE_PERCENT_DEFAULT;
- if (jvmmempcarg == null)
+ if (jvmmempcarg == null && useProps)
{
jvmmempcarg = System.getProperty(MAX_HEAPSIZE_PERCENT_PROPERTY_NAME);
}
{
if (jvmmempc != null)
{
- float trypercent = Float.parseFloat(jvmmempc);
- if (0 < trypercent && trypercent <= 100f)
+ int trypercent = Integer.parseInt(jvmmempc);
+ if (0 <= trypercent && trypercent <= 100)
{
percent = trypercent;
}
else
{
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME
- + "' should be in range 1..100. Using default " + percent
- + "%");
+ + "' should be in range 0..100. Using default " + percent
+ + "%", quiet);
}
}
} catch (NumberFormatException e)
{
- System.out.println("MemorySetting property '"
+ setAdjustmentMessage("MemorySetting property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg
- + ") badly formatted");
+ + ") badly formatted", quiet);
}
// catch everything in case of no com.sun.management.OperatingSystemMXBean
{
mempc = physicalMem - LEAVE_FREE_MIN_MEMORY;
reducedmempc = true;
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg
+ ") too large. Leaving free space for OS and reducing to ("
- + mempc + ").");
+ + mempc + ").", quiet);
}
// check for minimum application memsize
{
if (reducedmempc)
{
- System.out.println("Reduced MemorySetting (" + mempc
+ setAdjustmentMessage("Reduced MemorySetting (" + mempc
+ ") too small. Increasing to application minimum ("
- + APPLICATION_MIN_MEMORY + ").");
+ + APPLICATION_MIN_MEMORY + ").", quiet);
}
else
{
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' ("
+ jvmmempcarg + ") too small. Using minimum ("
- + APPLICATION_MIN_MEMORY + ").");
+ + APPLICATION_MIN_MEMORY + ").", quiet);
}
mempc = APPLICATION_MIN_MEMORY;
}
{
// not enough memory for application, just try and grab what we can!
mempc = physicalMem;
- System.out.println(
+ setAdjustmentMessage(
"Not enough physical memory for application. Ignoring MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' ("
+ jvmmempcarg
+ "). Using maximum memory available ("
- + physicalMem + ").");
+ + physicalMem + ").",
+ quiet);
}
} catch (Throwable t)
{
memoryPercentError = true;
- System.out.println(
- "Problem calling GetMemory.getPhysicalMemory(). Likely to be problem with com.sun.management.OperatingSystemMXBean");
+ setAdjustmentMessage(
+ "Problem calling GetMemory.getPhysicalMemory(). Likely to be problem with com.sun.management.OperatingSystemMXBean",
+ quiet);
t.printStackTrace();
}
// == null))
&& memmax > NOMEM_MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE)
{
- System.out.println(
+ setAdjustmentMessage(
"Capping maximum memory to " + NOMEM_MAX_HEAPSIZE_GB_DEFAULT
- + "g due to failure to read physical memory size.");
+ + "g due to failure to read physical memory size.",
+ quiet);
memmax = NOMEM_MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
}
return maxMemLong;
}
-}
\ No newline at end of file
+ public static boolean isValidMemoryString(String text)
+ {
+ if (text.length() > 0)
+ {
+ char lastChar = text.charAt(text.length() - 1);
+ char[] otherChars = text.substring(0, text.length() - 1)
+ .toCharArray();
+ for (char c : otherChars)
+ {
+ if (c < '0' || c > '9')
+ {
+ return false;
+ }
+ }
+ if ((lastChar < '0' || lastChar > '9') && memorySuffixes
+ .indexOf(Character.toLowerCase(lastChar)) == -1)
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ public static long memoryStringToLong(String memString)
+ throws NumberFormatException
+ {
+ if (!isValidMemoryString(memString)) // not valid
+ {
+ throw (new NumberFormatException("Not a valid memory string"));
+ }
+ char suffix = Character
+ .toLowerCase(memString.charAt(memString.length() - 1));
+ if ('0' <= suffix && suffix <= '9') // no suffix
+ {
+ return Long.valueOf(memString);
+ }
+ if (memorySuffixes.indexOf(suffix) == -1) // suffix is unknown
+ {
+ return -1;
+ }
+
+ long multiplier = (long) Math.pow(2,
+ memorySuffixes.indexOf(suffix) * 10); // note order of suffixes in
+ // memorySuffixes important
+ // here!
+ // parse the arg. NumberFormatExceptions passed on to calling method
+ long mem = Long
+ .parseLong(memString.substring(0, memString.length() - 1));
+ if (mem == 0)
+ {
+ return 0;
+ }
+
+ // apply multiplier only if result is not too big (i.e. bigger than a long)
+ if (Long.MAX_VALUE / mem > multiplier)
+ {
+ return multiplier * mem;
+ }
+ else
+ {
+ // number too big for a Long. Limit to Long.MAX_VALUE
+ System.out.println("Memory parsing of '" + memString
+ + "' produces number too big. Limiting to Long.MAX_VALUE="
+ + Long.MAX_VALUE);
+ return Long.MAX_VALUE;
+ }
+ }
+
+ public static String memoryLongToString(long mem)
+ {
+ return memoryLongToString(mem, "%.3f");
+ }
+
+ public static String memoryLongToString(long mem, String format)
+ {
+ int exponent = 0;
+ float num = mem;
+ char suffix = 'b';
+
+ for (int i = 0; i < memorySuffixes.length(); i++)
+ {
+ char s = Character.toUpperCase(memorySuffixes.charAt(i));
+ if (mem < (long) Math.pow(2, exponent + 10)
+ || i == memorySuffixes.length() - 1) // last suffix
+ {
+ suffix = s;
+ num = (float) (mem / Math.pow(2, exponent));
+ break;
+ }
+ exponent += 10;
+ }
+
+ return String.format(format, num) + suffix;
+ }
+
+ private static String ADJUSTMENT_MESSAGE = null;
+
+ private static void setAdjustmentMessage(String reason, boolean quiet)
+ {
+ ADJUSTMENT_MESSAGE = reason;
+ if (!quiet)
+ {
+ System.out.println(reason);
+ }
+ }
+
+ public static void clearAdjustmentMessage()
+ {
+ ADJUSTMENT_MESSAGE = null;
+ }
+
+ public static String getAdjustmentMessage()
+ {
+ return ADJUSTMENT_MESSAGE;
+ }
+
+}
*/
package jalview.commands;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
if ((caseChange == TO_UPPER && doCommand)
|| (caseChange == TO_LOWER && !doCommand))
{
- newSeq.append(sequence.substring(start, end).toUpperCase());
+ newSeq.append(sequence.substring(start, end).toUpperCase(Locale.ROOT));
}
else if ((caseChange == TO_LOWER && doCommand)
|| (caseChange == TO_UPPER && !doCommand))
{
- newSeq.append(sequence.substring(start, end).toLowerCase());
+ newSeq.append(sequence.substring(start, end).toLowerCase(Locale.ROOT));
}
else
*/
package jalview.commands;
+import java.util.Locale;
+
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
new String(command.string[i]));
- if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
+ if (!nogaprep.toLowerCase(Locale.ROOT).equals(nogapold.toLowerCase(Locale.ROOT)))
{
// we may already have dataset and limits stashed...
if (newDSWasNeeded || newStartEndWasNeeded)
// old ds and edited ds are different, so
// create the new dataset sequence
SequenceI newds = new Sequence(oldds);
- newds.setSequence(fullseq.toUpperCase());
+ newds.setSequence(fullseq.toUpperCase(Locale.ROOT));
if (command.oldds == null)
{
// new
// start/end
String nogapalseq = AlignSeq.extractGaps(Comparison.GapChars,
- command.seqs[i].getSequenceAsString().toUpperCase());
+ command.seqs[i].getSequenceAsString().toUpperCase(Locale.ROOT));
int newStart = command.seqs[i].getDatasetSequence()
.getSequenceAsString().indexOf(nogapalseq);
if (newStart == -1)
*/
package jalview.datamodel;
-import jalview.util.MapList;
-import jalview.util.MappingUtils;
-
import java.util.AbstractList;
import java.util.ArrayList;
import java.util.List;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
+
/**
* Stores mapping between the columns of a protein alignment and a DNA alignment
* and a list of individual codon to amino acid mappings between sequences.
{
return mapping;
}
+
+ /**
+ * Returns true if the mapping covers the full length of the given sequence.
+ * This allows us to distinguish the CDS that codes for a protein from
+ * another overlapping CDS in the parent dna sequence.
+ *
+ * @param seq
+ * @return
+ */
+ public boolean covers(SequenceI seq)
+ {
+ return covers(seq,false,false);
+ }
+ /**
+ *
+ * @param seq
+ * @param localCover - when true - compare extent of seq's dataset sequence rather than the local extent
+ * @param either - when true coverage is required for either seq or the mapped sequence
+ * @return true if mapping covers full length of given sequence (or the other if either==true)
+ */
+ public boolean covers(SequenceI seq, boolean localCover,boolean either)
+ {
+ List<int[]> mappedRanges = null,otherRanges=null;
+ MapList mapList = mapping.getMap();
+ int mstart=seq.getStart(),mend=seq.getEnd(),ostart,oend;
+ ;
+ if (fromSeq == seq || fromSeq == seq.getDatasetSequence())
+ {
+ if (localCover && fromSeq !=seq)
+ {
+ mstart=fromSeq.getStart();
+ mend=fromSeq.getEnd();
+ }
+ mappedRanges = mapList.getFromRanges();
+ otherRanges=mapList.getToRanges();
+ ostart=mapping.to.getStart();
+ oend=mapping.to.getEnd();
+ }
+ else if (mapping.to == seq || mapping.to == seq.getDatasetSequence())
+ {
+ if (localCover && mapping.to !=seq)
+ {
+ mstart=mapping.to.getStart();
+ mend=mapping.to.getEnd();
+ }
+ mappedRanges = mapList.getToRanges();
+ otherRanges=mapList.getFromRanges();
+ ostart=fromSeq.getStart();
+ oend=fromSeq.getEnd();
+ }
+ else
+ {
+ return false;
+ }
+
+ /*
+ * check that each mapped range lies within the sequence range
+ * (necessary for circular CDS - example EMBL:J03321:AAA91567)
+ * and mapped length covers (at least) sequence length
+ */
+ int length = countRange(mappedRanges,mstart,mend);
+
+ if (length != -1)
+ {
+ // add 3 to mapped length to allow for a mapped stop codon
+ if (length + 3 >= (mend - mstart + 1))
+ {
+ return true;
+ }
+ }
+ if (either)
+ {
+ // also check coverage of the other range
+ length = countRange(otherRanges, ostart, oend);
+ if (length != -1)
+ {
+ if (length + 1 >= (oend - ostart + 1))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+ private int countRange(List<int[]> mappedRanges,int mstart,int mend)
+ {
+ int length=0;
+ for (int[] range : mappedRanges)
+ {
+ int from = Math.min(range[0], range[1]);
+ int to = Math.max(range[0], range[1]);
+ if (from < mstart || to > mend)
+ {
+ return -1;
+ }
+ length += (to - from + 1);
+ }
+ return length;
+ }
+
+ /**
+ * Adds any regions mapped to or from position {@code pos} in sequence
+ * {@code seq} to the given search results
+ * Note: recommend first using the .covers(,true,true) to ensure mapping covers both sequences
+ * @param seq
+ * @param pos
+ * @param sr
+ */
+ public void markMappedRegion(SequenceI seq, int pos, SearchResultsI sr)
+ {
+ int[] codon = null;
+ SequenceI mappedSeq = null;
+ SequenceI ds = seq.getDatasetSequence();
+ if (ds == null)
+ {
+ ds = seq;
+ }
+
+ if (this.fromSeq == seq || this.fromSeq == ds)
+ {
+ codon = this.mapping.map.locateInTo(pos, pos);
+ mappedSeq = this.mapping.to;
+ }
+ else if (this.mapping.to == seq || this.mapping.to == ds)
+ {
+ codon = this.mapping.map.locateInFrom(pos, pos);
+ mappedSeq = this.fromSeq;
+ }
+
+ if (codon != null)
+ {
+ for (int i = 0; i < codon.length; i += 2)
+ {
+ sr.addResult(mappedSeq, codon[i], codon[i + 1]);
+ }
+ }
+ }
}
private List<SequenceToSequenceMapping> mappings;
}
/**
+ * Return the corresponding aligned or dataset dna sequence for given amino
+ * acid sequence, or null if not found. returns the sequence from the first
+ * mapping found that involves the protein sequence.
*
- * @param sequenceRef
- * @return null or corresponding aaSeq entry for dnaSeq entry
+ * @param aaSeqRef
+ * @return
*/
public SequenceI getDnaForAaSeq(SequenceI aaSeqRef)
{
/**
* Add search results for regions in other sequences that translate or are
- * translated from a particular position in seq
+ * translated from a particular position in seq (which may be an aligned or
+ * dataset sequence)
*
* @param seq
* @param index
public void markMappedRegion(SequenceI seq, int index,
SearchResultsI results)
{
- int[] codon;
SequenceI ds = seq.getDatasetSequence();
- for (SequenceToSequenceMapping ssm : mappings)
+ if (ds == null)
{
- if (ssm.fromSeq == seq || ssm.fromSeq == ds)
- {
- codon = ssm.mapping.map.locateInTo(index, index);
- if (codon != null)
- {
- for (int i = 0; i < codon.length; i += 2)
- {
- results.addResult(ssm.mapping.to, codon[i], codon[i + 1]);
- }
- }
- }
- else if (ssm.mapping.to == seq || ssm.mapping.to == ds)
- {
- {
- codon = ssm.mapping.map.locateInFrom(index, index);
- if (codon != null)
- {
- for (int i = 0; i < codon.length; i += 2)
- {
- results.addResult(ssm.fromSeq, codon[i], codon[i + 1]);
- }
- }
- }
- }
+ ds = seq;
}
- }
-
- /**
- * Returns the DNA codon positions (base 1) for the given position (base 1) in
- * a mapped protein sequence, or null if no mapping is found.
- *
- * Intended for use in aligning cDNA to match aligned protein. Only the first
- * mapping found is returned, so not suitable for use if multiple protein
- * sequences are mapped to the same cDNA (but aligning cDNA as protein is
- * ill-defined for this case anyway).
- *
- * @param seq
- * the DNA dataset sequence
- * @param aaPos
- * residue position (base 1) in a protein sequence
- * @return
- */
- public int[] getDnaPosition(SequenceI seq, int aaPos)
- {
- /*
- * Adapted from markMappedRegion().
- */
- MapList ml = null;
- int i = 0;
for (SequenceToSequenceMapping ssm : mappings)
{
- if (ssm.fromSeq == seq)
- {
- ml = getdnaToProt()[i];
- break;
+ if (ssm.covers(seq,true,true)) {
+ ssm.markMappedRegion(ds, index, results);
}
- i++;
}
- return ml == null ? null : ml.locateInFrom(aaPos, aaPos);
}
/**
* Two AlignedCodonFrame objects are equal if they hold the same ordered list
* of mappings
*
- * @see SequenceToSequenceMapping#
+ * @see SequenceToSequenceMapping#equals
*/
@Override
public boolean equals(Object obj)
{
return mappings;
}
+
+ /**
+ * Returns the first mapping found which is between the two given sequences,
+ * and covers the full extent of both.
+ *
+ * @param seq1
+ * @param seq2
+ * @return
+ */
+ public SequenceToSequenceMapping getCoveringMapping(SequenceI seq1,
+ SequenceI seq2)
+ {
+ for (SequenceToSequenceMapping mapping : mappings)
+ {
+ if (mapping.covers(seq2) && mapping.covers(seq1))
+ {
+ return mapping;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Returns the first mapping found which is between the given dataset sequence
+ * and another, is a triplet mapping (3:1 or 1:3), and covers the full extent
+ * of both sequences involved
+ *
+ * @param seq
+ * @return
+ */
+ public SequenceToSequenceMapping getCoveringCodonMapping(SequenceI seq)
+ {
+ for (SequenceToSequenceMapping mapping : mappings)
+ {
+ if (mapping.getMapping().getMap().isTripletMap()
+ && mapping.covers(seq))
+ {
+ if (mapping.fromSeq == seq
+ && mapping.covers(mapping.getMapping().getTo()))
+ {
+ return mapping;
+ }
+ else if (mapping.getMapping().getTo() == seq
+ && mapping.covers(mapping.fromSeq))
+ {
+ return mapping;
+ }
+ }
+ }
+ return null;
+ }
}
*/
package jalview.datamodel;
+import java.util.Locale;
+
import jalview.analysis.Rna;
import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.analysis.WUSSParseException;
{
if (seqname && this.sequenceRef != null)
{
- int i = description.toLowerCase().indexOf("<html>");
+ int i = description.toLowerCase(Locale.ROOT).indexOf("<html>");
if (i > -1)
{
// move the html tag to before the sequence reference.
*/
package jalview.datamodel;
+import java.util.Locale;
+
import jalview.api.DBRefEntryI;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
int sourceKey = Integer.MIN_VALUE;
String canonicalSourceName;
+
+ boolean isCanonicalAccession=false;
/*
* maps from associated sequence to the database sequence's coordinate system
*/
public DBRefEntry(String source, String version, String accessionId)
{
- this(source, version, accessionId, null);
+ this(source, version, accessionId, null,false);
}
/**
*
* @param source
+ * may not be null
+ * @param version
+ * may be null
+ * @param accessionId
+ * may be null
+ */
+ public DBRefEntry(String source, String version, String accessionId, Mapping map)
+ {
+ this(source, version, accessionId, map,false);
+ }
+ /**
+ *
+ * @param source
* canonical source (turned to uppercase; cannot be null)
* @param version
* (source dependent version string or null)
* numbering or null)
*/
public DBRefEntry(String source, String version, String accessionId,
- Mapping map)
+ Mapping map,boolean isCanonical)
{
- this.source = source.toUpperCase();
+ this.source = source.toUpperCase(Locale.ROOT);
setVersion(version);
this.accessionId = accessionId;
this.map = map;
+ this.isCanonicalAccession=isCanonical;
}
/**
: new String(entry.getVersion())),
(entry.getAccessionId() == null ? ""
: new String(entry.getAccessionId())),
- (entry.getMap() == null ? null : new Mapping(entry.getMap())));
+ (entry.getMap() == null ? null : new Mapping(entry.getMap())),entry.isCanonical());
}
@Override
return true;
}
+ boolean improved=false;
/*
* source must either match or be both null
*/
return false;
}
+ if (!isCanonicalAccession && other.isCanonical())
+ {
+ isCanonicalAccession = true;
+ improved = true;
+ }
+ else
+ {
+ if (isCanonicalAccession && !other.isCanonical())
+ {
+ // other is not an authoritative source of canonical accessions
+ return false;
+ }
+ }
/*
* if my version is null, "0" or "source:0" then replace with other version,
* otherwise the versions have to match
if (version != null && (otherVersion == null
|| !version.equalsIgnoreCase(otherVersion)))
{
- return false;
+ // FIXME: there may be a problem with old version strings not allowing
+ // updating of dbrefentries
+ return improved;
}
}
/*
- * if I have no mapping, take that of the other dbref
+ * if I have no mapping, take that of the other dbref
+ * - providing it had a version and so do I
*/
if (map == null)
{
public void setAccessionId(String accessionId)
{
this.accessionId = accessionId;
-// this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase();
+// this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase(Locale.ROOT);
}
/**
{
this.source = source;
-// this.source = (source == null ? "" : source).toUpperCase();
+// this.source = (source == null ? "" : source).toUpperCase(Locale.ROOT);
// this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source);
// this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName);
}
public void setVersion(String version)
{
this.version = version;
- this.ucversion = (version == null ? null : version.toUpperCase());
+ this.ucversion = (version == null ? null : version.toUpperCase(Locale.ROOT));
}
@Override
public String getCanonicalSourceName() {
return (canonicalSourceName == null ? (canonicalSourceName = DBRefUtils.getCanonicalName(this.source)) : canonicalSourceName);
}
+
+ /**
+ *
+ * @param canonical
+ */
+ public void setCanonical(boolean canonical)
+ {
+ isCanonicalAccession = canonical;
+ }
+ /**
+ *
+ * @return true if this is the primary canonical accession for the database source
+ */
+ public boolean isCanonical()
+ {
+ // TODO Auto-generated method stub
+ return isCanonicalAccession;
+ }
}
* @author JimP
*
*/
+import java.util.Locale;
+
public class DBRefSource
{
public static final String UNIPROT = "UNIPROT";
- public static final String UP_NAME = "UNIPROT_NAME".toUpperCase();
+ public static final String UP_NAME = "UNIPROT_NAME".toUpperCase(Locale.ROOT);
/**
* Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
*/
- public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
+ public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase(Locale.ROOT);
public static final String ENSEMBL = "ENSEMBL";
public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
public static final String EMBL = "EMBL";
public static final String EMBLCDS = "EMBLCDS";
- public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase();
+ public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase(Locale.ROOT);
public static final String PDB = "PDB";
public static final String PFAM = "PFAM";
public static final String RFAM = "RFAM";
- public static final String GENEDB = "GeneDB".toUpperCase();
+ public static final String GENEDB = "GeneDB".toUpperCase(Locale.ROOT);
public static final String PDB_CANONICAL_NAME = PDB;
// see if there is a primary reference that derived this reference.
for (int i = allSources.length; --i >= 0;)
{
- if (ucversion.startsWith(allSources[i])) // BH 2019.01.25 .toUpperCase() unnecessary here for allSources
+ if (ucversion.startsWith(allSources[i])) // BH 2019.01.25 .toUpperCase(Locale.ROOT) unnecessary here for allSources
{
// by convention, many secondary references inherit the primary
// reference's
*/
package jalview.datamodel;
+import java.util.Locale;
+
import java.util.HashSet;
import java.util.List;
import java.util.Set;
* e.g. C,G,T gives variants G and T for base C
*/
Set<String> variantPeptides = new HashSet<>();
- String[] alleles = alls.toUpperCase().split(",");
+ String[] alleles = alls.toUpperCase(Locale.ROOT).split(",");
StringBuilder vars = new StringBuilder();
for (String allele : alleles)
{
- allele = allele.trim().toUpperCase();
+ allele = allele.trim().toUpperCase(Locale.ROOT);
if (allele.length() > 1 || "-".equals(allele))
{
continue; // multi-locus variant
*/
final int i = cdsPos == codonPos[0] ? 0
: (cdsPos == codonPos[1] ? 1 : 2);
- variantCodon[i] = allele.toUpperCase().charAt(0);
+ variantCodon[i] = allele.toUpperCase(Locale.ROOT).charAt(0);
if (variantCodon[i] == baseCodon[i])
{
continue;
public int[] getMappedPositions(int begin, int end)
{
MapList map = mapping.getMap();
- return mapping.to == featureSequence ? map.locateInFrom(begin, end)
- : map.locateInTo(begin, end);
+ return mapping.to == featureSequence ? map.getOverlapsInFrom(begin, end)
+ : map.getOverlapsInTo(begin, end);
}
/**
*/
package jalview.datamodel;
-import jalview.util.Comparison;
-import jalview.util.MapList;
-
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.Vector;
+import jalview.util.Comparison;
+import jalview.util.MapList;
+
public class Mapping
{
/**
}
/**
- * gets boundary in direction of mapping
- *
- * @param position
- * in mapped reference frame
- * @return int{start, end} positions in associated sequence (in direction of
- * mapped word)
- */
- public int[] getWord(int mpos)
- {
- if (map != null)
- {
- return map.getToWord(mpos);
- }
- return null;
- }
-
- /**
* width of mapped unit in associated sequence
*
*/
private static final int PDB_ID_LENGTH = 4;
+ /**
+ * property set when id is a 'manufactured' identifier from the structure data's filename
+ */
+ private static final String FAKED_ID = "faked_pdbid";
+ /**
+ * property set when the id is authoritative, and should be used in preference to any identifiers in the structure data
+ */
+ private static final String AUTHORITATIVE_ID = "authoritative_pdbid";
+
private String file;
private String type;
{
// TODO is FILE needed; if not is this enum needed, or can we
// use FileFormatI for PDB, MMCIF?
- PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), FILE("?", "?");
+ PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), BCIF("bcif","bcif"),FILE("?", "?");
/*
* file extension for cached structure file; must be one that
return false; // shouldn't happen
}
- /*
- * id has to match (ignoring case)
- */
- if (!getId().equalsIgnoreCase(newId))
- {
- return false;
- }
+ boolean idMatches = getId().equalsIgnoreCase(newId);
/*
* Don't update if associated with different structure files
*/
String newFile = newEntry.getFile();
- if (newFile != null && getFile() != null && !newFile.equals(getFile()))
+ if (newFile != null && getFile() != null)
{
- return false;
+ if (!newFile.equals(getFile()))
+ {
+ return false;
+ }
+ else
+ {
+ // files match.
+ if (!idMatches)
+ {
+ // this shouldn't happen, but could do if the id from the
+ // file is not the same as the id from the authority that provided
+ // the file
+ if (!newEntry.fakedPDBId() && !isAuthoritative())
+ {
+ return false;
+ } // otherwise we can update
+ }
+ }
+ }
+ else
+ {
+ // one has data, one doesn't ..
+ if (!idMatches)
+ {
+ return false;
+ } // otherwise maybe can update
}
/*
*/
String key = newProps.nextElement();
Object value = newEntry.getProperty(key);
+ if (FAKED_ID.equals(key) || AUTHORITATIVE_ID.equals(key))
+ {
+ // we never update the fake ID property
+ continue;
+ }
if (!value.equals(getProperty(key)))
{
setProperty(key, value);
}
return true;
}
+
+ public void setAuthoritative(boolean isAuthoritative)
+ {
+ setProperty(AUTHORITATIVE_ID, Boolean.valueOf(isAuthoritative));
+ }
+
+ /**
+ *
+ * @return true if the identifier should be preferred over any identifiers
+ * embedded in the structure data
+ */
+ public boolean isAuthoritative()
+ {
+ if (_hasProperty(AUTHORITATIVE_ID))
+ {
+ return ((Boolean)getProperty(AUTHORITATIVE_ID));
+ }
+ return false;
+ }
+
+ /**
+ * set when Jalview has manufactured the ID using a local filename
+ * @return
+ */
+ public boolean fakedPDBId()
+ {
+ if (_hasProperty(FAKED_ID))
+ {
+ return true;
+ }
+ return false;
+ }
+ public void setFakedPDBId(boolean faked)
+ {
+ if (faked)
+ {
+ setProperty(FAKED_ID, Boolean.TRUE);
+ }
+ else
+ {
+ if (properties!=null) {
+ properties.remove(FAKED_ID);
+ }
+ }
+ }
+
+ private boolean _hasProperty(final String key)
+ {
+ return (properties != null && properties.containsKey(key));
+ }
+
+ private static final String RETRIEVE_FROM = "RETRIEVE_FROM";
+
+ private static final String PROVIDER = "PROVIDER";
+
+ private static final String MODELPAGE = "PROVIDERPAGE";
+
+ /**
+ * Permanent URI for retrieving the original structure data
+ *
+ * @param urlStr
+ */
+ public void setRetrievalUrl(String urlStr)
+ {
+ setProperty(RETRIEVE_FROM, urlStr);
+ }
+
+ public boolean hasRetrievalUrl()
+ {
+ return _hasProperty(RETRIEVE_FROM);
+ }
+
+ /**
+ * get the Permanent URI for retrieving the original structure data
+ */
+ public String getRetrievalUrl()
+ {
+ return (String) getProperty(RETRIEVE_FROM);
+ }
+
+ /**
+ * Data provider name - from 3D Beacons
+ *
+ * @param provider
+ */
+ public void setProvider(String provider)
+ {
+ setProperty(PROVIDER, provider);
+ }
+
+ /**
+ * Get Data provider name - from 3D Beacons
+ *
+ */
+ public String getProvider()
+ {
+ return (String) getProperty(PROVIDER);
+ }
+
+ /**
+ * Permanent URI for retrieving the original structure data
+ *
+ * @param urlStr
+ */
+ public void setProviderPage(String urlStr)
+ {
+ setProperty(MODELPAGE, urlStr);
+ }
+
+ /**
+ * get the Permanent URI for retrieving the original structure data
+ */
+ public String getProviderPage()
+ {
+ return (String) getProperty(MODELPAGE);
+ }
+
+ public boolean hasProviderPage()
+ {
+ return _hasProperty(MODELPAGE);
+ }
+
+ public boolean hasProvider()
+ {
+ return _hasProperty(PROVIDER);
+ }
}
}
/**
- * Two SearchResults are considered equal if they contain the same matches in
- * the same order.
+ * Two SearchResults are considered equal if they contain the same matches
+ * (Sequence, start position, end position) in the same order
+ *
+ * @see Match#equals(Object)
*/
@Override
public boolean equals(Object obj)
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label)
{
+ return getAlignmentAnnotations(calcId, label, null, true);
+ }
+
+ @Override
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label, String description)
+ {
+ return getAlignmentAnnotations(calcId, label, description, false);
+ }
+
+ private List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label, String description, boolean ignoreDescription)
+ {
List<AlignmentAnnotation> result = new ArrayList<>();
if (this.annotation != null)
{
for (AlignmentAnnotation ann : annotation)
{
- if (ann.calcId != null && ann.calcId.equals(calcId)
- && ann.label != null && ann.label.equals(label))
+ if ((ann.calcId != null && ann.calcId.equals(calcId))
+ && (ann.label != null && ann.label.equals(label))
+ && ((ignoreDescription && description == null)
+ || (ann.description != null
+ && ann.description.equals(description))))
+
{
result.add(ann);
}
String consequence = "";
if (mf != null)
{
- int[] beginRange = mf.getMappedPositions(begin, begin);
- int[] endRange = mf.getMappedPositions(end, end);
- int from = beginRange[0];
- int to = endRange[endRange.length - 1];
+ int[] localRange = mf.getMappedPositions(begin, end);
+ int from = localRange[0];
+ int to = localRange[localRange.length - 1];
String s = mf.isFromCds() ? "Peptide Location" : "Coding location";
sb.append(String.format(ROW_DATA, s, seqName, from == to ? from
: from + (isContactFeature() ? ":" : "-") + to));
String label);
/**
+ * Returns a (possibly empty) list of any annotations that match on given
+ * calcId (source), label (type) and description (observation instance).
+ * Null values do not match.
+ *
+ * @param calcId
+ * @param label
+ * @param description
+ */
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label, String description);
+ /**
* create a new dataset sequence (if necessary) for this sequence and sets
* this sequence to refer to it. This call will move any features or
* references on the sequence onto the dataset. It will also make a duplicate
*/
package jalview.datamodel.features;
+import java.util.Locale;
+
import jalview.datamodel.SequenceFeature;
import jalview.util.MessageManager;
import jalview.util.matcher.Condition;
firstField = descriptor.substring(0, nextSpacePos);
leftToParse = descriptor.substring(nextSpacePos + 1).trim();
}
- String lower = firstField.toLowerCase();
- if (lower.startsWith(LABEL.toLowerCase()))
+ String lower = firstField.toLowerCase(Locale.ROOT);
+ if (lower.startsWith(LABEL.toLowerCase(Locale.ROOT)))
{
byLabel = true;
}
- else if (lower.startsWith(SCORE.toLowerCase()))
+ else if (lower.startsWith(SCORE.toLowerCase(Locale.ROOT)))
{
byScore = true;
}
}
Condition condition = matcher.getCondition();
- sb.append(SPACE).append(condition.toString().toLowerCase());
+ sb.append(SPACE).append(condition.toString().toLowerCase(Locale.ROOT));
if (condition.isNumeric())
{
sb.append(SPACE).append(matcher.getPattern());
*/
package jalview.datamodel.features;
+import java.util.Locale;
+
import jalview.datamodel.SequenceFeature;
import jalview.util.MessageManager;
if (!first)
{
String joiner = andConditions ? AND_18N : OR_I18N;
- sb.append(SPACE).append(joiner.toLowerCase()).append(SPACE);
+ sb.append(SPACE).append(joiner.toLowerCase(Locale.ROOT)).append(SPACE);
}
first = false;
if (multiple)
SequenceOntologyI so = SequenceOntologyFactory.getInstance();
@Override
- public boolean isFeatureDisplayed(String type)
+ public boolean isFeatureHidden(String type)
{
- return (so.isA(type, SequenceOntologyI.EXON)
- || so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT));
+ return (!so.isA(type, SequenceOntologyI.EXON)
+ && !so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT));
}
@Override
*/
package jalview.ext.ensembl;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.util.JSONUtils;
{
fetchDivisions();
}
- return divisions.get(division.toUpperCase());
+ return divisions.get(division.toUpperCase(Locale.ROOT));
}
/**
/*
* for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
*/
- divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ensemblDomain);
+ divisions.put(DBRefSource.ENSEMBL.toUpperCase(Locale.ROOT), ensemblDomain);
try
{
@SuppressWarnings("unchecked")
while (rvals.hasNext())
{
String division = rvals.next().toString();
- divisions.put(division.toUpperCase(), ensemblGenomesDomain);
+ divisions.put(division.toUpperCase(Locale.ROOT), ensemblGenomesDomain);
}
} catch (IOException | ParseException | NumberFormatException e)
{
*/
package jalview.ext.ensembl;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.GeneLociI;
import jalview.datamodel.GeneLocus;
chromosome, map);
} catch (NullPointerException | NumberFormatException e)
{
- Cache.log.error("Error looking up gene loci: " + e.getMessage());
+ Console.error("Error looking up gene loci: " + e.getMessage());
e.printStackTrace();
}
return null;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Dna;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
if (upx.size() > 1)
{
- Cache.log.warn(
+ Console.warn(
"Implementation issue - multiple uniprot acc on product sequence.");
}
}
*/
package jalview.ext.htsjdk;
-import jalview.bin.Cache;
-
import java.io.Closeable;
import java.io.File;
import java.io.IOException;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFFileReader;
import htsjdk.variant.vcf.VCFHeader;
+import jalview.bin.Console;
/**
* A thin wrapper for htsjdk classes to read either plain, or compressed, or
}
else
{
- Cache.log.error("File not found: " + filePath);
+ Console.error("File not found: " + filePath);
}
}
import java.util.StringTokenizer;
import java.util.Vector;
+import javax.swing.SwingUtilities;
+
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolSelectionListener;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
import jalview.api.SequenceRenderer;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.gui.AppJmol;
import jalview.gui.IProgressIndicator;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
+import jalview.ws.dbsources.Pdb;
import javajs.util.BS;
public abstract class JalviewJmolBinding extends AAStructureBindingModel
setStructureCommands(new JmolCommands());
/*
* viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
- * "jalviewJmol", ap.av.applet .getDocumentBase(),
- * ap.av.applet.getCodeBase(), "", this);
+ * "jalviewJmol", ap.av.applet .getDocumentBase(), ap.av.applet.getCodeBase(),
+ * "", this);
*
* jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
*/
private String jmolScript(String script)
{
- Cache.log.debug(">>Jmol>> " + script);
+ Console.debug(">>Jmol>> " + script);
String s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
- Cache.log.debug("<<Jmol<< " + s);
+ Console.debug("<<Jmol<< " + s);
return s;
}
for (int i = 0; i < modelCount; ++i)
{
/*
- * defensive check for null as getModelFileName can return null
- * even when model count ms.mc is > 0
+ * defensive check for null as getModelFileName can return null even when model
+ * count ms.mc is > 0
*/
filePath = jmolViewer.ms.getModelFileName(i);
if (filePath != null && !mset.contains(filePath))
}
/*
- * highlight position on alignment(s); if some text is returned,
- * show this as a second line on the structure hover tooltip
+ * highlight position on alignment(s); if some text is returned, show this as a
+ * second line on the structure hover tooltip
*/
String label = getSsm().mouseOverStructure(pdbResNum, chainId,
pdbfilename);
/*
* { if (history != null && strStatus != null &&
- * !strStatus.equals("Script completed")) { history.append("\n" + strStatus);
- * } }
+ * !strStatus.equals("Script completed")) { history.append("\n" + strStatus); }
+ * }
*/
public void notifyAtomPicked(int atomIndex, String strInfo,
@Override
public void notifyCallback(CBK type, Object[] data)
{
+ /*
+ * ensure processed in AWT thread to avoid risk of deadlocks
+ */
+ SwingUtilities.invokeLater(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ processCallback(type, data);
+ }
+ });
+ }
+
+ /**
+ * Processes one callback notification from Jmol
+ *
+ * @param type
+ * @param data
+ */
+ protected void processCallback(CBK type, Object[] data)
+ {
try
{
switch (type)
FeatureRenderer fr = getFeatureRenderer(null);
if (fr != null)
{
- fr.featuresAdded();
+ FeatureSettingsModelI colours = new Pdb().getFeatureColourScheme();
+ ((AppJmol) getViewer()).getAlignmentPanel().av
+ .applyFeaturesStyle(colours);
}
refreshGUI();
loadNotifiesHandled++;
public abstract void sendConsoleEcho(String strEcho); /*
* { showConsole(true);
*
- * history.append("\n" +
- * strEcho); }
+ * history.append("\n" + strEcho); }
*/
// /End JmolStatusListener
import jalview.structure.StructureCommandsBase;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.util.Comparison;
import jalview.util.Platform;
*/
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec)
+ AtomSpecModel atomSpec, AtomSpecType backbone)
{
StringBuilder sb = new StringBuilder(64);
String refModel = refAtoms.getModels().iterator().next();
* command examples don't include modelspec with atoms, getAtomSpec does;
* it works, so leave it as it is for simplicity
*/
- sb.append(getAtomSpec(atomSpec, true)).append("}{");
- sb.append(getAtomSpec(refAtoms, true)).append("}");
+ sb.append(getAtomSpec(atomSpec, backbone)).append("}{");
+ sb.append(getAtomSpec(refAtoms, backbone)).append("}");
sb.append(" ROTATE TRANSLATE ");
sb.append(getCommandSeparator());
/*
* show residues used for superposition as ribbon
*/
- sb.append("select ").append(getAtomSpec(atomSpec, false)).append("|");
- sb.append(getAtomSpec(refAtoms, false)).append(getCommandSeparator())
+ sb.append("select ").append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY)).append("|");
+ sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY)).append(getCommandSeparator())
.append("cartoons");
return Arrays.asList(new StructureCommand(sb.toString()));
* a separate clause in the {@code compare} (superposition) command.
*/
@Override
- public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(128);
*/
package jalview.ext.jmol;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import org.jmol.modelset.ModelSet;
import org.jmol.viewer.Viewer;
+import com.stevesoft.pat.Regex;
+
import mc_view.Atom;
import mc_view.PDBChain;
import mc_view.Residue;
{
Viewer viewer = null;
+ private boolean alphaFoldModel;
+
public JmolParser(boolean immediate, Object inFile,
DataSourceType sourceType) throws IOException
{
// }
// ;
// instead, we distinguish .cif from non-.cif by filename
- setStructureFileType(getDataName().toLowerCase().endsWith(".cif")
+ setStructureFileType(getDataName().toLowerCase(Locale.ROOT).endsWith(".cif")
? PDBEntry.Type.MMCIF.toString()
: "PDB");
}
return viewer;
}
+
+ public static Regex getNewAlphafoldValidator()
+ {
+ Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+ validator.setIgnoreCase(true);
+ return validator;
+ }
+ PDBEntry.Type jmolFiletype=null;
+ /**
+ * resolve a jmol filetype string and update the jmolFiletype field accordingly
+ * @param jmolIdentifiedFileType
+ * @return true if filetype was identified as MMCIF, PDB
+ */
+ public boolean updateFileType(String jmolIdentifiedFileType)
+ {
+ if (jmolIdentifiedFileType == null
+ || jmolIdentifiedFileType.trim().equals(""))
+ {
+ return false;
+ }
+ if ("mmcif".equalsIgnoreCase(jmolIdentifiedFileType)) {
+ jmolFiletype = PDBEntry.Type.MMCIF;
+ return true;
+ }
+ if ("pdb".equalsIgnoreCase(jmolIdentifiedFileType))
+ {
+ jmolFiletype = PDBEntry.Type.PDB;
+ return true;
+ }
+ return false;
+ }
+
public void transformJmolModelToJalview(ModelSet ms) throws IOException
{
try
{
+ Regex alphaFold = getNewAlphafoldValidator();
String lastID = "";
List<SequenceI> rna = new ArrayList<SequenceI>();
List<SequenceI> prot = new ArrayList<SequenceI>();
PDBChain tmpchain;
String pdbId = (String) ms.getInfo(0, "title");
-
+ boolean isMMCIF = false;
+ String jmolFileType_String = (String) ms.getInfo(0, "fileType");
+ if (updateFileType(jmolFileType_String))
+ {
+ setStructureFileType(jmolFiletype.toString());
+ }
+
+ isMMCIF = PDBEntry.Type.MMCIF.equals(jmolFiletype);
+
if (pdbId == null)
{
setId(safeName(getDataName()));
{
setId(pdbId);
setPDBIdAvailable(true);
+ alphaFoldModel = alphaFold.search(pdbId) && isMMCIF;
+
}
List<Atom> significantAtoms = convertSignificantAtoms(ms);
for (Atom tmpatom : significantAtoms)
tmpchain.atoms.addElement(tmpatom);
} else
{
- tmpchain = new PDBChain(getId(), tmpatom.chain);
+ String tempFString=null;
+ if (isAlphafoldModel())
+ {
+ tempFString = "Alphafold Reliability";
+ }
+
+ tmpchain = new PDBChain(getId(), tmpatom.chain,tempFString);
getChains().add(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
}
}
+ private boolean isAlphafoldModel()
+ {
+ return alphaFoldModel;
+ }
+
private List<Atom> convertSignificantAtoms(ModelSet ms)
{
List<Atom> significantAtoms = new ArrayList<Atom>();
/**
* Helper method that adds an AlignmentAnnotation for secondary structure to
- * the sequence, provided at least one secondary structure prediction has been
+ * the sequence, provided at least one secondary structure assignment has been
* made
*
* @param modelTitle
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec)
+ AtomSpecModel atomSpec, AtomSpecType specType)
{
+
// https://pymolwiki.org/index.php/Super
List<StructureCommandI> commands = new ArrayList<>();
- String refAtomsAlphaOnly = getAtomSpec(refAtoms, true);
- String atomSpec2AlphaOnly = getAtomSpec(atomSpec, true);
- commands.add(new StructureCommand("super", refAtomsAlphaOnly,
- atomSpec2AlphaOnly));
+ String refAtomsAlphaOnly = "("+getAtomSpec(refAtoms, specType)+" and (altloc '' or altloc 'a'))";
+ String atomSpec2AlphaOnly = "("+getAtomSpec(atomSpec, specType)+" and (altloc '' or altloc 'a'))";
+ // pair_fit mobile -> reference
+ commands.add(new StructureCommand("pair_fit",
+ atomSpec2AlphaOnly, refAtomsAlphaOnly));
/*
* and show superposed residues as cartoon
*/
- String refAtomsAll = getAtomSpec(refAtoms, false);
- String atomSpec2All = getAtomSpec(atomSpec, false);
+ String refAtomsAll = getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY);
+ String atomSpec2All = getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY);
commands.add(new StructureCommand("show", "cartoon",
refAtomsAll + " " + atomSpec2All));
* @see https://pymolwiki.org/index.php/Selection_Macros
*/
@Override
- public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(64);
boolean first = true;
}
}
sb.append("/");
- if (alphaOnly)
+ if (specType == AtomSpecType.ALPHA)
{
sb.append("CA");
}
+ if (specType == AtomSpecType.PHOSPHATE)
+ {
+ sb.append("P");
+ }
}
}
return sb.toString();
StringBuilder sb = new StringBuilder(128);
sb.append("p.").append(attributeName).append("='")
.append(attributeValue).append("'");
- String atomSpec = getAtomSpec(atomSpecModel, false);
+ String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
return new StructureCommand("iterate", atomSpec, sb.toString());
}
import java.util.List;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.Preferences;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
int rc = conn.getResponseCode();
if (rc != HttpURLConnection.HTTP_OK)
{
- Cache.log.error(
+ Console.error(
String.format("Error status from %s: %d", rpcUrl, rc));
return result;
}
} catch (SocketException e)
{
// thrown when 'quit' command is sent to PyMol
- Cache.log.warn(String.format("Request to %s returned %s", rpcUrl,
+ Console.warn(String.format("Request to %s returned %s", rpcUrl,
e.toString()));
} catch (Exception e)
{
{
out.close();
}
+ if (Console.isTraceEnabled())
+ {
+ Console.trace("Sent: " + command.toString());
+ if (result != null)
+ {
+ Console.trace("Received: " + result);
+ }
+ }
}
return result;
}
this.pymolXmlRpcPort = getPortNumber();
if (pymolXmlRpcPort > 0)
{
- Cache.log.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
+ Console.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
}
else
{
error += "Failed to read PyMOL XMLRPC port number";
- Cache.log.error(error);
+ Console.error(error);
pymolProcess.destroy();
pymolProcess = null;
}
}
} catch (Exception e)
{
- Cache.log.error("Failed to get REST port number from " + responses
+ Console.error("Failed to get REST port number from " + responses
+ ": " + e.getMessage());
// logger.error("Failed to get REST port number from " + responses + ": "
// + e.getMessage());
}
if (port == 0)
{
- Cache.log.error("Failed to start PyMOL with XMLRPC, response was: "
+ Console.error("Failed to start PyMOL with XMLRPC, response was: "
+ responses);
}
- Cache.log.error("PyMOL started with XMLRPC on port " + port);
+ Console.error("PyMOL started with XMLRPC on port " + port);
return port;
}
*/
package jalview.ext.rbvi.chimera;
+import java.util.Locale;
+
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsBase;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.util.ColorUtils;
/**
StringBuilder sb = new StringBuilder(128);
sb.append("setattr res ").append(attributeName).append(" '")
.append(attributeValue).append("' ");
- sb.append(getAtomSpec(atomSpecModel, false));
+ sb.append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY));
return new StructureCommand(sb.toString());
}
* Chimera treats an attribute name ending in 'color' as colour-valued;
* Jalview doesn't, so prevent this by appending an underscore
*/
- if (attName.toUpperCase().endsWith("COLOR"))
+ if (attName.toUpperCase(Locale.ROOT).endsWith("COLOR"))
{
attName += "_";
}
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
- AtomSpecModel spec)
+ AtomSpecModel spec, AtomSpecType backbone)
{
/*
* Form Chimera match command to match spec to ref
* @see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
*/
StringBuilder cmd = new StringBuilder();
- String atomSpecAlphaOnly = getAtomSpec(spec, true);
- String refSpecAlphaOnly = getAtomSpec(ref, true);
+ String atomSpecAlphaOnly = getAtomSpec(spec, backbone);
+ String refSpecAlphaOnly = getAtomSpec(ref, backbone);
cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly);
/*
* show superposed residues as ribbon
*/
- String atomSpec = getAtomSpec(spec, false);
- String refSpec = getAtomSpec(ref, false);
+ String atomSpec = getAtomSpec(spec, AtomSpecType.RESIDUE_ONLY);
+ String refSpec = getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY);
cmd.append("; ribbon ");
cmd.append(atomSpec).append("|").append(refSpec).append("; focus");
* <pre>
*
* @param model
- * @param alphaOnly
+ * @param specType
* @return
* @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
*/
@Override
- public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(128);
boolean firstModel = true;
sb.append("|");
}
firstModel = false;
- appendModel(sb, model, atomSpec, alphaOnly);
+ appendModel(sb, model, atomSpec, specType);
}
return sb.toString();
}
* @param alphaOnly
*/
protected void appendModel(StringBuilder sb, String model,
- AtomSpecModel atomSpec, boolean alphaOnly)
+ AtomSpecModel atomSpec, AtomSpecType specType)
{
sb.append("#").append(model).append(":");
firstPositionForModel = false;
}
}
- if (alphaOnly)
+ if (specType == AtomSpecType.ALPHA)
{
/*
* restrict to alpha carbon, no alternative locations
* (needed to ensuring matching atom counts for superposition)
*/
- // TODO @P instead if RNA - add nucleotide flag to AtomSpecModel?
sb.append("@CA").append(NO_ALTLOCS);
}
+ if (specType == AtomSpecType.PHOSPHATE)
+ {
+ sb.append("@P").append(NO_ALTLOCS);
+ }
}
@Override
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
/**
* Routines for generating ChimeraX commands for Jalview/ChimeraX binding
public class ChimeraXCommands extends ChimeraCommands
{
// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#resattr
- private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("info resattr");
+ private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand(
+ "info resattr");
// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/exit.html
- private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand("exit");
+ private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand(
+ "exit");
// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#notify
- private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("info notify stop selection jalview");
+ private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand(
+ "info notify stop selection jalview");
- private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("info notify stop models jalview");
+ private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand(
+ "info notify stop models jalview");
// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#selection
private static final StructureCommand GET_SELECTION = new StructureCommand(
}
/**
- * Returns a viewer command to set the given residue attribute value on
- * residues specified by the AtomSpecModel, for example
+ * Returns a viewer command to set the given residue attribute value on residues
+ * specified by the AtomSpecModel, for example
*
* <pre>
* setattr #0/A:3-9,14-20,39-43 res jv_strand 'strand' create true
String attributeValue, AtomSpecModel atomSpecModel)
{
StringBuilder sb = new StringBuilder(128);
- sb.append("setattr ").append(getAtomSpec(atomSpecModel, false));
+ sb.append("setattr ").append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY));
sb.append(" res ").append(attributeName).append(" '")
.append(attributeValue).append("'");
sb.append(" create true");
* Returns the range(s) formatted as a ChimeraX atomspec, for example
* <p>
* #1/A:2-20,30-40/B:10-20|#2/A:12-30
+ * <p>
+ * Note there is no need to explicitly exclude ALTLOC atoms when
+ * {@code alphaOnly == true}, as this is the default behaviour of ChimeraX (a
+ * change from Chimera)
*
* @return
*/
@Override
- public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(128);
boolean firstModel = true;
}
firstModel = false;
appendModel(sb, model, atomSpec);
- if (alphaOnly)
+ if (specType == AtomSpecType.ALPHA)
{
- // TODO @P if RNA - add nucleotide flag to AtomSpecModel?
sb.append("@CA");
}
- // todo: is there ChimeraX syntax to exclude altlocs?
+ if (specType == AtomSpecType.PHOSPHATE)
+ {
+ sb.append("@P");
+ }
}
return sb.toString();
}
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
- AtomSpecModel spec)
+ AtomSpecModel spec, AtomSpecType backbone)
{
/*
* Form ChimeraX match command to match spec to ref
* @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/align.html
*/
StringBuilder cmd = new StringBuilder();
- String atomSpec = getAtomSpec(spec, true);
- String refSpec = getAtomSpec(ref, true);
+ String atomSpec = getAtomSpec(spec, backbone);
+ String refSpec = getAtomSpec(ref, backbone);
cmd.append("align ").append(atomSpec).append(" toAtoms ")
.append(refSpec);
* show superposed residues as ribbon, others as chain
*/
cmd.append("; ribbon ");
- cmd.append(getAtomSpec(spec, false)).append("|");
- cmd.append(getAtomSpec(ref, false)).append("; view");
+ cmd.append(getAtomSpec(spec, AtomSpecType.RESIDUE_ONLY)).append("|");
+ cmd.append(getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY)).append("; view");
return Arrays.asList(new StructureCommand(cmd.toString()));
}
public List<StructureCommandI> startNotifications(String uri)
{
List<StructureCommandI> cmds = new ArrayList<>();
- cmds.add(new StructureCommand("info notify start models jalview prefix ModelChanged url " + uri));
- cmds.add(new StructureCommand("info notify start selection jalview prefix SelectionChanged url " + uri));
+ cmds.add(new StructureCommand(
+ "info notify start models jalview prefix ModelChanged url "
+ + uri));
+ cmds.add(new StructureCommand(
+ "info notify start selection jalview prefix SelectionChanged url "
+ + uri));
return cmds;
}
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
if (getResponse)
{
reply = lastReply;
- if (Cache.log.isDebugEnabled()) {
- Cache.log.debug(
+ if (Console.isDebugEnabled()) {
+ Console.debug(
"Response from command ('" + cmd + "') was:\n" + lastReply);
}
}
+ else
+ {
+ if (Console.isDebugEnabled())
+ {
+ Console.debug("Command executed: " + cmd);
+ }
+ }
return reply;
}
{
return;
}
-
+ if (!found)
+ {
+ // not a valid residue label command, so clear
+ cmd.setLength(0);
+ }
/*
- * unshow the label for the previous residue
+ * prepend with command
+ * to unshow the label for the previous residue
*/
if (lastHighlightCommand != null)
{
- executeCommand(false, null, new StructureCommand("~" + lastHighlightCommand));
+ cmd.insert(0, ";");
+ cmd.insert(0,lastHighlightCommand);
+ cmd.insert(0,"~");
+
}
- if (found)
- {
- executeCommand(false, null, new StructureCommand(command));
+ if (cmd.length()>0) {
+ executeCommand(true, null, new StructureCommand(cmd.toString()));
+ }
+
+ if (found) {
+ this.lastHighlightCommand = command;
}
- this.lastHighlightCommand = command;
}
/**
atomSpecs.add(spec);
} catch (IllegalArgumentException e)
{
- Cache.log.error("Failed to parse atomspec: " + atomSpec);
+ Console.error("Failed to parse atomspec: " + atomSpec);
}
}
return atomSpecs;
spec = parseAtomSpec(atomSpec);
} catch (IllegalArgumentException e)
{
- Cache.log.error("Problem parsing atomspec " + atomSpec);
+ Console.error("Problem parsing atomspec " + atomSpec);
continue;
}
import org.biojava.nbio.ontology.io.OboParser;
import org.biojava.nbio.ontology.utils.Annotation;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.io.gff.SequenceOntologyI;
/**
}
}
long elapsed = System.currentTimeMillis() - now;
- Cache.log.info("Loaded Sequence Ontology from " + zipFile + " ("
+ Console.info("Loaded Sequence Ontology from " + zipFile + " ("
+ elapsed + "ms)");
} catch (Exception e)
{
boolean oldTermIsObsolete = isObsolete(replaced);
if (newTermIsObsolete && !oldTermIsObsolete)
{
- Cache.log.debug("Ignoring " + term.getName()
+ Console.debug("Ignoring " + term.getName()
+ " as obsolete and duplicated by "
+ replaced.getName());
term = replaced;
}
else if (!newTermIsObsolete && oldTermIsObsolete)
{
- Cache.log.debug("Ignoring " + replaced.getName()
+ Console.debug("Ignoring " + replaced.getName()
+ " as obsolete and duplicated by " + term.getName());
}
else
{
- Cache.log.debug("Warning: " + term.getName()
+ Console.debug("Warning: " + term.getName()
+ " has replaced " + replaced.getName()
+ " for lookup of '" + description + "'");
}
{
if (!termsNotFound.contains(term))
{
- Cache.log.error("SO term " + term + " invalid");
+ Console.error("SO term " + term + " invalid");
termsNotFound.add(term);
}
}
package jalview.fts.api;
import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
/**
* Fetch index of the primary key column for the dynamic table
- *
+ * TODO: consider removing 'hasRefSeq' - never used in code
* @param wantedFields
* the available table columns
* @param hasRefSeq
* @return the default response page size
*/
public int getDefaultResponsePageSize();
+
+ public String[] getPreferencesColumnsFor(PreferenceSource source);
}
--- /dev/null
+package jalview.fts.api;
+
+import java.util.Collection;
+
+public interface StructureFTSRestClientI
+{
+
+ Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns();
+
+}
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
import jalview.fts.api.FTSRestClientI;
+import jalview.fts.api.StructureFTSRestClientI;
import jalview.fts.service.pdb.PDBFTSRestClient;
import java.util.ArrayList;
import javax.swing.table.AbstractTableModel;
import javax.swing.table.TableModel;
import javax.swing.table.TableRowSorter;
-
+/**
+ * Helps render GUI allowing control of which columns to show for entries returned from an FTS query.
+ * TODO: push down FTSClient specific code
+ *
+ * @author tcofoegbu
+ *
+ */
@SuppressWarnings("serial")
public class FTSDataColumnPreferences extends JScrollPane
{
if (source.equals(PreferenceSource.STRUCTURE_CHOOSER)
|| source.equals(PreferenceSource.PREFERENCES))
{
- structSummaryColumns = ((PDBFTSRestClient) ftsRestClient)
+ structSummaryColumns = ((StructureFTSRestClientI) ftsRestClient)
.getAllDefaultDisplayedStructureDataColumns();
}
allFTSDataColumns.addAll(ftsRestClient.getAllFTSDataColumns());
this.getViewport().add(tbl_FTSDataColumnPrefs);
this.currentSource = source;
- String[] columnNames = null;
- switch (source)
- {
- case SEARCH_SUMMARY:
- columnNames = new String[] { "", "Display", "Group" };
- break;
- case STRUCTURE_CHOOSER:
- columnNames = new String[] { "", "Display", "Group" };
- break;
- case PREFERENCES:
- columnNames = new String[] { "PDB Field", "Show in search summary",
- "Show in structure summary" };
- break;
- default:
- break;
- }
+ String[] columnNames = ftsRestClient.getPreferencesColumnsFor(source);
- Object[][] data = new Object[allFTSDataColumns.size() - 1][3];
+ Object[][] data = new Object[allFTSDataColumns.size()][3];
int x = 0;
for (FTSDataColumnI field : allFTSDataColumns)
- {
+ {
+ //System.out.println("allFTSDataColumns==" + allFTSDataColumns);
if (field.getName().equalsIgnoreCase("all"))
{
continue;
data[x++] = new Object[] { ftsRestClient
.getAllDefaultDisplayedFTSDataColumns().contains(field),
field.getName(), field.getGroup() };
+ //System.out.println(" PUIS " + field.getName() + " ET AUSSI " + field.getGroup() + "X = " + x);
break;
case STRUCTURE_CHOOSER:
data[x++] = new Object[] { structSummaryColumns.contains(field),
*/
package jalview.fts.core;
+import java.util.Locale;
+
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Collection;
+import java.util.HashMap;
import java.util.Objects;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
+import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
import jalview.fts.api.FTSRestClientI;
/**
private int defaultResponsePageSize = 100;
+ protected HashMap<String,String> mockQueries = null;
+
protected FTSRestClient()
{
public DataTypeI getDataType()
{
final String[] dataTypeString = lineData[2].split("\\|");
- final String classString = dataTypeString[0].toUpperCase();
+ final String classString = dataTypeString[0].toUpperCase(Locale.ROOT);
return new DataTypeI()
{
if (dataTypeString.length > 1
&& dataTypeString[1] != null)
{
- switch (dataTypeString[1].toUpperCase())
+ switch (dataTypeString[1].toUpperCase(Locale.ROOT))
{
case "T":
case "TRUE":
"Couldn't find data column with name : " + nameOrCode);
}
+ /**
+ *
+ * @param instance
+ * @param mocks {{working query, working response}, ...}
+ */
+ public static void createMockFTSRestClient(FTSRestClient instance,String[][] mocks)
+ {
+ instance.setMock(mocks);
+ }
+
@Override
public FTSDataColumnGroupI getDataColumnGroupById(String id)
throws Exception
return String.valueOf(code) + " " + message;
}
+ public static void unMock(FTSRestClient instance)
+ {
+ instance.mockQueries=null;
+ }
+
protected String getResourceFile(String fileName)
{
String result = "";
return defaultResponsePageSize;
}
+ protected void setMock(String[][] mocks)
+ {
+ if (mocks==null) {
+ mockQueries=null;
+ return;
+ }
+ mockQueries=new HashMap<String,String>();
+ for (String[] mock:mocks)
+ {
+ mockQueries.put(mock[0],mock[1]);
+ }
+ }
+
+ protected boolean isMocked()
+ {
+ return mockQueries!=null;
+ }
+
+ @Override
+ public String[] getPreferencesColumnsFor(PreferenceSource source)
+ {
+ String[] columnNames = null;
+ switch (source)
+ {
+ case SEARCH_SUMMARY:
+ columnNames = new String[] { "", "Display", "Group" };
+ break;
+ default:
+ // non structure sources don't return any other kind of preferences columns
+ break;
+ }
+ return columnNames;
+ }
}
{
this.offSet = offSet;
}
+
+ /**
+ * locate column given field name
+ * @param string - field name
+ * @return -1 if not located
+ */
+ public int getFieldIndex(String string)
+ {
+ int i=associatedSequence!=null ? 1 : 0;
+ for (FTSDataColumnI field:wantedFields)
+ {
+ if (field.getName().equals(string))
+ {
+ return i;
+ }
+ i++;
+ }
+ return -1;
+ }
}
public class FTSRestResponse
{
private int numberOfItemsFound;
-
+
private String responseTime;
private Collection<FTSData> searchSummary;
btn_autosearch.setText(MessageManager.getString("option.autosearch"));
btn_autosearch.setToolTipText(
MessageManager.getString("option.enable_disable_autosearch"));
+ // disable autosearch by default
btn_autosearch.setSelected(!Platform.isJS()
- && Cache.getDefault(getAutosearchPreference(), true));
+ && Cache.getDefault(getAutosearchPreference(), false));
btn_autosearch.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- jalview.bin.Cache.setProperty(getAutosearchPreference(),
+ Cache.setProperty(getAutosearchPreference(),
Boolean.toString(btn_autosearch.isSelected()));
}
});
import java.util.Map;
import java.util.Objects;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
}
} catch (Exception mfe)
{
- jalview.bin.Cache.log.debug("Exception accessing urls", mfe);
+ Console.debug("Exception accessing urls", mfe);
continue;
}
int colCounter = 0;
*/
package jalview.fts.service.pdb;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
import java.net.URI;
+import java.nio.CharBuffer;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Iterator;
import jalview.fts.api.FTSData;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
+import jalview.fts.api.StructureFTSRestClientI;
+import jalview.fts.core.FTSDataColumnPreferences;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.core.FTSRestClient;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
* @author tcnofoegbu
*/
public class PDBFTSRestClient extends FTSRestClient
+ implements StructureFTSRestClientI
{
private static FTSRestClientI instance = null;
// Build request parameters for the REST Request
- // BH 2018 the trick here is to coerce the classes in Javascript to be
- // different from the ones in Java yet still allow this to be correct for Java
+ // BH 2018 the trick here is to coerce the classes in Javascript to be
+ // different from the ones in Java yet still allow this to be correct for
+ // Java
Client client;
Class<ClientResponse> clientResponseClass;
if (Platform.isJS())
URI uri = webResource.getURI();
- // System.out.println(uri);
-
- // Execute the REST request
- ClientResponse clientResponse = webResource
- .accept(MediaType.APPLICATION_JSON).get(clientResponseClass );
-
+ System.out.println(uri);
+ ClientResponse clientResponse = null;
+ int responseStatus = -1;
// Get the JSON string from the response object or directly from the
// client (JavaScript)
Map<String, Object> jsonObj = null;
String responseString = null;
- // System.out.println("query >>>>>>> " + pdbRestRequest.toString());
+ System.out.println("query >>>>>>> " + pdbRestRequest.toString());
+
+ if (!isMocked())
+ {
+ // Execute the REST request
+ clientResponse = webResource.accept(MediaType.APPLICATION_JSON)
+ .get(clientResponseClass);
+ responseStatus = clientResponse.getStatus();
+ }
+ else
+ {
+ // mock response
+ if (mockQueries.containsKey(uri.toString()))
+ {
+ responseStatus = 200;
+ }
+ else
+ {
+ // FIXME - may cause unexpected exceptions for callers when mocked
+ responseStatus = 400;
+ }
+ }
// Check the response status and report exception if one occurs
- int responseStatus = clientResponse.getStatus();
switch (responseStatus)
{
case 200:
- if (Platform.isJS())
+
+ if (isMocked())
{
- jsonObj = clientResponse.getEntity(Map.class);
+ responseString = mockQueries.get(uri.toString());
}
else
{
- responseString = clientResponse.getEntity(String.class);
+ if (Platform.isJS())
+ {
+ jsonObj = clientResponse.getEntity(Map.class);
+ }
+ else
+ {
+ responseString = clientResponse.getEntity(String.class);
+ }
}
break;
case 400:
- throw new Exception(parseJsonExceptionString(responseString));
+ throw new Exception(isMocked() ? "400 response (Mocked)"
+ : parseJsonExceptionString(responseString));
default:
throw new Exception(
getMessageByHTTPStatusCode(responseStatus, "PDB"));
return parsePDBJsonResponse(responseString, jsonObj, pdbRestRequest);
} catch (Exception e)
{
+ if (e.getMessage() == null)
+ {
+ throw (e);
+ }
String exceptionMsg = e.getMessage();
if (exceptionMsg.contains("SocketException"))
{
* @return the processed error message from the JSON string
*/
@SuppressWarnings("unchecked")
-public static String parseJsonExceptionString(String jsonErrorResponse)
+ public static String parseJsonExceptionString(String jsonErrorResponse)
{
StringBuilder errorMessage = new StringBuilder(
"\n============= PDB Rest Client RunTime error =============\n");
-
-// {
-// "responseHeader":{
-// "status":0,
-// "QTime":0,
-// "params":{
-// "q":"(text:q93xj9_soltu) AND molecule_sequence:['' TO *] AND status:REL",
-// "fl":"pdb_id,title,experimental_method,resolution",
-// "start":"0",
-// "sort":"overall_quality desc",
-// "rows":"500",
-// "wt":"json"}},
-// "response":{"numFound":1,"start":0,"docs":[
-// {
-// "experimental_method":["X-ray diffraction"],
-// "pdb_id":"4zhp",
-// "resolution":2.46,
-// "title":"The crystal structure of Potato ferredoxin I with 2Fe-2S cluster"}]
-// }}
-//
+ // {
+ // "responseHeader":{
+ // "status":0,
+ // "QTime":0,
+ // "params":{
+ // "q":"(text:q93xj9_soltu) AND molecule_sequence:['' TO *] AND status:REL",
+ // "fl":"pdb_id,title,experimental_method,resolution",
+ // "start":"0",
+ // "sort":"overall_quality desc",
+ // "rows":"500",
+ // "wt":"json"}},
+ // "response":{"numFound":1,"start":0,"docs":[
+ // {
+ // "experimental_method":["X-ray diffraction"],
+ // "pdb_id":"4zhp",
+ // "resolution":2.46,
+ // "title":"The crystal structure of Potato ferredoxin I with 2Fe-2S
+ // cluster"}]
+ // }}
+ //
try
{
- Map<String, Object> jsonObj = (Map<String, Object>) JSONUtils.parse(jsonErrorResponse);
- Map<String, Object> errorResponse = (Map<String, Object>) jsonObj.get("error");
+ Map<String, Object> jsonObj = (Map<String, Object>) JSONUtils
+ .parse(jsonErrorResponse);
+ Map<String, Object> errorResponse = (Map<String, Object>) jsonObj
+ .get("error");
Map<String, Object> responseHeader = (Map<String, Object>) jsonObj
.get("responseHeader");
- Map<String, Object> paramsObj = (Map<String, Object>) responseHeader.get("params");
+ Map<String, Object> paramsObj = (Map<String, Object>) responseHeader
+ .get("params");
String status = responseHeader.get("status").toString();
String message = errorResponse.get("msg").toString();
String query = paramsObj.get("q").toString();
{
if (jsonObj == null)
{
- jsonObj = (Map<String, Object>) JSONUtils.parse(pdbJsonResponseString);
+ jsonObj = (Map<String, Object>) JSONUtils
+ .parse(pdbJsonResponseString);
}
- Map<String, Object> pdbResponse = (Map<String, Object>) jsonObj.get("response");
- String queryTime = ((Map<String, Object>) jsonObj.get("responseHeader"))
- .get("QTime").toString();
+ Map<String, Object> pdbResponse = (Map<String, Object>) jsonObj
+ .get("response");
+ String queryTime = ((Map<String, Object>) jsonObj
+ .get("responseHeader")).get("QTime").toString();
int numFound = Integer
.valueOf(pdbResponse.get("numFound").toString());
List<Object> docs = (List<Object>) pdbResponse.get("docs");
- // add in any alphafold bits at the top
- result = AlphafoldRestClient.getFTSData(pdbRestRequest);
+
+ result = new ArrayList<FTSData>();
if (numFound > 0)
{
- for (Iterator<Object> docIter = docs.iterator(); docIter
- .hasNext();)
+ for (Iterator<Object> docIter = docs.iterator(); docIter.hasNext();)
{
Map<String, Object> doc = (Map<String, Object>) docIter.next();
result.add(getFTSData(doc, pdbRestRequest));
}
}
- searchResult.setNumberOfItemsFound(result.size());
+ // this is the total number found by the query,
+ // rather than the set returned in SearchSummary
+ searchResult.setNumberOfItemsFound(numFound);
searchResult.setResponseTime(queryTime);
searchResult.setSearchSummary(result);
for (FTSDataColumnI field : diplayFields)
{
+ // System.out.println("Field " + field);
String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
: pdbJsonDoc.get(field.getCode()).toString();
+ // System.out.println("Field Data : " + fieldData);
if (field.isPrimaryKeyColumn())
{
primaryKey = fieldData;
private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
+ @Override
public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
{
if (allDefaultDisplayedStructureDataColumns == null
}
return allDefaultDisplayedStructureDataColumns;
}
-
-
+
+ @Override
+ public String[] getPreferencesColumnsFor(PreferenceSource source)
+ {
+ String[] columnNames = null;
+ switch (source)
+ {
+ case SEARCH_SUMMARY:
+ columnNames = new String[] { "", "Display", "Group" };
+ break;
+ case STRUCTURE_CHOOSER:
+ columnNames = new String[] { "", "Display", "Group" };
+ break;
+ case PREFERENCES:
+ columnNames = new String[] { "PDB Field", "Show in search summary",
+ "Show in structure summary" };
+ break;
+ default:
+ break;
+ }
+ return columnNames;
+ }
}
--- /dev/null
+/tdbresttest2.java
--- /dev/null
+package jalview.fts.service.threedbeacons;
+
+import java.util.Map;
+import java.util.Objects;
+
+import jalview.fts.api.FTSData;
+
+/**
+ * TDB result bean - holds filtered fields for GUI and essential metadata fields
+ * for back end
+ *
+ * @author jprocter
+ *
+ */
+public class TDB_FTSData implements FTSData
+{
+ String primaryKey;
+
+ Object[] summaryRowData;
+
+ /*
+ * fields in the JSON object
+ */
+ public static String Uniprot_Id= "id";
+ public static String Uniprot_Start= "uniprot_start";
+ public static String Uniprot_End= "uniprot_end";
+ public static String Provider= "provider";
+ public static String Model_id= "model_identifier";
+ public static String Model_Category= "model_category";
+ public static String Model_Type= "model_type";
+ public static String Model_Title="model_title";
+ public static String Resolution= "resolution";
+ public static String Confidence= "confidence_avg_local_score";
+ public static String Confidence_Score_Type= "confidence_type";
+ public static String Confidence_Score_Version= "confidence_version";
+ public static String Coverage= "coverage";
+ public static String Sequence_Identity= "sequence_identity";
+ public static String Created_Date= "created";
+ public static String UniProt_Accession= "uniprot_accession";
+ public static String Url= "model_url";
+ public static String Page_URL= "model_page_url";
+ public static String Ensemble_Sample_Url= "ensembl_sample_url";
+
+ /**
+ * original response from server
+ */
+ Map<String, Object> tdb_entry;
+
+ public TDB_FTSData(String primaryKey,
+ Map<String, Object> tdbJsonStructure, Object[] summaryData)
+ {
+ this.primaryKey = primaryKey;
+ tdb_entry = tdbJsonStructure;
+ this.summaryRowData = summaryData;
+ }
+
+ public Object getField(String key)
+ {
+ return tdb_entry.get(key);
+ }
+
+ @Override
+ public Object[] getSummaryData()
+ {
+ return summaryRowData;
+ }
+
+ @Override
+ public Object getPrimaryKey()
+ {
+ return primaryKey;
+ }
+
+ /**
+ * Returns a string representation of this object;
+ */
+ @Override
+ public String toString()
+ {
+ StringBuilder summaryFieldValues = new StringBuilder();
+ for (Object summaryField : summaryRowData)
+ {
+ summaryFieldValues
+ .append(summaryField == null ? " " : summaryField.toString())
+ .append("\t");
+ }
+ return summaryFieldValues.toString();
+ }
+
+ /**
+ * Returns hash code value for this object
+ */
+ @Override
+ public int hashCode()
+ {
+ return Objects.hash(primaryKey, this.toString());
+ }
+
+ @Override
+ public boolean equals(Object that)
+ {
+ return this.toString().equals(that.toString());
+ }
+
+ public String getProvider()
+ {
+ return (String) getField(Provider);
+ }
+
+ public String getModelViewUrl()
+ {
+ return (String) getField(Page_URL);
+ }
+
+ public String getModelId()
+ {
+ return (String) getField(Model_id);
+ }
+
+}
--- /dev/null
+package jalview.fts.service.threedbeacons;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+
+import javax.swing.SwingUtilities;
+
+import org.json.JSONArray;
+import org.json.JSONObject;
+
+import jalview.bin.Console;
+import jalview.datamodel.AlignmentI;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.core.GFTSPanel;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.gui.SequenceFetcher;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
+
+@SuppressWarnings("serial")
+public class TDBeaconsFTSPanel extends GFTSPanel
+{
+ private static String defaultFTSFrameTitle = MessageManager
+ .getString("label.pdb_sequence_fetcher");
+
+ private static Map<String, Integer> tempUserPrefs = new HashMap<>();
+
+ private static final String THREEDB_FTS_CACHE_KEY = "CACHE.THREEDB_FTS";
+
+ private static final String THREEDB_AUTOSEARCH = "FTS.THREEDB.AUTOSEARCH";
+
+ private static HttpURLConnection connection;
+
+ public TDBeaconsFTSPanel(SequenceFetcher fetcher)
+ {
+ // no ID retrieval option for TD Beacons just now
+ super(null);
+ pageLimit = TDBeaconsFTSRestClient.getInstance()
+ .getDefaultResponsePageSize();
+ this.seqFetcher = fetcher;
+ this.progressIndicator = (fetcher == null) ? null
+ : fetcher.getProgressIndicator();
+ }
+
+ @Override
+ public void searchAction(boolean isFreshSearch)
+ {
+ mainFrame.requestFocusInWindow();
+ if (isFreshSearch)
+ {
+ offSet = 0;
+ }
+ new Thread()
+ {
+ @Override
+ public void run()
+ {
+ reset();
+ boolean allowEmptySequence = false;
+ if (getTypedText().length() > 0)
+ {
+ setSearchInProgress(true);
+ long startTime = System.currentTimeMillis();
+
+ String searchTarget = ((FTSDataColumnI) cmb_searchTarget
+ .getSelectedItem()).getCode();
+ wantedFields = TDBeaconsFTSRestClient.getInstance()
+ .getAllDefaultDisplayedFTSDataColumns();
+ String searchTerm = getTypedText(); // to add : decodeSearchTerm
+
+ FTSRestRequest request = new FTSRestRequest();
+ request.setAllowEmptySeq(allowEmptySequence);
+ request.setResponseSize(100);
+ // expect it to be uniprot accesssion
+ request.setSearchTerm(searchTerm + ".json");
+ request.setOffSet(offSet);
+ request.setWantedFields(wantedFields);
+ FTSRestClientI tdbRestClient = TDBeaconsFTSRestClient
+ .getInstance();
+ FTSRestResponse resultList;
+ try
+ {
+ resultList = tdbRestClient.executeRequest(request);
+ } catch (Exception e)
+ {
+ setErrorMessage(e.getMessage());
+ checkForErrors();
+ setSearchInProgress(false);
+ return;
+ }
+
+ if (resultList.getSearchSummary() != null
+ && resultList.getSearchSummary().size() > 0)
+ {
+ getResultTable().setModel(FTSRestResponse.getTableModel(request,
+ resultList.getSearchSummary()));
+ FTSRestResponse.configureTableColumn(getResultTable(),
+ wantedFields, tempUserPrefs);
+ getResultTable().setVisible(true);
+ }
+
+ long endTime = System.currentTimeMillis();
+ totalResultSetCount = resultList.getNumberOfItemsFound();
+ resultSetCount = resultList.getSearchSummary() == null ? 0
+ : resultList.getSearchSummary().size();
+ String result = (resultSetCount > 0)
+ ? MessageManager.getString("label.results")
+ : MessageManager.getString("label.result");
+
+ if (isPaginationEnabled() && resultSetCount > 0)
+ {
+ String f1 = totalNumberformatter
+ .format(Integer.valueOf(offSet + 1));
+ String f2 = totalNumberformatter
+ .format(Integer.valueOf(offSet + resultSetCount));
+ String f3 = totalNumberformatter
+ .format(Integer.valueOf(totalResultSetCount));
+ updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
+ + " " + f1 + " to " + f2 + " of " + f3 + " " + " ("
+ + (endTime - startTime) + " milli secs)");
+ }
+ else
+ {
+ updateSearchFrameTitle(defaultFTSFrameTitle + " - "
+ + resultSetCount + " " + result + " ("
+ + (endTime - startTime) + " milli secs)");
+ }
+
+ setSearchInProgress(false);
+ refreshPaginatorState();
+ updateSummaryTableSelections();
+ }
+ txt_search.updateCache();
+ }
+ }.start();
+ }
+
+ @Override
+ public void okAction()
+ {
+ // mainFrame.dispose();
+ disableActionButtons();
+ StringBuilder selectedIds = new StringBuilder();
+ final HashSet<String> selectedIdsSet = new HashSet<>();
+ int primaryKeyColIndex = 0;
+ try
+ {
+ primaryKeyColIndex = getFTSRestClient()
+ .getPrimaryKeyColumIndex(wantedFields, false);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ int[] selectedRows = getResultTable().getSelectedRows();
+ String searchTerm = getTypedText();
+ for (int summaryRow : selectedRows)
+ {
+ String idStr = getResultTable()
+ .getValueAt(summaryRow, primaryKeyColIndex).toString();
+ selectedIdsSet.add(idStr);
+ }
+
+ for (String idStr : paginatorCart)
+ {
+ selectedIdsSet.add(idStr);
+ }
+
+ for (String selectedId : selectedIdsSet)
+ {
+ selectedIds.append(selectedId).append(";");
+ }
+
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ AlignmentI allSeqs = null;
+ FormatAdapter fl = new jalview.io.FormatAdapter();
+ for (String tdbURL : selectedIdsSet)
+ {
+ try
+ {
+ // retrieve the structure via its URL
+ AlignmentI tdbAl = fl.readFile(tdbURL, DataSourceType.URL,
+ FileFormat.MMCif);
+
+ // TODO: pad structure according to its Uniprot Start so all line up w.r.t. the Uniprot reference sequence
+ // TODO: give the structure a sensible name (not the giant URL *:o) )
+ if (tdbAl != null)
+ {
+ if (allSeqs != null)
+ {
+ allSeqs.append(tdbAl);
+ }
+ else
+ {
+ allSeqs = tdbAl;
+ }
+ }
+ } catch (Exception x)
+ {
+ Console.warn(
+ "Couldn't retrieve 3d-beacons model for uniprot id"
+ + searchTerm + " : " + tdbURL,
+ x);
+ }
+ }
+ seqFetcher.parseResult(allSeqs,
+ "3D-Beacons models for " + searchTerm, FileFormat.MMCif,
+ null);
+
+ }
+ });
+ delayAndEnableActionButtons();
+ }
+
+ @Override
+ public FTSRestClientI getFTSRestClient()
+ {
+ return TDBeaconsFTSRestClient.getInstance();
+ }
+
+ @Override
+ public String getFTSFrameTitle()
+ {
+ return defaultFTSFrameTitle;
+ }
+
+ @Override
+ public boolean isPaginationEnabled()
+ {
+ return true;
+ }
+
+ @Override
+ public Map<String, Integer> getTempUserPrefs()
+ {
+ return tempUserPrefs;
+ }
+
+ @Override
+ public String getCacheKey()
+ {
+ return THREEDB_FTS_CACHE_KEY;
+ }
+
+ @Override
+ public String getAutosearchPreference()
+ {
+ return THREEDB_AUTOSEARCH;
+ }
+
+ @Override
+ protected void showHelp()
+ {
+ System.out.println("No help implemented yet.");
+
+ }
+
+ public static String decodeSearchTerm(String enteredText)
+ {
+ // no multiple query support yet
+ return enteredText;
+ }
+}
--- /dev/null
+package jalview.fts.service.threedbeacons;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+
+import javax.ws.rs.core.MediaType;
+
+import org.json.simple.parser.ParseException;
+
+import com.sun.jersey.api.client.Client;
+import com.sun.jersey.api.client.ClientResponse;
+import com.sun.jersey.api.client.WebResource;
+import com.sun.jersey.api.client.config.DefaultClientConfig;
+
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.api.StructureFTSRestClientI;
+import jalview.fts.core.FTSRestClient;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.util.JSONUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+public class TDBeaconsFTSRestClient extends FTSRestClient
+ implements StructureFTSRestClientI
+{
+ /**
+ * production server URI
+ */
+ private static String TDB_PROD_API="https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+ /**
+ * dev server URI
+ */
+ private static String TDB_DEV_API="https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+ private static String DEFAULT_THREEDBEACONS_DOMAIN = TDB_PROD_API;
+
+ public static FTSRestClientI instance = null;
+
+ protected TDBeaconsFTSRestClient()
+ {
+ }
+ @SuppressWarnings("unchecked")
+ @Override
+ public FTSRestResponse executeRequest(FTSRestRequest tdbRestRequest)
+ throws Exception
+ {
+ try
+ {
+ String query = tdbRestRequest.getSearchTerm();
+ Client client;
+ Class<ClientResponse> clientResponseClass;
+ if (Platform.isJS())
+ {
+ // JavaScript only
+ client = (Client) (Object) new jalview.javascript.web.Client();
+ clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ client = Client.create(new DefaultClientConfig());
+ clientResponseClass = ClientResponse.class;
+ }
+
+ WebResource webResource;
+ webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN+query);
+
+ URI uri = webResource.getURI();
+ System.out.println(uri.toString());
+
+ // Execute the REST request
+ ClientResponse clientResponse;
+ if (isMocked()) {
+ clientResponse = null;
+ }
+ else
+ {
+ clientResponse = webResource.accept(MediaType.APPLICATION_JSON)
+ .get(clientResponseClass);
+ }
+
+ // Get the JSON string from the response object or directly from the
+ // client (JavaScript)
+ Map<String, Object> jsonObj = null;
+ String responseString = null;
+
+ // Check the response status and report exception if one occurs
+ int responseStatus = isMocked() ? (mockQueries.containsKey(query) ? 200 : 404) : clientResponse.getStatus();
+ switch (responseStatus)
+ {
+ // if success
+ case 200:
+ if (Platform.isJS())
+ {
+ jsonObj = clientResponse.getEntity(Map.class);
+ }
+ else
+ {
+ responseString = isMocked() ? mockQueries.get(query): clientResponse.getEntity(String.class);
+ }
+ break;
+ case 400:
+ throw new Exception(parseJsonExceptionString(responseString));
+ case 404:
+ return emptyTDBeaconsJsonResponse();
+ default:
+ throw new Exception(
+ getMessageByHTTPStatusCode(responseStatus, "3DBeacons"));
+ }
+ // Process the response and return the result to the caller.
+ return parseTDBeaconsJsonResponse(responseString, jsonObj,
+ tdbRestRequest);
+ } catch (Exception e)
+ {
+ String exceptionMsg = e.getMessage();
+ if (exceptionMsg != null)
+ {
+ if (exceptionMsg.contains("SocketException"))
+ {
+ // No internet connection
+ throw new Exception(MessageManager.getString(
+ "exception.unable_to_detect_internet_connection"));
+ }
+ else if (exceptionMsg.contains("UnknownHostException"))
+ {
+ // The server is unreachable
+ throw new Exception(MessageManager.formatMessage(
+ "exception.fts_server_unreachable", "3DB Hub"));
+ }
+ }
+ throw e;
+
+ }
+
+ }
+
+ /**
+ * returns response for when the 3D-Beacons service doesn't have a record for
+ * the given query - in 2.11.2 this triggers a failover to the PDBe FTS
+ *
+ * @return null
+ */
+ private FTSRestResponse emptyTDBeaconsJsonResponse()
+ {
+ return null;
+ }
+
+ public String setSearchTerm(String term)
+ {
+ return term;
+ }
+
+ public static FTSRestResponse parseTDBeaconsJsonResponse(
+ String tdbJsonResponseString, FTSRestRequest tdbRestRequest)
+ {
+ return parseTDBeaconsJsonResponse(tdbJsonResponseString,
+ (Map<String, Object>) null, tdbRestRequest);
+ }
+
+ @SuppressWarnings("unchecked")
+ public static FTSRestResponse parseTDBeaconsJsonResponse(
+ String tdbJsonResponseString, Map<String, Object> jsonObj,
+ FTSRestRequest tdbRestRequest)
+ {
+ FTSRestResponse searchResult = new FTSRestResponse();
+ List<FTSData> result = null;
+
+ try
+ {
+ if (jsonObj == null)
+ {
+ jsonObj = (Map<String, Object>) JSONUtils
+ .parse(tdbJsonResponseString);
+ }
+
+ Object uniprot_entry = jsonObj.get("uniprot_entry");
+ // TODO: decide if anything from uniprot_entry needs to be reported via
+ // the FTSRestResponse object
+ // Arnaud added seqLength = (Long) ((Map<String, Object>)
+ // jsonObj.get("uniprot_entry")).get("sequence_length");
+
+ List<Object> structures = (List<Object>) jsonObj.get("structures");
+ result = new ArrayList<>();
+
+ int numFound = 0;
+ for (Iterator<Object> strucIter = structures.iterator(); strucIter
+ .hasNext();)
+ {
+ Map<String, Object> structure = (Map<String, Object>) strucIter
+ .next();
+ result.add(getFTSData(structure, tdbRestRequest));
+ numFound++;
+ }
+
+ searchResult.setNumberOfItemsFound(numFound);
+ searchResult.setSearchSummary(result);
+
+ } catch (ParseException e)
+ {
+ e.printStackTrace();
+ }
+ return searchResult;
+ }
+
+ private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
+ FTSRestRequest tdbRequest)
+ {
+ String primaryKey = null;
+ Object[] summaryRowData;
+
+ SequenceI associatedSequence;
+
+ Collection<FTSDataColumnI> displayFields = tdbRequest.getWantedFields();
+ SequenceI associatedSeq = tdbRequest.getAssociatedSequence();
+ int colCounter = 0;
+ summaryRowData = new Object[(associatedSeq != null)
+ ? displayFields.size() + 1
+ : displayFields.size()];
+ if (associatedSeq != null)
+ {
+ associatedSequence = associatedSeq;
+ summaryRowData[0] = associatedSequence;
+ colCounter = 1;
+ }
+
+ for (FTSDataColumnI field : displayFields)
+ {
+ String fieldData = (tdbJsonStructure.get(field.getCode()) == null)
+ ? " "
+ : tdbJsonStructure.get(field.getCode()).toString();
+ // System.out.println("Field : " + field + " Data : " + fieldData);
+ if (field.isPrimaryKeyColumn())
+ {
+ primaryKey = fieldData;
+ summaryRowData[colCounter++] = primaryKey;
+ }
+ else if (fieldData == null || fieldData.trim().isEmpty())
+ {
+ summaryRowData[colCounter++] = null;
+ }
+ else
+ {
+ try
+ {
+ summaryRowData[colCounter++] = (field.getDataType()
+ .getDataTypeClass() == Integer.class)
+ ? Integer.valueOf(fieldData)
+ : (field.getDataType()
+ .getDataTypeClass() == Double.class)
+ ? Double.valueOf(fieldData)
+ : fieldData;
+ } catch (Exception e)
+ {
+ // e.printStackTrace();
+ System.out.println("offending value:" + fieldData + fieldData);
+ }
+ }
+ }
+ final String primaryKey1 = primaryKey;
+ final Object[] summaryRowData1 = summaryRowData;
+
+ return new TDB_FTSData(primaryKey, tdbJsonStructure, summaryRowData1);
+ }
+
+ // private static FTSData getFTSData(Map<String, Object> doc,
+ // FTSRestRequest tdbRestRequest)
+ // {
+ // String primaryKey = null;
+ //
+ // Object[] summaryRowData;
+ //
+ // Collection<FTSDataColumnI> displayFields =
+ // tdbRestRequest.getWantedFields();
+ // int colCounter = 0;
+ // summaryRowData = new Object[displayFields.size() + 1];
+ //
+ // return null;
+ // }
+
+ private String parseJsonExceptionString(String jsonErrorString)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getColumnDataConfigFileName()
+ {
+ return "/fts/tdbeacons_data_columns.txt";
+ }
+
+ public static FTSRestClientI getInstance()
+ {
+ if (instance == null)
+ {
+ instance = new TDBeaconsFTSRestClient();
+ }
+ return instance;
+ }
+
+ private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
+
+ public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
+ {
+ if (allDefaultDisplayedStructureDataColumns == null
+ || allDefaultDisplayedStructureDataColumns.isEmpty())
+ {
+ allDefaultDisplayedStructureDataColumns = new ArrayList<>();
+ allDefaultDisplayedStructureDataColumns
+ .addAll(super.getAllDefaultDisplayedFTSDataColumns());
+ }
+ return allDefaultDisplayedStructureDataColumns;
+ }
+
+ @Override
+ public String[] getPreferencesColumnsFor(PreferenceSource source)
+ {
+ String[] columnNames = null;
+ switch (source)
+ {
+ case SEARCH_SUMMARY:
+ columnNames = new String[] { "", "Display", "Group" };
+ break;
+ case STRUCTURE_CHOOSER:
+ columnNames = new String[] { "", "Display", "Group" };
+ break;
+ case PREFERENCES:
+ columnNames = new String[] { "3DB Beacons Field", "Show in search summary",
+ "Show in structure summary" };
+ break;
+ default:
+ break;
+ }
+ return columnNames;
+ }
+}
*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.util.MessageManager;
import jalview.util.Platform;
public void handleQuitRequestWith(
QuitEvent e, QuitResponse r)
{
- boolean confirmQuit = jalview.bin.Cache
+ boolean confirmQuit = Cache
.getDefault(
jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT,
true);
*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import jalview.api.ViewStyleI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.bin.Jalview;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
// modifyPID.setEnabled(false);
}
- String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+ String sortby = Cache.getDefault("SORT_ALIGNMENT",
"No sort");
if (sortby.equals("Id"))
wrapMenuItem_actionPerformed(null);
}
- if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+ if (Cache.getDefault("SHOW_OVERVIEW", false))
{
this.overviewMenuItem_actionPerformed(null);
}
}
}
});
- if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+ if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
.indexOf("devel") > -1
- || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+ || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
.indexOf("test") > -1)
{
formatMenu.add(vsel);
}
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().moveCursor(0, 1);
+ alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
}
break;
}
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().moveCursor(0, -1);
+ alignPanel.getSeqPanel().moveCursor(0, -1,evt.isShiftDown());
}
break;
}
else
{
- alignPanel.getSeqPanel().moveCursor(-1, 0);
+ alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
}
break;
}
else
{
- alignPanel.getSeqPanel().moveCursor(1, 0);
+ alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
}
break;
*/
public String getVersion()
{
- return jalview.bin.Cache.getProperty("VERSION");
+ return Cache.getProperty("VERSION");
}
public FeatureRenderer getFeatureRenderer()
}
else
{
- Cache.log.error(MessageManager
+ Console.error(MessageManager
.formatMessage("label.couldnt_save_file", new Object[]
{ lastFilenameSaved }));
}
BackupFiles backupfiles = null;
if (doBackup)
{
- Cache.log.trace(
+ Console.trace(
"ALIGNFRAME making backupfiles object for " + file);
backupfiles = new BackupFiles(file);
}
{
String tempFilePath = doBackup ? backupfiles.getTempFilePath()
: file;
- Cache.log.trace("ALIGNFRAME setting PrintWriter");
+ Console.trace("ALIGNFRAME setting PrintWriter");
PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
if (backupfiles != null)
{
- Cache.log.trace("ALIGNFRAME about to write to temp file "
+ Console.trace("ALIGNFRAME about to write to temp file "
+ backupfiles.getTempFilePath());
}
out.print(output);
- Cache.log.trace("ALIGNFRAME about to close file");
+ Console.trace("ALIGNFRAME about to close file");
out.close();
- Cache.log.trace("ALIGNFRAME closed file");
+ Console.trace("ALIGNFRAME closed file");
AlignFrame.this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format",
} catch (IOException e)
{
lastSaveSuccessful = false;
- Cache.log.error(
+ Console.error(
"ALIGNFRAME Something happened writing the temp file");
- Cache.log.error(e.getMessage());
- Cache.log.debug(Cache.getStackTraceString(e));
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
} catch (Exception ex)
{
lastSaveSuccessful = false;
- Cache.log.error(
+ Console.error(
"ALIGNFRAME Something unexpected happened writing the temp file");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
if (doBackup)
{
backupfiles.setWriteSuccess(lastSaveSuccessful);
- Cache.log.debug("ALIGNFRAME writing temp file was "
+ Console.debug("ALIGNFRAME writing temp file was "
+ (lastSaveSuccessful ? "" : "NOT ") + "successful");
// do the backup file roll and rename the temp file to actual file
- Cache.log.trace(
+ Console.trace(
"ALIGNFRAME about to rollBackupsAndRenameTempFile");
lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
- Cache.log.debug(
+ Console.debug(
"ALIGNFRAME performed rollBackupsAndRenameTempFile "
+ (lastSaveSuccessful ? "" : "un")
+ "successfully");
public void associatedData_actionPerformed(ActionEvent e)
{
final JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
String tooltip = MessageManager
.getString("label.load_jalview_annotations");
public void run()
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ Cache.setProperty("LAST_DIRECTORY", choice);
loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
}
});
{
if (originalSource != viewport)
{
- Cache.log.warn(
+ Console.warn(
"Implementation worry: mismatch of viewport origin for undo");
}
originalSource.updateHiddenColumns();
if (originalSource != viewport)
{
- Cache.log.warn(
+ Console.warn(
"Implementation worry: mismatch of viewport origin for redo");
}
originalSource.updateHiddenColumns();
@Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
- new Finder(alignPanel);
+ new Finder(alignPanel, false, null);
}
/**
{
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.select_newick_like_tree_file"));
jws2servs.attachWSMenuEntry(webService, me);
for (Jws2Instance sv : jws2servs.getServices())
{
- if (sv.description.toLowerCase().contains("jpred"))
+ if (sv.description.toLowerCase(Locale.ROOT).contains("jpred"))
{
for (JMenuItem jmi : legacyItems)
{
}
} catch (Exception e)
{
- Cache.log.debug(
+ Console.debug(
"Exception during web service menu building process.",
e);
}
showProducts.setEnabled(showp);
} catch (Exception e)
{
- Cache.log.warn(
+ Console.warn(
"canShowProducts threw an exception - please report to help@jalview.org",
e);
return false;
al = dna.translateCdna(codeTable);
} catch (Exception ex)
{
- jalview.bin.Cache.log.error(
+ Console.error(
"Exception during translation. Please report this !", ex);
final String msg = MessageManager.getString(
"label.error_when_translating_sequences_submit_bug_report");
}
} catch (Exception x)
{
- Cache.log.debug(
+ Console.debug(
"Exception when processing data source as T-COFFEE score file",
x);
tcf = null;
import jalview.api.FeaturesDisplayedI;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
- if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ if (seqsetid != null)
{
- Cache.log.debug(
+ Console.debug(
"Setting viewport's sequence set id : " + sequenceSetID);
}
- if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ if (viewId != null)
{
- Cache.log.debug("Setting viewport's view id : " + viewId);
+ Console.debug("Setting viewport's view id : " + viewId);
}
init();
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
- if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ if (seqsetid != null)
{
- Cache.log.debug(
+ Console.debug(
"Setting viewport's sequence set id : " + sequenceSetID);
}
- if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ if (viewId != null)
{
- Cache.log.debug("Setting viewport's view id : " + viewId);
+ Console.debug("Setting viewport's view id : " + viewId);
}
if (hiddenColumns != null)
// calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
if (needsUpdate)
{
- Cache.log.debug("trigger update for " + calcId);
+ Console.debug("trigger update for " + calcId);
}
}
try
{
newAlignFrame.setMaximum(
- jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
.getFeatureRenderer();
- List<String> origRenderOrder = new ArrayList(),
- origGroups = new ArrayList();
+ List<String> origRenderOrder = new ArrayList<>();
+ List<String> origGroups = new ArrayList<>();
// preserve original render order - allows differentiation between user configured colours and autogenerated ones
origRenderOrder.addAll(fr.getRenderOrder());
origGroups.addAll(fr.getFeatureGroups());
if (!mergeOnly)
{
// only clear displayed features if we are mergeing
- displayed.clear();
+ // displayed.clear();
}
// TODO this clears displayed.featuresRegistered - do we care?
//
{
displayed.setVisible(type);
}
+ else if (featureSettings.isFeatureHidden(type))
+ {
+ displayed.setHidden(type);
+ }
}
}
fr.orderFeatures(featureSettings);
}
fr.setTransparency(featureSettings.getTransparency());
+
+ fr.notifyFeaturesChanged();
}
public String getViewName()
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
// could not be validated and it is not clear if it is now being
// called. Log warning here in case it is called and unforeseen
// problems occur
- Cache.log.warn(
+ Console.warn(
"Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
// scroll to start of panel
}
else
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.warn("Closing alignment panel which is already closed.");
+ Console.warn("Closing alignment panel which is already closed.");
}
}
}
} catch (Exception ex)
{
}
-
if (b)
{
- alignFrame.setDisplayedView(this);
+ setAlignFrameView();
}
}
-
+ public void setAlignFrameView()
+ {
+ alignFrame.setDisplayedView(this);
+ }
+
@Override
public StructureSelectionManager getStructureSelectionManager()
{
*/
package jalview.gui;
+import java.util.Locale;
+
import jalview.api.FeatureRenderer;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
boolean nucleotide = ap.av.isNucleotide();
String complement = nucleotide
- ? MessageManager.getString("label.protein").toLowerCase()
+ ? MessageManager.getString("label.protein").toLowerCase(Locale.ROOT)
: "CDS";
JLabel label = new JLabel(
MessageManager.formatMessage("label.include_linked_features",
*/
package jalview.gui;
+import java.util.Locale;
+
import jalview.analysis.AlignSeq;
import jalview.analysis.AlignmentUtils;
import jalview.datamodel.Alignment;
// jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
// tooltips
String desc = aa.getDescription(true).trim();
- if (!desc.toLowerCase().startsWith(HTML_START_TAG))
+ if (!desc.toLowerCase(Locale.ROOT).startsWith(HTML_START_TAG))
{
tooltip.append(HTML_START_TAG);
desc = desc.replace("<", "<");
}
- else if (desc.toLowerCase().endsWith(HTML_END_TAG))
+ else if (desc.toLowerCase(Locale.ROOT).endsWith(HTML_END_TAG))
{
desc = desc.substring(0, desc.length() - HTML_END_TAG.length());
}
*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.Graphics;
import java.io.File;
-import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import javax.swing.event.InternalFrameEvent;
import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
import jalview.datamodel.StructureViewerModel.StructureData;
+import jalview.fts.service.alphafold.AlphafoldRestClient;
import jalview.gui.ImageExporter.ImageWriterI;
import jalview.gui.StructureViewer.ViewerType;
import jalview.structure.StructureCommand;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.ws.dbsources.EBIAlfaFold;
-import jalview.ws.dbsources.Pdb;
public class AppJmol extends StructureViewerBase
{
_started = true;
try
{
- List<String> files = fetchPdbFiles();
+ List<String> files = jmb.fetchPdbFiles(this);
if (files.size() > 0)
{
showFilesInViewer(files);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("When trying to open the Jmol viewer!", oomerror);
- Cache.log.debug("File locations are " + filesString);
+ Console.debug("File locations are " + filesString);
} catch (Exception ex)
{
- Cache.log.error("Couldn't open Jmol viewer!", ex);
+ Console.error("Couldn't open Jmol viewer!", ex);
ex.printStackTrace();
return;
}
{
new OOMWarning("When trying to add structures to the Jmol viewer!",
oomerror);
- Cache.log.debug("File locations are " + filesString);
+ Console.debug("File locations are " + filesString);
return;
} catch (Exception ex)
{
- Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ Console.error("Couldn't add files to Jmol viewer!", ex);
ex.printStackTrace();
return;
}
{
try
{
- Cache.log.debug("Waiting around for jmb notify.");
+ Console.debug("Waiting around for jmb notify.");
waitTotal += waitFor;
// Thread.sleep() throws an exception in JS
}
/**
- * Retrieves and saves as file any modelled PDB entries for which we do not
- * already have a file saved. Returns a list of absolute paths to structure
- * files which were either retrieved, or already stored but not modelled in
- * the structure viewer (i.e. files to add to the viewer display).
- *
- * @return
- */
- List<String> fetchPdbFiles()
- {
- // todo - record which pdbids were successfully imported.
- StringBuilder errormsgs = new StringBuilder();
-
- List<String> files = new ArrayList<>();
- String pdbid = "";
- try
- {
- String[] filesInViewer = jmb.getStructureFiles();
- // TODO: replace with reference fetching/transfer code (validate PDBentry
- // as a DBRef?)
- Pdb pdbclient = new Pdb();
- EBIAlfaFold afclient = new EBIAlfaFold();
-
- for (int pi = 0; pi < jmb.getPdbCount(); pi++)
- {
- String file = jmb.getPdbEntry(pi).getFile();
- if (file == null)
- {
- // todo: extract block as method and pull up (also ChimeraViewFrame)
- // retrieve the pdb and store it locally
- AlignmentI pdbseq = null;
- pdbid = jmb.getPdbEntry(pi).getId();
- long hdl = pdbid.hashCode() - System.currentTimeMillis();
- setProgressMessage(MessageManager
- .formatMessage("status.fetching_pdb", new String[]
- { pdbid }), hdl);
- try
- {
- if (afclient.isValidReference(pdbid))
- {
- pdbseq = afclient.getSequenceRecords(pdbid);
- } else {
- pdbseq = pdbclient.getSequenceRecords(pdbid);
- }
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- errormsgs.append("'").append(pdbid).append("'");
- } finally
- {
- setProgressMessage(
- MessageManager.getString("label.state_completed"), hdl);
- }
- if (pdbseq != null)
- {
- // just transfer the file name from the first sequence's first
- // PDBEntry
- file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
- .elementAt(0).getFile()).getAbsolutePath();
- jmb.getPdbEntry(pi).setFile(file);
- files.add(file);
- }
- else
- {
- errormsgs.append("'").append(pdbid).append("' ");
- }
- }
- else
- {
- if (filesInViewer != null && filesInViewer.length > 0)
- {
- addingStructures = true; // already files loaded.
- for (int c = 0; c < filesInViewer.length; c++)
- {
- if (Platform.pathEquals(filesInViewer[c], file))
- {
- file = null;
- break;
- }
- }
- }
- if (file != null)
- {
- files.add(file);
- }
- }
- }
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- errormsgs.append("When retrieving pdbfiles : current was: '")
- .append(pdbid).append("'");
- }
- if (errormsgs.length() > 0)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.pdb_entries_couldnt_be_retrieved", new String[]
- { errormsgs.toString() }),
- MessageManager.getString("label.couldnt_load_file"),
- JvOptionPane.ERROR_MESSAGE);
- }
- return files;
- }
-
- /**
* Outputs the Jmol viewer image as an image file, after prompting the user to
* choose a file and (for EPS) choice of Text or Lineart character rendering
* (unless a preference for this is set)
jmb.jmolViewer.renderScreenImage(g, width, height);
}
};
- String view = MessageManager.getString("action.view").toLowerCase();
+ String view = MessageManager.getString("action.view").toLowerCase(Locale.ROOT);
ImageExporter exporter = new ImageExporter(writer,
getProgressIndicator(), type, getTitle());
exporter.doExport(null, this, width, height, view);
import java.awt.Container;
import java.io.File;
+import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import jalview.api.AlignmentViewPanel;
import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.ws.dbsources.EBIAlfaFold;
+import jalview.ws.dbsources.Pdb;
+import jalview.ws.utils.UrlDownloadClient;
import javajs.util.BS;
public class AppJmolBinding extends JalviewJmolBinding
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception e)
{
- Cache.log.error("Failed to launch Jmol-associated url " + url, e);
+ Console.error("Failed to launch Jmol-associated url " + url, e);
// TODO: 2.6 : warn user if browser was not configured.
}
}
Platform.cacheFileData(f);
}
}
+
+ /**
+ * Retrieves and saves as file any modelled PDB entries for which we do not
+ * already have a file saved. Returns a list of absolute paths to structure
+ * files which were either retrieved, or already stored but not modelled in
+ * the structure viewer (i.e. files to add to the viewer display).
+ *
+ * Currently only used by Jmol - similar but different code used for Chimera/X
+ * and Pymol so still need to refactor
+ *
+ * @param structureViewer
+ * UI proxy for the structure viewer
+ * @return list of absolute paths to structures retrieved that need to be
+ * added to the display
+ */
+ public List<String> fetchPdbFiles(StructureViewerBase structureViewer)
+ {
+ // todo - record which pdbids were successfully imported.
+ StringBuilder errormsgs = new StringBuilder();
+
+ List<String> files = new ArrayList<>();
+ String pdbid = "";
+ try
+ {
+ String[] filesInViewer = getStructureFiles();
+ // TODO: replace with reference fetching/transfer code (validate PDBentry
+ // as a DBRef?)
+
+ for (int pi = 0; pi < getPdbCount(); pi++)
+ {
+ PDBEntry strucEntry = getPdbEntry(pi);
+
+ String file = strucEntry.getFile();
+ if (file == null)
+ {
+ pdbid = strucEntry.getId();
+ try{
+ file = structureViewer.fetchPdbFile(strucEntry);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("'").append(pdbid).append("'");
+ }
+ if (file!=null)
+ {
+ // success
+ files.add(file);
+ }
+ else
+ {
+ errormsgs.append("'").append(pdbid).append("' ");
+ }
+ }
+ else
+ {
+ if (filesInViewer != null && filesInViewer.length > 0)
+ {
+ structureViewer.setAddingStructures(true); // already files loaded.
+ for (int c = 0; c < filesInViewer.length; c++)
+ {
+ if (Platform.pathEquals(filesInViewer[c], file))
+ {
+ file = null;
+ break;
+ }
+ }
+ }
+ if (file != null)
+ {
+ files.add(file);
+ }
+ }
+ }
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("When retrieving pdbfiles : current was: '")
+ .append(pdbid).append("'");
+ }
+ if (errormsgs.length() > 0)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.pdb_entries_couldnt_be_retrieved", new String[]
+ { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ return files;
+ }
+
}
package jalview.gui;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
{
if (parent != null)
{
- Cache.log.debug("News window closed.");
+ Console.debug("News window closed.");
jd = null;
parent.showNews(false);
}
public BlogReader(Desktop desktop)
{
- Cache.log.debug("Constructing news reader.");
+ Console.debug("Constructing news reader.");
parent = desktop;
_channelModel = new ChannelListModel();
// Construct our jalview news channel
Channel chan = new Channel();
chan.setURL(
- jalview.bin.Cache.getDefault("JALVIEW_NEWS_RSS",
- jalview.bin.Cache.getDefault("www.jalview.org",
- "http://www.jalview.org")
+ Cache.getDefault("JALVIEW_NEWS_RSS",
+ Cache.getDefault("www.jalview.org",
+ "https://www.jalview.org")
+ "/feeds/desktop/rss"));
loadLastM();
_channelModel.addChannel(chan);
if (setvisible)
{
- Cache.log.debug("Will show jalview news automatically");
+ Console.debug("Will show jalview news automatically");
showNews();
}
- Cache.log.debug("Completed construction of reader.");
+ Console.debug("Completed construction of reader.");
}
MessageManager.getString("label.news_from_jalview"),
bounds.width, bounds.height);
jd.frame.setModalExclusionType(ModalExclusionType.NO_EXCLUDE);
- Cache.log.debug("Displaying news.");
+ Console.debug("Displaying news.");
jd.waitForInput();
}
}
}
if (chan != null && chan.getItems() != null)
{
- Cache.log.debug("Scanning news items: newsnew=" + newsnew
+ Console.debug("Scanning news items: newsnew=" + newsnew
+ " and lastDate is " + lastDate);
for (Item i : (List<Item>) chan.getItems())
{
{
String formatted = Cache
.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", lastDate);
- Cache.log.debug("Saved last read date as " + formatted);
+ Console.debug("Saved last read date as " + formatted);
}
}
}
{
// this tests the detection of new news based on the last read date stored
// in jalview properties
- jalview.bin.Cache.loadProperties(null);
- jalview.bin.Cache.initLogger();
+ Cache.loadProperties(null);
+ Console.initLogger();
// test will advance read date each time
Calendar today = Calendar.getInstance(),
lastread = Calendar.getInstance();
System.out.println("Set last date to " + formattedDate);
if (me.isNewsNew())
{
- Cache.log.debug("There is news to read.");
+ Console.debug("There is news to read.");
}
else
{
- Cache.log.debug("There is no new news.");
+ Console.debug("There is no new news.");
me.xf.setTitle("Testing : Last read is " + me.lastDate);
me.showNews();
me.xf.toFront();
}
- Cache.log.debug("Waiting for closure.");
+ Console.debug("Waiting for closure.");
do
{
try
if (me.isNewsNew())
{
- Cache.log.debug("Still new news after reader displayed.");
+ Console.debug("Still new news after reader displayed.");
}
if (lastread.getTime().before(me.lastDate))
{
- Cache.log.debug("The news was read.");
+ Console.debug("The news was read.");
lastread.setTime(me.lastDate);
}
else
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
private int myHeight = 150;
- /**
+ private JMenuItem writeFeatures=null;
+
+ private JMenu fetchAttributes=null;
+/**
* Initialise menu options.
*/
@Override
savemenu.setVisible(false); // not yet implemented
viewMenu.add(fitToWindow);
- JMenuItem writeFeatures = new JMenuItem(
+ writeFeatures = new JMenuItem(
MessageManager.getString("label.create_viewer_attributes"));
writeFeatures.setToolTipText(MessageManager
.getString("label.create_viewer_attributes_tip"));
});
viewerActionMenu.add(writeFeatures);
- final JMenu fetchAttributes = new JMenu(
- MessageManager.getString("label.fetch_chimera_attributes"));
+ fetchAttributes = new JMenu(
+ MessageManager.formatMessage("label.fetch_viewer_attributes",getViewerName()));
fetchAttributes.setToolTipText(
- MessageManager.getString("label.fetch_chimera_attributes_tip"));
+ MessageManager.formatMessage("label.fetch_viewer_attributes_tip",getViewerName()));
fetchAttributes.addMouseListener(new MouseAdapter()
{
});
viewerActionMenu.add(fetchAttributes);
}
-
+ @Override
+ protected void buildActionMenu()
+ {
+ super.buildActionMenu();
+ // add these back in after menu is refreshed
+ viewerActionMenu.add(writeFeatures);
+ viewerActionMenu.add(fetchAttributes);
+
+ };
/**
* Query the structure viewer for its residue attribute names and add them as
* items off the attributes menu
// todo pull up?
int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
statusBar.setText(
- MessageManager.formatMessage("label.attributes_set", count));
+ MessageManager.formatMessage("label.attributes_set", count, getViewerName()));
}
/**
initChimera();
} catch (Exception ex)
{
- Cache.log.error("Couldn't open Chimera viewer!", ex);
+ Console.error("Couldn't open Chimera viewer!", ex);
}
}
int num = -1;
oomerror);
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Couldn't open " + pe.getFile() + " in Chimera viewer!",
ex);
} finally
{
- Cache.log.debug("File locations are " + files);
+ Console.debug("File locations are " + files);
}
}
}
/*
* ensure that any newly discovered features (e.g. RESNUM)
- * are added to any open feature settings dialog
+ * are notified to the FeatureRenderer (and added to any
+ * open feature settings dialog)
*/
FeatureRenderer fr = getBinding().getFeatureRenderer(null);
if (fr != null)
import java.io.PipedOutputStream;
import java.io.PrintStream;
+import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
+import javax.swing.border.Border;
+import javax.swing.text.DefaultCaret;
-import org.apache.log4j.Level;
-import org.apache.log4j.SimpleLayout;
-
-import jalview.bin.Cache;
+import jalview.log.JLoggerI.LogLevel;
+import jalview.log.JLoggerLog4j;
+import jalview.log.JalviewAppender;
import jalview.util.ChannelProperties;
import jalview.util.MessageManager;
+import jalview.util.Platform;
/**
* Simple Jalview Java Console. Version 1 - allows viewing of console output
private int MIN_HEIGHT = 250;
- private JComboBox<Level> logLevelCombo = new JComboBox<Level>();
+ private JComboBox<LogLevel> logLevelCombo = new JComboBox<LogLevel>();
- protected Level startingLogLevel = Level.INFO;
+ protected LogLevel startingLogLevel = LogLevel.INFO;
public Console()
{
// textArea = cpt.getTextArea();
textArea = new JTextArea();
textArea.setEditable(false);
+ // autoscroll
+ DefaultCaret caret = (DefaultCaret) textArea.getCaret();
+ caret.setUpdatePolicy(DefaultCaret.ALWAYS_UPDATE);
+ // toggle autoscroll by clicking on the text area
+ Border pausedBorder = BorderFactory.createMatteBorder(2, 2, 2, 2,
+ textArea.getForeground());
+ Border noBorder = BorderFactory.createEmptyBorder(2, 2, 2, 2);
+ JScrollPane scrollPane = new JScrollPane(textArea);
+ scrollPane.setBorder(noBorder);
+ textArea.addMouseListener(new MouseAdapter()
+ {
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getButton() == MouseEvent.BUTTON1)
+ {
+ if (caret.getUpdatePolicy() == DefaultCaret.ALWAYS_UPDATE)
+ {
+ caret.setUpdatePolicy(DefaultCaret.NEVER_UPDATE);
+ scrollPane.setBorder(pausedBorder);
+ }
+ else
+ {
+ caret.setUpdatePolicy(DefaultCaret.ALWAYS_UPDATE);
+ textArea.setCaretPosition(textArea.getDocument().getLength());
+ scrollPane.setBorder(noBorder);
+ }
+ }
+ }
+ });
+
JButton clearButton = new JButton(
MessageManager.getString("action.clear"));
JButton copyToClipboardButton = new JButton(
JLabel logLevelLabel = new JLabel(
MessageManager.getString("label.log_level") + ":");
- // logLevelCombo.addItem(Level.ALL);
- logLevelCombo.addItem(Level.TRACE);
- logLevelCombo.addItem(Level.DEBUG);
- logLevelCombo.addItem(Level.INFO);
- logLevelCombo.addItem(Level.WARN);
- // logLevelCombo.addItem(Level.ERROR);
- // logLevelCombo.addItem(Level.FATAL);
- // logLevelCombo.addItem(Level.OFF);
+ // logLevelCombo.addItem(LogLevel.ALL);
+ logLevelCombo.addItem(LogLevel.TRACE);
+ logLevelCombo.addItem(LogLevel.DEBUG);
+ logLevelCombo.addItem(LogLevel.INFO);
+ logLevelCombo.addItem(LogLevel.WARN);
+ // logLevelCombo.addItem(LogLevel.ERROR);
+ // logLevelCombo.addItem(LogLevel.FATAL);
+ // logLevelCombo.addItem(LogLevel.ERROR);
+ // logLevelCombo.addItem(LogLevel.OFF);
// set startingLogLevel
- startingLogLevel = Cache.log == null ? Level.INFO
- : Cache.log.getLevel();
+ startingLogLevel = jalview.bin.Console.log == null ? LogLevel.INFO
+ : jalview.bin.Console.log.getLevel();
setChosenLogLevelCombo();
logLevelCombo.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- if (Cache.log != null)
+ if (jalview.bin.Console.log != null)
{
- Cache.log.setLevel((Level) logLevelCombo.getSelectedItem());
+ jalview.bin.Console.log.setLevel((LogLevel) logLevelCombo.getSelectedItem());
}
}
// frame = cpt;
frame.getContentPane().setLayout(new BorderLayout());
- frame.getContentPane().add(new JScrollPane(textArea),
- BorderLayout.CENTER);
+ frame.getContentPane().add(scrollPane, BorderLayout.CENTER);
JPanel southPanel = new JPanel();
southPanel.setLayout(new GridBagLayout());
setChosenLogLevelCombo(startingLogLevel);
}
- private void setChosenLogLevelCombo(Level setLogLevel)
+ private void setChosenLogLevelCombo(LogLevel setLogLevel)
{
logLevelCombo.setSelectedItem(setLogLevel);
if (!logLevelCombo.getSelectedItem().equals(setLogLevel))
{
// setLogLevel not (yet) in list
- if (setLogLevel != null && setLogLevel instanceof Level)
+ if (setLogLevel != null && setLogLevel instanceof LogLevel)
{
// add new item to list (might be set via .jalview_properties)
boolean added = false;
for (int i = 0; i < logLevelCombo.getItemCount(); i++)
{
- Level l = (Level) logLevelCombo.getItemAt(i);
- if (l.isGreaterOrEqual(setLogLevel))
+ LogLevel l = (LogLevel) logLevelCombo.getItemAt(i);
+ if (l.compareTo(setLogLevel) >= 0)
{
logLevelCombo.insertItemAt(setLogLevel, i);
added = true;
}
else
{
- logLevelCombo.setSelectedItem(Level.INFO);
+ logLevelCombo.setSelectedItem(LogLevel.INFO);
}
}
}
frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
// desktop.add(frame);
initConsole(false);
- JalviewAppender jappender = new JalviewAppender();
- jappender.setLayout(new SimpleLayout());
- JalviewAppender.setTextArea(textArea);
- org.apache.log4j.Logger.getRootLogger().addAppender(jappender);
+ LogLevel level = (LogLevel) logLevelCombo.getSelectedItem();
+ if (!Platform.isJS())
+ {
+ JalviewAppender jappender = new JalviewAppender(level);
+ JalviewAppender.setTextArea(textArea);
+ jappender.start();
+ if (jalview.bin.Console.log != null && jalview.bin.Console.log instanceof JLoggerLog4j)
+ {
+ JLoggerLog4j.addAppender(jalview.bin.Console.log, jappender);
+ }
+ }
}
public synchronized void stopConsole()
else
{
// reset log level to what it was before
- if (Cache.log != null)
+ if (jalview.bin.Console.log != null)
{
- Cache.log.setLevel(startingLogLevel);
+ jalview.bin.Console.log.setLevel(startingLogLevel);
}
unredirectStreams();
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
new OOMWarning("whilst fetching crossreferences", e);
} catch (Throwable e)
{
- Cache.log.error("Error when finding crossreferences", e);
+ Console.error("Error when finding crossreferences", e);
} finally
{
alignFrame.setProgressBar(MessageManager.formatMessage(
*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.GCutAndPasteHtmlTransfer;
// TODO: JAL-3048 JalviewFileChooser - Save option
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
// TODO: JAL-3048 JalviewFileChooser - Save option
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
*/
if (viewport != null && viewport.getAlignment() != null)
{
- if (proxyColourScheme != null)
- {
- viewport.applyFeaturesStyle(proxyColourScheme);
- }
((AlignViewport) viewport).addAlignment(al, title);
+ viewport.applyFeaturesStyle(proxyColourScheme);
}
else
{
try
{
af.setMaximum(
- jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (Exception ex)
{
}
*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
* @version $Revision: 1.155 $
*/
public class Desktop extends jalview.jbgui.GDesktop
- implements DropTargetListener, ClipboardOwner, IProgressIndicator,
- jalview.api.StructureSelectionManagerProvider
-{
+ implements DropTargetListener, ClipboardOwner, IProgressIndicator, jalview.api.StructureSelectionManagerProvider {
private static final String CITATION;
- static
- {
- URL bg_logo_url = ChannelProperties.getImageURL(
- "bg_logo." + String.valueOf(SplashScreen.logoSize));
- URL uod_logo_url = ChannelProperties.getImageURL(
- "uod_banner." + String.valueOf(SplashScreen.logoSize));
+ static {
+ URL bg_logo_url = ChannelProperties.getImageURL("bg_logo." + String.valueOf(SplashScreen.logoSize));
+ URL uod_logo_url = ChannelProperties.getImageURL("uod_banner." + String.valueOf(SplashScreen.logoSize));
boolean logo = (bg_logo_url != null || uod_logo_url != null);
StringBuilder sb = new StringBuilder();
- sb.append(
- "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.");
- if (logo)
- {
+ sb.append("<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.");
+ if (logo) {
sb.append("<br>");
}
- sb.append(bg_logo_url == null ? ""
- : "<img alt=\"Barton Group logo\" src=\""
- + bg_logo_url.toString() + "\">");
+ sb.append(bg_logo_url == null ? "" : "<img alt=\"Barton Group logo\" src=\"" + bg_logo_url.toString() + "\">");
sb.append(uod_logo_url == null ? ""
- : " <img alt=\"University of Dundee shield\" src=\""
- + uod_logo_url.toString() + "\">");
+ : " <img alt=\"University of Dundee shield\" src=\"" + uod_logo_url.toString() + "\">");
sb.append(
- "<br><br>For help, see the FAQ at <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list");
+ "<br><br>For help, see the FAQ at <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list");
sb.append("<br><br>If you use Jalview, please cite:"
- + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
- + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
- + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033");
+ + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033");
CITATION = sb.toString();
}
* @param listener
* @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
*/
- public void addJalviewPropertyChangeListener(
- PropertyChangeListener listener)
- {
+ public void addJalviewPropertyChangeListener(PropertyChangeListener listener) {
changeSupport.addJalviewPropertyChangeListener(listener);
}
* @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
* java.beans.PropertyChangeListener)
*/
- public void addJalviewPropertyChangeListener(String propertyName,
- PropertyChangeListener listener)
- {
+ public void addJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) {
changeSupport.addJalviewPropertyChangeListener(propertyName, listener);
}
* @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
* java.beans.PropertyChangeListener)
*/
- public void removeJalviewPropertyChangeListener(String propertyName,
- PropertyChangeListener listener)
- {
- changeSupport.removeJalviewPropertyChangeListener(propertyName,
- listener);
+ public void removeJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) {
+ changeSupport.removeJalviewPropertyChangeListener(propertyName, listener);
}
/** Singleton Desktop instance */
public static MyDesktopPane desktop;
- public static MyDesktopPane getDesktop()
- {
+ public static MyDesktopPane getDesktop() {
// BH 2018 could use currentThread() here as a reference to a
// Hashtable<Thread, MyDesktopPane> in JavaScript
return desktop;
static int fileLoadingCount = 0;
- class MyDesktopManager implements DesktopManager
- {
+ class MyDesktopManager implements DesktopManager {
private DesktopManager delegate;
- public MyDesktopManager(DesktopManager delegate)
- {
+ public MyDesktopManager(DesktopManager delegate) {
this.delegate = delegate;
}
@Override
- public void activateFrame(JInternalFrame f)
- {
- try
- {
+ public void activateFrame(JInternalFrame f) {
+ try {
delegate.activateFrame(f);
- } catch (NullPointerException npe)
- {
+ } catch (NullPointerException npe) {
Point p = getMousePosition();
instance.showPasteMenu(p.x, p.y);
}
}
@Override
- public void beginDraggingFrame(JComponent f)
- {
+ public void beginDraggingFrame(JComponent f) {
delegate.beginDraggingFrame(f);
}
@Override
- public void beginResizingFrame(JComponent f, int direction)
- {
+ public void beginResizingFrame(JComponent f, int direction) {
delegate.beginResizingFrame(f, direction);
}
@Override
- public void closeFrame(JInternalFrame f)
- {
+ public void closeFrame(JInternalFrame f) {
delegate.closeFrame(f);
}
@Override
- public void deactivateFrame(JInternalFrame f)
- {
+ public void deactivateFrame(JInternalFrame f) {
delegate.deactivateFrame(f);
}
@Override
- public void deiconifyFrame(JInternalFrame f)
- {
+ public void deiconifyFrame(JInternalFrame f) {
delegate.deiconifyFrame(f);
}
@Override
- public void dragFrame(JComponent f, int newX, int newY)
- {
- if (newY < 0)
- {
+ public void dragFrame(JComponent f, int newX, int newY) {
+ if (newY < 0) {
newY = 0;
}
delegate.dragFrame(f, newX, newY);
}
@Override
- public void endDraggingFrame(JComponent f)
- {
+ public void endDraggingFrame(JComponent f) {
delegate.endDraggingFrame(f);
desktop.repaint();
}
@Override
- public void endResizingFrame(JComponent f)
- {
+ public void endResizingFrame(JComponent f) {
delegate.endResizingFrame(f);
desktop.repaint();
}
@Override
- public void iconifyFrame(JInternalFrame f)
- {
+ public void iconifyFrame(JInternalFrame f) {
delegate.iconifyFrame(f);
}
@Override
- public void maximizeFrame(JInternalFrame f)
- {
+ public void maximizeFrame(JInternalFrame f) {
delegate.maximizeFrame(f);
}
@Override
- public void minimizeFrame(JInternalFrame f)
- {
+ public void minimizeFrame(JInternalFrame f) {
delegate.minimizeFrame(f);
}
@Override
- public void openFrame(JInternalFrame f)
- {
+ public void openFrame(JInternalFrame f) {
delegate.openFrame(f);
}
@Override
- public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
- int newHeight)
- {
- if (newY < 0)
- {
+ public void resizeFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) {
+ if (newY < 0) {
newY = 0;
}
delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
}
@Override
- public void setBoundsForFrame(JComponent f, int newX, int newY,
- int newWidth, int newHeight)
- {
+ public void setBoundsForFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) {
delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight);
}
/**
* Creates a new Desktop object.
*/
- public Desktop()
- {
+ public Desktop() {
super();
/**
- * A note to implementors. It is ESSENTIAL that any activities that might
- * block are spawned off as threads rather than waited for during this
- * constructor.
+ * A note to implementors. It is ESSENTIAL that any activities that might block
+ * are spawned off as threads rather than waited for during this constructor.
*/
instance = this;
doConfigureStructurePrefs();
- setTitle(ChannelProperties.getProperty("app_name") + " "
- + Cache.getProperty("VERSION"));
+ setTitle(ChannelProperties.getProperty("app_name") + " " + Cache.getProperty("VERSION"));
/**
- * Set taskbar "grouped windows" name for linux desktops (works in GNOME and KDE).
- * This uses sun.awt.X11.XToolkit.awtAppClassName which is not officially documented or
- * guaranteed to exist, so we access it via reflection.
- * There appear to be unfathomable criteria about what this string can contain, and it if doesn't
- * meet those criteria then "java" (KDE) or "jalview-bin-Jalview" (GNOME) is used.
- * "Jalview", "Jalview Develop" and "Jalview Test" seem okay, but "Jalview non-release" does not.
- * The reflection access may generate a warning:
- * WARNING: An illegal reflective access operation has occurred
- * WARNING: Illegal reflective access by jalview.gui.Desktop () to field sun.awt.X11.XToolkit.awtAppClassName
- * which I don't think can be avoided.
+ * Set taskbar "grouped windows" name for linux desktops (works in GNOME and
+ * KDE). This uses sun.awt.X11.XToolkit.awtAppClassName which is not officially
+ * documented or guaranteed to exist, so we access it via reflection. There
+ * appear to be unfathomable criteria about what this string can contain, and it
+ * if doesn't meet those criteria then "java" (KDE) or "jalview-bin-Jalview"
+ * (GNOME) is used. "Jalview", "Jalview Develop" and "Jalview Test" seem okay,
+ * but "Jalview non-release" does not. The reflection access may generate a
+ * warning: WARNING: An illegal reflective access operation has occurred
+ * WARNING: Illegal reflective access by jalview.gui.Desktop () to field
+ * sun.awt.X11.XToolkit.awtAppClassName which I don't think can be avoided.
*/
- if (Platform.isLinux())
- {
- try
- {
+ if (Platform.isLinux()) {
+ try {
Toolkit xToolkit = Toolkit.getDefaultToolkit();
Field[] declaredFields = xToolkit.getClass().getDeclaredFields();
Field awtAppClassNameField = null;
- if (Arrays.stream(declaredFields).anyMatch(f -> f.getName().equals("awtAppClassName")))
- {
- awtAppClassNameField = xToolkit.getClass()
- .getDeclaredField("awtAppClassName");
+ if (Arrays.stream(declaredFields).anyMatch(f -> f.getName().equals("awtAppClassName"))) {
+ awtAppClassNameField = xToolkit.getClass().getDeclaredField("awtAppClassName");
}
String title = ChannelProperties.getProperty("app_name");
- if (awtAppClassNameField != null)
- {
+ if (awtAppClassNameField != null) {
awtAppClassNameField.setAccessible(true);
awtAppClassNameField.set(xToolkit, title);
+ } else {
+ jalview.bin.Console.debug("XToolkit: awtAppClassName not found");
}
- else
- {
- Cache.log.debug("XToolkit: awtAppClassName not found");
- }
- } catch (Exception e)
- {
- Cache.debug("Error setting awtAppClassName");
- Cache.trace(Cache.getStackTraceString(e));
+ } catch (Exception e) {
+ jalview.bin.Console.debug("Error setting awtAppClassName");
+ jalview.bin.Console.trace(Cache.getStackTraceString(e));
}
}
/**
- * APQHandlers sets handlers for About, Preferences and Quit actions peculiar to macOS's application menu.
- * APQHandlers will check to see if a handler is supported before setting it.
+ * APQHandlers sets handlers for About, Preferences and Quit actions peculiar to
+ * macOS's application menu. APQHandlers will check to see if a handler is
+ * supported before setting it.
*/
- try
- {
+ try {
APQHandlers.setAPQHandlers(this);
- } catch (Throwable t)
- {
- Cache.warn("Error setting APQHandlers: " + t.toString());
- Cache.trace(Cache.getStackTraceString(t));
+ } catch (Exception e) {
+ System.out.println("Cannot set APQHandlers");
+ // e.printStackTrace();
+ } catch (Throwable t) {
+ jalview.bin.Console.warn("Error setting APQHandlers: " + t.toString());
+ jalview.bin.Console.trace(Cache.getStackTraceString(t));
}
setIconImages(ChannelProperties.getIconList());
- addWindowListener(new WindowAdapter()
- {
+ addWindowListener(new WindowAdapter() {
@Override
- public void windowClosing(WindowEvent ev)
- {
+ public void windowClosing(WindowEvent ev) {
quit();
}
});
showMemusage.setSelected(selmemusage);
desktop.setBackground(Color.white);
- this.setIconImages(ChannelProperties.getIconList());
-
getContentPane().setLayout(new BorderLayout());
// alternate config - have scrollbars - see notes in JAL-153
// JScrollPane sp = new JScrollPane();
// getContentPane().add(sp, BorderLayout.CENTER);
// BH 2018 - just an experiment to try unclipped JInternalFrames.
- if (Platform.isJS())
- {
+ if (Platform.isJS()) {
getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
}
// This line prevents Windows Look&Feel resizing all new windows to maximum
// if previous window was maximised
- desktop.setDesktopManager(new MyDesktopManager(
- (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
- : Platform.isAMacAndNotJS()
- ? new AquaInternalFrameManager(
- desktop.getDesktopManager())
- : desktop.getDesktopManager())));
+ desktop.setDesktopManager(new MyDesktopManager((Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
+ : Platform.isAMacAndNotJS() ? new AquaInternalFrameManager(desktop.getDesktopManager())
+ : desktop.getDesktopManager())));
Rectangle dims = getLastKnownDimensions("");
- if (dims != null)
- {
+ if (dims != null) {
setBounds(dims);
- }
- else
- {
+ } else {
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
int xPos = Math.max(5, (screenSize.width - 900) / 2);
int yPos = Math.max(5, (screenSize.height - 650) / 2);
checkURLLinks();
// Spawn a thread that shows the splashscreen
- if (!nosplash)
- {
- SwingUtilities.invokeLater(new Runnable()
- {
+ if (!nosplash) {
+ SwingUtilities.invokeLater(new Runnable() {
@Override
- public void run()
- {
+ public void run() {
new SplashScreen(true);
}
});
// Thread off a new instance of the file chooser - this reduces the time
// it
// takes to open it later on.
- new Thread(new Runnable()
- {
+ new Thread(new Runnable() {
@Override
- public void run()
- {
- Cache.log.debug("Filechooser init thread started.");
+ public void run() {
+ jalview.bin.Console.debug("Filechooser init thread started.");
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
- fileFormat);
- Cache.log.debug("Filechooser init thread finished.");
+ JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+ jalview.bin.Console.debug("Filechooser init thread finished.");
}
}).start();
// Add the service change listener
- changeSupport.addJalviewPropertyChangeListener("services",
- new PropertyChangeListener()
- {
+ changeSupport.addJalviewPropertyChangeListener("services", new PropertyChangeListener() {
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- Cache.log.debug("Firing service changed event for "
- + evt.getNewValue());
- JalviewServicesChanged(evt);
- }
- });
+ @Override
+ public void propertyChange(PropertyChangeEvent evt) {
+ jalview.bin.Console.debug("Firing service changed event for " + evt.getNewValue());
+ JalviewServicesChanged(evt);
+ }
+ });
}
this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
- this.addWindowListener(new WindowAdapter()
- {
+ this.addWindowListener(new WindowAdapter() {
@Override
- public void windowClosing(WindowEvent evt)
- {
+ public void windowClosing(WindowEvent evt) {
quit();
}
});
MouseAdapter ma;
- this.addMouseListener(ma = new MouseAdapter()
- {
+ this.addMouseListener(ma = new MouseAdapter() {
@Override
- public void mousePressed(MouseEvent evt)
- {
+ public void mousePressed(MouseEvent evt) {
if (evt.isPopupTrigger()) // Mac
{
showPasteMenu(evt.getX(), evt.getY());
}
@Override
- public void mouseReleased(MouseEvent evt)
- {
+ public void mouseReleased(MouseEvent evt) {
if (evt.isPopupTrigger()) // Windows
{
showPasteMenu(evt.getX(), evt.getY());
*
* @return
*/
- public boolean showExperimental()
- {
- String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES,
- Boolean.FALSE.toString());
+ public boolean showExperimental() {
+ String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES, Boolean.FALSE.toString());
return Boolean.valueOf(experimental).booleanValue();
}
- public void doConfigureStructurePrefs()
- {
+ public void doConfigureStructurePrefs() {
// configure services
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(this);
- if (Cache.getDefault(Preferences.ADD_SS_ANN, true))
- {
- ssm.setAddTempFacAnnot(
- Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
- ssm.setProcessSecondaryStructure(
- Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
- ssm.setSecStructServices(
- Cache.getDefault(Preferences.USE_RNAVIEW, true));
- }
- else
- {
+ StructureSelectionManager ssm = StructureSelectionManager.getStructureSelectionManager(this);
+ if (Cache.getDefault(Preferences.ADD_SS_ANN, true)) {
+ ssm.setAddTempFacAnnot(Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
+ ssm.setProcessSecondaryStructure(Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
+ // JAL-3915 - RNAView is no longer an option so this has no effect
+ ssm.setSecStructServices(Cache.getDefault(Preferences.USE_RNAVIEW, false));
+ } else {
ssm.setAddTempFacAnnot(false);
ssm.setProcessSecondaryStructure(false);
ssm.setSecStructServices(false);
}
}
- public void checkForNews()
- {
+ public void checkForNews() {
final Desktop me = this;
// Thread off the news reader, in case there are connection problems.
- new Thread(new Runnable()
- {
+ new Thread(new Runnable() {
@Override
- public void run()
- {
- Cache.log.debug("Starting news thread.");
+ public void run() {
+ jalview.bin.Console.debug("Starting news thread.");
jvnews = new BlogReader(me);
showNews.setVisible(true);
- Cache.log.debug("Completed news thread.");
+ jalview.bin.Console.debug("Completed news thread.");
}
}).start();
}
- public void getIdentifiersOrgData()
- {
- // Thread off the identifiers fetcher
- new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- Cache.log.debug("Downloading data from identifiers.org");
- try
- {
- UrlDownloadClient.download(IdOrgSettings.getUrl(),
- IdOrgSettings.getDownloadLocation());
- } catch (IOException e)
- {
- Cache.log.debug("Exception downloading identifiers.org data"
- + e.getMessage());
+ public void getIdentifiersOrgData() {
+ if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null) {
+ // Thread off the identifiers fetcher
+ new Thread(new Runnable() {
+ @Override
+ public void run() {
+ jalview.bin.Console.debug("Downloading data from identifiers.org");
+ try {
+ UrlDownloadClient.download(IdOrgSettings.getUrl(), IdOrgSettings.getDownloadLocation());
+ } catch (IOException e) {
+ jalview.bin.Console.debug("Exception downloading identifiers.org data" + e.getMessage());
+ }
}
- }
- }).start();
-
+ }).start();
+ }
}
@Override
- protected void showNews_actionPerformed(ActionEvent e)
- {
+ protected void showNews_actionPerformed(ActionEvent e) {
showNews(showNews.isSelected());
}
- void showNews(boolean visible)
- {
- Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
+ void showNews(boolean visible) {
+ jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news.");
showNews.setSelected(visible);
- if (visible && !jvnews.isVisible())
- {
- new Thread(new Runnable()
- {
+ if (visible && !jvnews.isVisible()) {
+ new Thread(new Runnable() {
@Override
- public void run()
- {
+ public void run() {
long now = System.currentTimeMillis();
- Desktop.instance.setProgressBar(
- MessageManager.getString("status.refreshing_news"), now);
+ Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_news"), now);
jvnews.refreshNews();
Desktop.instance.setProgressBar(null, now);
jvnews.showNews();
/**
* recover the last known dimensions for a jalview window
*
- * @param windowName
- * - empty string is desktop, all other windows have unique prefix
+ * @param windowName - empty string is desktop, all other windows have unique
+ * prefix
* @return null or last known dimensions scaled to current geometry (if last
* window geom was known)
*/
- Rectangle getLastKnownDimensions(String windowName)
- {
+ Rectangle getLastKnownDimensions(String windowName) {
// TODO: lock aspect ratio for scaling desktop Bug #0058199
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
String x = Cache.getProperty(windowName + "SCREEN_X");
String y = Cache.getProperty(windowName + "SCREEN_Y");
String width = Cache.getProperty(windowName + "SCREEN_WIDTH");
String height = Cache.getProperty(windowName + "SCREEN_HEIGHT");
- if ((x != null) && (y != null) && (width != null) && (height != null))
- {
- int ix = Integer.parseInt(x), iy = Integer.parseInt(y),
- iw = Integer.parseInt(width), ih = Integer.parseInt(height);
- if (Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
- {
+ if ((x != null) && (y != null) && (width != null) && (height != null)) {
+ int ix = Integer.parseInt(x), iy = Integer.parseInt(y), iw = Integer.parseInt(width),
+ ih = Integer.parseInt(height);
+ if (Cache.getProperty("SCREENGEOMETRY_WIDTH") != null) {
// attempt #1 - try to cope with change in screen geometry - this
// version doesn't preserve original jv aspect ratio.
// take ratio of current screen size vs original screen size.
- double sw = ((1f * screenSize.width) / (1f * Integer
- .parseInt(Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
- double sh = ((1f * screenSize.height) / (1f * Integer
- .parseInt(Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
+ double sw = ((1f * screenSize.width) / (1f * Integer.parseInt(Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
+ double sh = ((1f * screenSize.height) / (1f * Integer.parseInt(Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
// rescale the bounds depending upon the current screen geometry.
ix = (int) (ix * sw);
iw = (int) (iw * sw);
iy = (int) (iy * sh);
ih = (int) (ih * sh);
- while (ix >= screenSize.width)
- {
- Cache.log.debug(
- "Window geometry location recall error: shifting horizontal to within screenbounds.");
+ while (ix >= screenSize.width) {
+ jalview.bin.Console.debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
ix -= screenSize.width;
}
- while (iy >= screenSize.height)
- {
- Cache.log.debug(
- "Window geometry location recall error: shifting vertical to within screenbounds.");
+ while (iy >= screenSize.height) {
+ jalview.bin.Console.debug("Window geometry location recall error: shifting vertical to within screenbounds.");
iy -= screenSize.height;
}
- Cache.log.debug(
- "Got last known dimensions for " + windowName + ": x:" + ix
- + " y:" + iy + " width:" + iw + " height:" + ih);
+ jalview.bin.Console.debug("Got last known dimensions for " + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
+ + " height:" + ih);
}
// return dimensions for new instance
return new Rectangle(ix, iy, iw, ih);
return null;
}
- void showPasteMenu(int x, int y)
- {
+ void showPasteMenu(int x, int y) {
JPopupMenu popup = new JPopupMenu();
- JMenuItem item = new JMenuItem(
- MessageManager.getString("label.paste_new_window"));
- item.addActionListener(new ActionListener()
- {
+ JMenuItem item = new JMenuItem(MessageManager.getString("label.paste_new_window"));
+ item.addActionListener(new ActionListener() {
@Override
- public void actionPerformed(ActionEvent evt)
- {
+ public void actionPerformed(ActionEvent evt) {
paste();
}
});
popup.show(this, x, y);
}
- public void paste()
- {
- try
- {
+ public void paste() {
+ try {
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
Transferable contents = c.getContents(this);
- if (contents != null)
- {
- String file = (String) contents
- .getTransferData(DataFlavor.stringFlavor);
+ if (contents != null) {
+ String file = (String) contents.getTransferData(DataFlavor.stringFlavor);
- FileFormatI format = new IdentifyFile().identify(file,
- DataSourceType.PASTE);
+ FileFormatI format = new IdentifyFile().identify(file, DataSourceType.PASTE);
new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
}
- } catch (Exception ex)
- {
- System.out.println(
- "Unable to paste alignment from system clipboard:\n" + ex);
+ } catch (Exception ex) {
+ System.out.println("Unable to paste alignment from system clipboard:\n" + ex);
}
}
/**
* Adds and opens the given frame to the desktop
*
- * @param frame
- * Frame to show
- * @param title
- * Visible Title
- * @param w
- * width
- * @param h
- * height
- */
- public static synchronized void addInternalFrame(
- final JInternalFrame frame, String title, int w, int h)
- {
+ * @param frame Frame to show
+ * @param title Visible Title
+ * @param w width
+ * @param h height
+ */
+ public static synchronized void addInternalFrame(final JInternalFrame frame, String title, int w, int h) {
addInternalFrame(frame, title, true, w, h, true, false);
}
/**
* Add an internal frame to the Jalview desktop
*
- * @param frame
- * Frame to show
- * @param title
- * Visible Title
- * @param makeVisible
- * When true, display frame immediately, otherwise, caller must call
- * setVisible themselves.
- * @param w
- * width
- * @param h
- * height
- */
- public static synchronized void addInternalFrame(
- final JInternalFrame frame, String title, boolean makeVisible,
- int w, int h)
- {
+ * @param frame Frame to show
+ * @param title Visible Title
+ * @param makeVisible When true, display frame immediately, otherwise, caller
+ * must call setVisible themselves.
+ * @param w width
+ * @param h height
+ */
+ public static synchronized void addInternalFrame(final JInternalFrame frame, String title, boolean makeVisible, int w,
+ int h) {
addInternalFrame(frame, title, makeVisible, w, h, true, false);
}
/**
* Add an internal frame to the Jalview desktop and make it visible
*
- * @param frame
- * Frame to show
- * @param title
- * Visible Title
- * @param w
- * width
- * @param h
- * height
- * @param resizable
- * Allow resize
- */
- public static synchronized void addInternalFrame(
- final JInternalFrame frame, String title, int w, int h,
- boolean resizable)
- {
+ * @param frame Frame to show
+ * @param title Visible Title
+ * @param w width
+ * @param h height
+ * @param resizable Allow resize
+ */
+ public static synchronized void addInternalFrame(final JInternalFrame frame, String title, int w, int h,
+ boolean resizable) {
addInternalFrame(frame, title, true, w, h, resizable, false);
}
/**
* Add an internal frame to the Jalview desktop
*
- * @param frame
- * Frame to show
- * @param title
- * Visible Title
- * @param makeVisible
- * When true, display frame immediately, otherwise, caller must call
- * setVisible themselves.
- * @param w
- * width
- * @param h
- * height
- * @param resizable
- * Allow resize
- * @param ignoreMinSize
- * Do not set the default minimum size for frame
- */
- public static synchronized void addInternalFrame(
- final JInternalFrame frame, String title, boolean makeVisible,
- int w, int h, boolean resizable, boolean ignoreMinSize)
- {
+ * @param frame Frame to show
+ * @param title Visible Title
+ * @param makeVisible When true, display frame immediately, otherwise, caller
+ * must call setVisible themselves.
+ * @param w width
+ * @param h height
+ * @param resizable Allow resize
+ * @param ignoreMinSize Do not set the default minimum size for frame
+ */
+ public static synchronized void addInternalFrame(final JInternalFrame frame, String title, boolean makeVisible, int w,
+ int h, boolean resizable, boolean ignoreMinSize) {
// TODO: allow callers to determine X and Y position of frame (eg. via
// bounds object).
// the current window title
frame.setTitle(title);
- if (frame.getWidth() < 1 || frame.getHeight() < 1)
- {
+ if (frame.getWidth() < 1 || frame.getHeight() < 1) {
frame.setSize(w, h);
}
// THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
// IF JALVIEW IS RUNNING HEADLESS
// ///////////////////////////////////////////////
if (instance == null || (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true")))
- {
+ && System.getProperty("java.awt.headless").equals("true"))) {
return;
}
openFrameCount++;
- if (!ignoreMinSize)
- {
- frame.setMinimumSize(
- new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT));
+ if (!ignoreMinSize) {
+ frame.setMinimumSize(new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT));
// Set default dimension for Alignment Frame window.
// The Alignment Frame window could be added from a number of places,
// hence,
// I did this here in order not to miss out on any Alignment frame.
- if (frame instanceof AlignFrame)
- {
- frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH,
- ALIGN_FRAME_DEFAULT_MIN_HEIGHT));
+ if (frame instanceof AlignFrame) {
+ frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH, ALIGN_FRAME_DEFAULT_MIN_HEIGHT));
}
}
frame.setIconifiable(resizable);
frame.setOpaque(Platform.isJS());
- if (frame.getX() < 1 && frame.getY() < 1)
- {
- frame.setLocation(xOffset * openFrameCount,
- yOffset * ((openFrameCount - 1) % 10) + yOffset);
+ if (frame.getX() < 1 && frame.getY() < 1) {
+ frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount - 1) % 10) + yOffset);
}
/*
- * add an entry for the new frame in the Window menu
- * (and remove it when the frame is closed)
+ * add an entry for the new frame in the Window menu (and remove it when the
+ * frame is closed)
*/
final JMenuItem menuItem = new JMenuItem(title);
- frame.addInternalFrameListener(new InternalFrameAdapter()
- {
+ frame.addInternalFrameListener(new InternalFrameAdapter() {
@Override
- public void internalFrameActivated(InternalFrameEvent evt)
- {
+ public void internalFrameActivated(InternalFrameEvent evt) {
JInternalFrame itf = desktop.getSelectedFrame();
- if (itf != null)
- {
- if (itf instanceof AlignFrame)
- {
+ if (itf != null) {
+ if (itf instanceof AlignFrame) {
Jalview.setCurrentAlignFrame((AlignFrame) itf);
}
itf.requestFocus();
}
@Override
- public void internalFrameClosed(InternalFrameEvent evt)
- {
+ public void internalFrameClosed(InternalFrameEvent evt) {
PaintRefresher.RemoveComponent(frame);
/*
- * defensive check to prevent frames being
- * added half off the window
+ * defensive check to prevent frames being added half off the window
*/
- if (openFrameCount > 0)
- {
+ if (openFrameCount > 0) {
openFrameCount--;
}
/*
* ensure no reference to alignFrame retained by menu item listener
*/
- if (menuItem.getActionListeners().length > 0)
- {
+ if (menuItem.getActionListeners().length > 0) {
menuItem.removeActionListener(menuItem.getActionListeners()[0]);
}
windowMenu.remove(menuItem);
}
});
- menuItem.addActionListener(new ActionListener()
- {
+ menuItem.addActionListener(new ActionListener() {
@Override
- public void actionPerformed(ActionEvent e)
- {
- try
- {
+ public void actionPerformed(ActionEvent e) {
+ try {
frame.setSelected(true);
frame.setIcon(false);
- } catch (java.beans.PropertyVetoException ex)
- {
- // System.err.println(ex.toString());
+ } catch (java.beans.PropertyVetoException ex) {
+
}
}
});
windowMenu.add(menuItem);
frame.toFront();
- try
- {
+ try {
frame.setSelected(true);
frame.requestFocus();
- } catch (java.beans.PropertyVetoException ve)
- {
- } catch (java.lang.ClassCastException cex)
- {
- Cache.log.warn(
- "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
- cex);
+ } catch (java.beans.PropertyVetoException ve) {
+ } catch (java.lang.ClassCastException cex) {
+ jalview.bin.Console.warn(
+ "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
+ cex);
}
}
/**
- * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close
- * the window
+ * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close the
+ * window
*
* @param frame
*/
- private static void setKeyBindings(JInternalFrame frame)
- {
+ private static void setKeyBindings(JInternalFrame frame) {
@SuppressWarnings("serial")
- final Action closeAction = new AbstractAction()
- {
+ final Action closeAction = new AbstractAction() {
@Override
- public void actionPerformed(ActionEvent e)
- {
+ public void actionPerformed(ActionEvent e) {
frame.dispose();
}
};
/*
* set up key bindings for Ctrl-W and Cmd-W, with the same (Close) action
*/
- KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- InputEvent.CTRL_DOWN_MASK);
- KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
+ KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, InputEvent.CTRL_DOWN_MASK);
+ KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
- InputMap inputMap = frame
- .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
+ InputMap inputMap = frame.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
String ctrlW = ctrlWKey.toString();
inputMap.put(ctrlWKey, ctrlW);
inputMap.put(cmdWKey, ctrlW);
}
@Override
- public void lostOwnership(Clipboard clipboard, Transferable contents)
- {
- if (!internalCopy)
- {
+ public void lostOwnership(Clipboard clipboard, Transferable contents) {
+ if (!internalCopy) {
Desktop.jalviewClipboard = null;
}
}
@Override
- public void dragEnter(DropTargetDragEvent evt)
- {
+ public void dragEnter(DropTargetDragEvent evt) {
}
@Override
- public void dragExit(DropTargetEvent evt)
- {
+ public void dragExit(DropTargetEvent evt) {
}
@Override
- public void dragOver(DropTargetDragEvent evt)
- {
+ public void dragOver(DropTargetDragEvent evt) {
}
@Override
- public void dropActionChanged(DropTargetDragEvent evt)
- {
+ public void dropActionChanged(DropTargetDragEvent evt) {
}
/**
* DOCUMENT ME!
*
- * @param evt
- * DOCUMENT ME!
+ * @param evt DOCUMENT ME!
*/
@Override
- public void drop(DropTargetDropEvent evt)
- {
+ public void drop(DropTargetDropEvent evt) {
boolean success = true;
// JAL-1552 - acceptDrop required before getTransferable call for
// Java's Transferable for native dnd
List<Object> files = new ArrayList<>();
List<DataSourceType> protocols = new ArrayList<>();
- try
- {
+ try {
Desktop.transferFromDropTarget(files, protocols, evt, t);
- } catch (Exception e)
- {
+ } catch (Exception e) {
e.printStackTrace();
success = false;
}
- if (files != null)
- {
- try
- {
- for (int i = 0; i < files.size(); i++)
- {
+ if (files != null) {
+ try {
+ for (int i = 0; i < files.size(); i++) {
// BH 2018 File or String
Object file = files.get(i);
String fileName = file.toString();
- DataSourceType protocol = (protocols == null)
- ? DataSourceType.FILE
- : protocols.get(i);
+ DataSourceType protocol = (protocols == null) ? DataSourceType.FILE : protocols.get(i);
FileFormatI format = null;
- if (fileName.endsWith(".jar"))
- {
+ if (fileName.endsWith(".jar")) {
format = FileFormat.Jalview;
- }
- else
- {
+ } else {
format = new IdentifyFile().identify(file, protocol);
}
- if (file instanceof File)
- {
+ if (file instanceof File) {
Platform.cacheFileData((File) file);
}
new FileLoader().LoadFile(null, file, protocol, format);
}
- } catch (Exception ex)
- {
+ } catch (Exception ex) {
success = false;
}
}
/**
* DOCUMENT ME!
*
- * @param e
- * DOCUMENT ME!
+ * @param e DOCUMENT ME!
*/
@Override
- public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
- {
+ public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) {
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser chooser = JalviewFileChooser.forRead(
- Cache.getProperty("LAST_DIRECTORY"), fileFormat,
- BackupFiles.getEnabled());
+ JalviewFileChooser chooser = JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat,
+ BackupFiles.getEnabled());
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(
- MessageManager.getString("label.open_local_file"));
+ chooser.setDialogTitle(MessageManager.getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
- chooser.setResponseHandler(0, new Runnable()
- {
+ chooser.setResponseHandler(0, new Runnable() {
@Override
- public void run()
- {
+ public void run() {
File selectedFile = chooser.getSelectedFile();
Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
/*
* Call IdentifyFile to verify the file contains what its extension implies.
- * Skip this step for dynamically added file formats, because
- * IdentifyFile does not know how to recognise them.
+ * Skip this step for dynamically added file formats, because IdentifyFile does
+ * not know how to recognise them.
*/
- if (FileFormats.getInstance().isIdentifiable(format))
- {
- try
- {
- format = new IdentifyFile().identify(selectedFile,
- DataSourceType.FILE);
- } catch (FileFormatException e)
- {
+ if (FileFormats.getInstance().isIdentifiable(format)) {
+ try {
+ format = new IdentifyFile().identify(selectedFile, DataSourceType.FILE);
+ } catch (FileFormatException e) {
// format = null; //??
}
}
- new FileLoader().LoadFile(viewport, selectedFile,
- DataSourceType.FILE, format);
+ new FileLoader().LoadFile(viewport, selectedFile, DataSourceType.FILE, format);
}
});
chooser.showOpenDialog(this);
* @param viewport
*/
@Override
- public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
- {
+ public void inputURLMenuItem_actionPerformed(AlignViewport viewport) {
// This construct allows us to have a wider textfield
// for viewing
- JLabel label = new JLabel(
- MessageManager.getString("label.input_file_url"));
+ JLabel label = new JLabel(MessageManager.getString("label.input_file_url"));
JPanel panel = new JPanel(new GridLayout(2, 1));
panel.add(label);
/*
- * the URL to fetch is input in
- * Java: an editable combobox with history
- * JS: (pending JAL-3038) a plain text field
+ * the URL to fetch is input in Java: an editable combobox with history JS:
+ * (pending JAL-3038) a plain text field
*/
JComponent history;
String urlBase = "https://www.";
- if (Platform.isJS())
- {
+ if (Platform.isJS()) {
history = new JTextField(urlBase, 35);
- }
- else
+ } else
/**
* Java only
*
asCombo.setEditable(true);
asCombo.addItem(urlBase);
String historyItems = Cache.getProperty("RECENT_URL");
- if (historyItems != null)
- {
- for (String token : historyItems.split("\\t"))
- {
+ if (historyItems != null) {
+ for (String token : historyItems.split("\\t")) {
asCombo.addItem(token);
}
}
Object[] options = new Object[] { MessageManager.getString("action.ok"),
MessageManager.getString("action.cancel") };
- Runnable action = new Runnable()
- {
+ Runnable action = new Runnable() {
@Override
- public void run()
- {
+ public void run() {
@SuppressWarnings("unchecked")
- String url = (history instanceof JTextField
- ? ((JTextField) history).getText()
- : ((JComboBox<String>) history).getEditor().getItem()
- .toString().trim());
-
- if (url.toLowerCase().endsWith(".jar"))
- {
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- FileFormat.Jalview);
+ String url = (history instanceof JTextField ? ((JTextField) history).getText()
+ : ((JComboBox<String>) history).getEditor().getItem().toString().trim());
+
+ if (url.toLowerCase(Locale.ROOT).endsWith(".jar")) {
+ if (viewport != null) {
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL, FileFormat.Jalview);
+ } else {
+ new FileLoader().LoadFile(url, DataSourceType.URL, FileFormat.Jalview);
}
- else
- {
- new FileLoader().LoadFile(url, DataSourceType.URL,
- FileFormat.Jalview);
- }
- }
- else
- {
+ } else {
FileFormatI format = null;
- try
- {
+ try {
format = new IdentifyFile().identify(url, DataSourceType.URL);
- } catch (FileFormatException e)
- {
+ } catch (FileFormatException e) {
// TODO revise error handling, distinguish between
// URL not found and response not valid
}
- if (format == null)
- {
- String msg = MessageManager
- .formatMessage("label.couldnt_locate", url);
+ if (format == null) {
+ String msg = MessageManager.formatMessage("label.couldnt_locate", url);
JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
- MessageManager.getString("label.url_not_found"),
- JvOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.url_not_found"), JvOptionPane.WARNING_MESSAGE);
return;
}
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- format);
- }
- else
- {
+ if (viewport != null) {
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL, format);
+ } else {
new FileLoader().LoadFile(url, DataSourceType.URL, format);
}
}
}
};
- String dialogOption = MessageManager
- .getString("label.input_alignment_from_url");
- JvOptionPane.newOptionDialog(desktop).setResponseHandler(0, action)
- .showInternalDialog(panel, dialogOption,
- JvOptionPane.YES_NO_CANCEL_OPTION,
- JvOptionPane.PLAIN_MESSAGE, null, options,
- MessageManager.getString("action.ok"));
+ String dialogOption = MessageManager.getString("label.input_alignment_from_url");
+ JvOptionPane.newOptionDialog(desktop).setResponseHandler(0, action).showInternalDialog(panel, dialogOption,
+ JvOptionPane.YES_NO_CANCEL_OPTION, JvOptionPane.PLAIN_MESSAGE, null, options,
+ MessageManager.getString("action.ok"));
}
/**
* Opens the CutAndPaste window for the user to paste an alignment in to
*
- * @param viewPanel
- * - if not null, the pasted alignment is added to the current
- * alignment; if null, to a new alignment window
+ * @param viewPanel - if not null, the pasted alignment is added to the current
+ * alignment; if null, to a new alignment window
*/
@Override
- public void inputTextboxMenuItem_actionPerformed(
- AlignmentViewPanel viewPanel)
- {
+ public void inputTextboxMenuItem_actionPerformed(AlignmentViewPanel viewPanel) {
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(viewPanel);
- Desktop.addInternalFrame(cap,
- MessageManager.getString("label.cut_paste_alignmen_file"), true,
- 600, 500);
+ Desktop.addInternalFrame(cap, MessageManager.getString("label.cut_paste_alignmen_file"), true, 600, 500);
}
/*
* Exit the program
*/
@Override
- public void quit()
- {
+ public void quit() {
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
- storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
- getWidth(), getHeight()));
+ storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y, getWidth(), getHeight()));
- if (jconsole != null)
- {
+ if (jconsole != null) {
storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
jconsole.stopConsole();
}
- if (jvnews != null)
- {
+ if (jvnews != null) {
storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
}
- if (dialogExecutor != null)
- {
+ if (dialogExecutor != null) {
dialogExecutor.shutdownNow();
}
closeAll_actionPerformed(null);
- if (groovyConsole != null)
- {
+ if (groovyConsole != null) {
// suppress a possible repeat prompt to save script
groovyConsole.setDirty(false);
groovyConsole.exit();
System.exit(0);
}
- private void storeLastKnownDimensions(String string, Rectangle jc)
- {
- Cache.log.debug("Storing last known dimensions for " + string + ": x:"
- + jc.x + " y:" + jc.y + " width:" + jc.width + " height:"
- + jc.height);
+ private void storeLastKnownDimensions(String string, Rectangle jc) {
+ jalview.bin.Console.debug("Storing last known dimensions for " + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+ + " height:" + jc.height);
Cache.setProperty(string + "SCREEN_X", jc.x + "");
Cache.setProperty(string + "SCREEN_Y", jc.y + "");
/**
* DOCUMENT ME!
*
- * @param e
- * DOCUMENT ME!
+ * @param e DOCUMENT ME!
*/
@Override
- public void aboutMenuItem_actionPerformed(ActionEvent e)
- {
- new Thread(new Runnable()
- {
+ public void aboutMenuItem_actionPerformed(ActionEvent e) {
+ new Thread(new Runnable() {
@Override
- public void run()
- {
+ public void run() {
new SplashScreen(false);
}
}).start();
/**
* Returns the html text for the About screen, including any available version
- * number, build details, author details and citation reference, but without
- * the enclosing {@code html} tags
+ * number, build details, author details and citation reference, but without the
+ * enclosing {@code html} tags
*
* @return
*/
- public String getAboutMessage()
- {
+ public String getAboutMessage() {
StringBuilder message = new StringBuilder(1024);
- message.append("<div style=\"font-family: sans-serif;\">")
- .append("<h1><strong>Version: ")
- .append(Cache.getProperty("VERSION")).append("</strong></h1>")
- .append("<strong>Built: <em>")
- .append(Cache.getDefault("BUILD_DATE", "unknown"))
- .append("</em> from ").append(Cache.getBuildDetailsForSplash())
- .append("</strong>");
+ message.append("<div style=\"font-family: sans-serif;\">").append("<h1><strong>Version: ")
+ .append(Cache.getProperty("VERSION")).append("</strong></h1>").append("<strong>Built: <em>")
+ .append(Cache.getDefault("BUILD_DATE", "unknown")).append("</em> from ")
+ .append(Cache.getBuildDetailsForSplash()).append("</strong>");
String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking");
- if (latestVersion.equals("Checking"))
- {
+ if (latestVersion.equals("Checking")) {
// JBP removed this message for 2.11: May be reinstated in future version
// message.append("<br>...Checking latest version...</br>");
- }
- else if (!latestVersion.equals(Cache.getProperty("VERSION")))
- {
+ } else if (!latestVersion.equals(Cache.getProperty("VERSION"))) {
boolean red = false;
- if (Cache.getProperty("VERSION").toLowerCase()
- .indexOf("automated build") == -1)
- {
+ if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT).indexOf("automated build") == -1) {
red = true;
// Displayed when code version and jnlp version do not match and code
// version is not a development build
message.append("<div style=\"color: #FF0000;font-style: bold;\">");
}
- message.append("<br>!! Version ")
- .append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
- .append(" is available for download from ")
- .append(Cache.getDefault("www.jalview.org",
- "https://www.jalview.org"))
- .append(" !!");
- if (red)
- {
+ message.append("<br>!! Version ").append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
+ .append(" is available for download from ")
+ .append(Cache.getDefault("www.jalview.org", "https://www.jalview.org")).append(" !!");
+ if (red) {
message.append("</div>");
}
}
* Action on requesting Help documentation
*/
@Override
- public void documentationMenuItem_actionPerformed()
- {
- try
- {
- if (Platform.isJS())
- {
+ public void documentationMenuItem_actionPerformed() {
+ try {
+ if (Platform.isJS()) {
BrowserLauncher.openURL("https://www.jalview.org/help.html");
- }
- else
+ } else
/**
* Java only
*
{
Help.showHelpWindow();
}
- } catch (Exception ex)
- {
+ } catch (Exception ex) {
System.err.println("Error opening help: " + ex.getMessage());
}
}
@Override
- public void closeAll_actionPerformed(ActionEvent e)
- {
+ public void closeAll_actionPerformed(ActionEvent e) {
// TODO show a progress bar while closing?
JInternalFrame[] frames = desktop.getAllFrames();
- for (int i = 0; i < frames.length; i++)
- {
- try
- {
+ for (int i = 0; i < frames.length; i++) {
+ try {
frames[i].setClosed(true);
- } catch (java.beans.PropertyVetoException ex)
- {
+ } catch (java.beans.PropertyVetoException ex) {
}
}
Jalview.setCurrentAlignFrame(null);
* reset state of singleton objects as appropriate (clear down session state
* when all windows are closed)
*/
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(this);
- if (ssm != null)
- {
+ StructureSelectionManager ssm = StructureSelectionManager.getStructureSelectionManager(this);
+ if (ssm != null) {
ssm.resetAll();
}
}
@Override
- public void raiseRelated_actionPerformed(ActionEvent e)
- {
+ public void raiseRelated_actionPerformed(ActionEvent e) {
reorderAssociatedWindows(false, false);
}
@Override
- public void minimizeAssociated_actionPerformed(ActionEvent e)
- {
+ public void minimizeAssociated_actionPerformed(ActionEvent e) {
reorderAssociatedWindows(true, false);
}
- void closeAssociatedWindows()
- {
+ void closeAssociatedWindows() {
reorderAssociatedWindows(false, true);
}
* ActionEvent)
*/
@Override
- protected void garbageCollect_actionPerformed(ActionEvent e)
- {
+ protected void garbageCollect_actionPerformed(ActionEvent e) {
// We simply collect the garbage
- Cache.log.debug("Collecting garbage...");
+ jalview.bin.Console.debug("Collecting garbage...");
System.gc();
- Cache.log.debug("Finished garbage collection.");
+ jalview.bin.Console.debug("Finished garbage collection.");
}
/*
* (non-Javadoc)
*
- * @see
- * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
- * )
+ * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.
+ * ActionEvent )
*/
@Override
- protected void showMemusage_actionPerformed(ActionEvent e)
- {
+ protected void showMemusage_actionPerformed(ActionEvent e) {
desktop.showMemoryUsage(showMemusage.isSelected());
}
* )
*/
@Override
- protected void showConsole_actionPerformed(ActionEvent e)
- {
+ protected void showConsole_actionPerformed(ActionEvent e) {
showConsole(showConsole.isSelected());
}
*
* @param selected
*/
- void showConsole(boolean selected)
- {
+ void showConsole(boolean selected) {
// TODO: decide if we should update properties file
if (jconsole != null) // BH 2018
{
showConsole.setSelected(selected);
- Cache.setProperty("SHOW_JAVA_CONSOLE",
- Boolean.valueOf(selected).toString());
+ Cache.setProperty("SHOW_JAVA_CONSOLE", Boolean.valueOf(selected).toString());
jconsole.setVisible(selected);
}
}
- void reorderAssociatedWindows(boolean minimize, boolean close)
- {
+ void reorderAssociatedWindows(boolean minimize, boolean close) {
JInternalFrame[] frames = desktop.getAllFrames();
- if (frames == null || frames.length < 1)
- {
+ if (frames == null || frames.length < 1) {
return;
}
AlignmentViewport source = null, target = null;
- if (frames[0] instanceof AlignFrame)
- {
+ if (frames[0] instanceof AlignFrame) {
source = ((AlignFrame) frames[0]).getCurrentView();
- }
- else if (frames[0] instanceof TreePanel)
- {
+ } else if (frames[0] instanceof TreePanel) {
source = ((TreePanel) frames[0]).getViewPort();
- }
- else if (frames[0] instanceof PCAPanel)
- {
+ } else if (frames[0] instanceof PCAPanel) {
source = ((PCAPanel) frames[0]).av;
- }
- else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
- {
+ } else if (frames[0].getContentPane() instanceof PairwiseAlignPanel) {
source = ((PairwiseAlignPanel) frames[0].getContentPane()).av;
}
- if (source != null)
- {
- for (int i = 0; i < frames.length; i++)
- {
+ if (source != null) {
+ for (int i = 0; i < frames.length; i++) {
target = null;
- if (frames[i] == null)
- {
+ if (frames[i] == null) {
continue;
}
- if (frames[i] instanceof AlignFrame)
- {
+ if (frames[i] instanceof AlignFrame) {
target = ((AlignFrame) frames[i]).getCurrentView();
- }
- else if (frames[i] instanceof TreePanel)
- {
+ } else if (frames[i] instanceof TreePanel) {
target = ((TreePanel) frames[i]).getViewPort();
- }
- else if (frames[i] instanceof PCAPanel)
- {
+ } else if (frames[i] instanceof PCAPanel) {
target = ((PCAPanel) frames[i]).av;
- }
- else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
- {
+ } else if (frames[i].getContentPane() instanceof PairwiseAlignPanel) {
target = ((PairwiseAlignPanel) frames[i].getContentPane()).av;
}
- if (source == target)
- {
- try
- {
- if (close)
- {
+ if (source == target) {
+ try {
+ if (close) {
frames[i].setClosed(true);
- }
- else
- {
+ } else {
frames[i].setIcon(minimize);
- if (!minimize)
- {
+ if (!minimize) {
frames[i].toFront();
}
}
- } catch (java.beans.PropertyVetoException ex)
- {
+ } catch (java.beans.PropertyVetoException ex) {
}
}
}
/**
* DOCUMENT ME!
*
- * @param e
- * DOCUMENT ME!
+ * @param e DOCUMENT ME!
*/
@Override
- protected void preferences_actionPerformed(ActionEvent e)
- {
+ protected void preferences_actionPerformed(ActionEvent e) {
Preferences.openPreferences();
}
* Jalview project file
*/
@Override
- public void saveState_actionPerformed()
- {
+ public void saveState_actionPerformed() {
saveState_actionPerformed(false);
}
- public void saveState_actionPerformed(boolean saveAs)
- {
+ public void saveState_actionPerformed(boolean saveAs) {
java.io.File projectFile = getProjectFile();
// autoSave indicates we already have a file and don't need to ask
- boolean autoSave = projectFile != null && !saveAs
- && BackupFiles.getEnabled();
+ boolean autoSave = projectFile != null && !saveAs && BackupFiles.getEnabled();
// System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
// saveAs="+saveAs+", Backups
// "+(BackupFiles.getEnabled()?"enabled":"disabled"));
boolean approveSave = false;
- if (!autoSave)
- {
- JalviewFileChooser chooser = new JalviewFileChooser("jvp",
- "Jalview Project");
+ if (!autoSave) {
+ JalviewFileChooser chooser = new JalviewFileChooser("jvp", "Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.save_state"));
int value = chooser.showSaveDialog(this);
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
+ if (value == JalviewFileChooser.APPROVE_OPTION) {
projectFile = chooser.getSelectedFile();
setProjectFile(projectFile);
approveSave = true;
}
}
- if (approveSave || autoSave)
- {
+ if (approveSave || autoSave) {
final Desktop me = this;
final java.io.File chosenFile = projectFile;
- new Thread(new Runnable()
- {
+ new Thread(new Runnable() {
@Override
- public void run()
- {
+ public void run() {
// TODO: refactor to Jalview desktop session controller action.
- setProgressBar(MessageManager.formatMessage(
- "label.saving_jalview_project", new Object[]
- { chosenFile.getName() }), chosenFile.hashCode());
+ setProgressBar(
+ MessageManager.formatMessage("label.saving_jalview_project", new Object[] { chosenFile.getName() }),
+ chosenFile.hashCode());
Cache.setProperty("LAST_DIRECTORY", chosenFile.getParent());
// TODO catch and handle errors for savestate
// TODO prevent user from messing with the Desktop whilst we're saving
- try
- {
+ try {
boolean doBackup = BackupFiles.getEnabled();
- BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile)
- : null;
+ BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null;
- new Jalview2XML().saveState(
- doBackup ? backupfiles.getTempFile() : chosenFile);
+ new Jalview2XML().saveState(doBackup ? backupfiles.getTempFile() : chosenFile);
- if (doBackup)
- {
+ if (doBackup) {
backupfiles.setWriteSuccess(true);
backupfiles.rollBackupsAndRenameTempFile();
}
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Whilst saving current state to "
- + chosenFile.getName(), oom);
- } catch (Exception ex)
- {
- Cache.log.error("Problems whilst trying to save to "
- + chosenFile.getName(), ex);
+ } catch (OutOfMemoryError oom) {
+ new OOMWarning("Whilst saving current state to " + chosenFile.getName(), oom);
+ } catch (Exception ex) {
+ jalview.bin.Console.error("Problems whilst trying to save to " + chosenFile.getName(), ex);
JvOptionPane.showMessageDialog(me,
- MessageManager.formatMessage(
- "label.error_whilst_saving_current_state_to",
- new Object[]
- { chosenFile.getName() }),
- MessageManager.getString("label.couldnt_save_project"),
- JvOptionPane.WARNING_MESSAGE);
+ MessageManager.formatMessage("label.error_whilst_saving_current_state_to",
+ new Object[] { chosenFile.getName() }),
+ MessageManager.getString("label.couldnt_save_project"), JvOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, chosenFile.hashCode());
}
}
@Override
- public void saveAsState_actionPerformed(ActionEvent e)
- {
+ public void saveAsState_actionPerformed(ActionEvent e) {
saveState_actionPerformed(true);
}
- private void setProjectFile(File choice)
- {
+ private void setProjectFile(File choice) {
this.projectFile = choice;
}
- public File getProjectFile()
- {
+ public File getProjectFile() {
return this.projectFile;
}
* Jalview project
*/
@Override
- public void loadState_actionPerformed()
- {
+ public void loadState_actionPerformed() {
final String[] suffix = new String[] { "jvp", "jar" };
- final String[] desc = new String[] { "Jalview Project",
- "Jalview Project (old)" };
- JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
- "Jalview Project", true, BackupFiles.getEnabled()); // last two
- // booleans:
- // allFiles,
+ final String[] desc = new String[] { "Jalview Project", "Jalview Project (old)" };
+ JalviewFileChooser chooser = new JalviewFileChooser(Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
+ "Jalview Project", true, BackupFiles.getEnabled()); // last two
+ // booleans:
+ // allFiles,
// allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
- chooser.setResponseHandler(0, new Runnable()
- {
+ chooser.setResponseHandler(0, new Runnable() {
@Override
- public void run()
- {
+ public void run() {
File selectedFile = chooser.getSelectedFile();
setProjectFile(selectedFile);
String choice = selectedFile.getAbsolutePath();
Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
- new Thread(new Runnable()
- {
+ new Thread(new Runnable() {
@Override
- public void run()
- {
- try
- {
+ public void run() {
+ try {
new Jalview2XML().loadJalviewAlign(selectedFile);
- } catch (OutOfMemoryError oom)
- {
+ } catch (OutOfMemoryError oom) {
new OOMWarning("Whilst loading project from " + choice, oom);
- } catch (Exception ex)
- {
- Cache.log.error(
- "Problems whilst loading project from " + choice, ex);
+ } catch (Exception ex) {
+ jalview.bin.Console.error("Problems whilst loading project from " + choice, ex);
JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.error_whilst_loading_project_from",
- new Object[]
- { choice }),
- MessageManager
- .getString("label.couldnt_load_project"),
- JvOptionPane.WARNING_MESSAGE);
+ MessageManager.formatMessage("label.error_whilst_loading_project_from", new Object[] { choice }),
+ MessageManager.getString("label.couldnt_load_project"), JvOptionPane.WARNING_MESSAGE);
}
}
}, "Project Loader").start();
}
@Override
- public void inputSequence_actionPerformed(ActionEvent e)
- {
+ public void inputSequence_actionPerformed(ActionEvent e) {
new SequenceFetcher(this);
}
ArrayList<JPanel> fileLoadingPanels = new ArrayList<>();
- public void startLoading(final Object fileName)
- {
- if (fileLoadingCount == 0)
- {
- fileLoadingPanels.add(addProgressPanel(MessageManager
- .formatMessage("label.loading_file", new Object[]
- { fileName })));
+ public void startLoading(final Object fileName) {
+ if (fileLoadingCount == 0) {
+ fileLoadingPanels
+ .add(addProgressPanel(MessageManager.formatMessage("label.loading_file", new Object[] { fileName })));
}
fileLoadingCount++;
}
- private JPanel addProgressPanel(String string)
- {
- if (progressPanel == null)
- {
+ private JPanel addProgressPanel(String string) {
+ if (progressPanel == null) {
progressPanel = new JPanel(new GridLayout(1, 1));
totalProgressCount = 0;
instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
thisprogress.add(progressBar, BorderLayout.CENTER);
progressPanel.add(thisprogress);
- ((GridLayout) progressPanel.getLayout()).setRows(
- ((GridLayout) progressPanel.getLayout()).getRows() + 1);
+ ((GridLayout) progressPanel.getLayout()).setRows(((GridLayout) progressPanel.getLayout()).getRows() + 1);
++totalProgressCount;
instance.validate();
return thisprogress;
int totalProgressCount = 0;
- private void removeProgressPanel(JPanel progbar)
- {
- if (progressPanel != null)
- {
- synchronized (progressPanel)
- {
+ private void removeProgressPanel(JPanel progbar) {
+ if (progressPanel != null) {
+ synchronized (progressPanel) {
progressPanel.remove(progbar);
GridLayout gl = (GridLayout) progressPanel.getLayout();
gl.setRows(gl.getRows() - 1);
- if (--totalProgressCount < 1)
- {
+ if (--totalProgressCount < 1) {
this.getContentPane().remove(progressPanel);
progressPanel = null;
}
validate();
}
- public void stopLoading()
- {
+ public void stopLoading() {
fileLoadingCount--;
- if (fileLoadingCount < 1)
- {
- while (fileLoadingPanels.size() > 0)
- {
+ if (fileLoadingCount < 1) {
+ while (fileLoadingPanels.size() > 0) {
removeProgressPanel(fileLoadingPanels.remove(0));
}
fileLoadingPanels.clear();
validate();
}
- public static int getViewCount(String alignmentId)
- {
+ public static int getViewCount(String alignmentId) {
AlignmentViewport[] aps = getViewports(alignmentId);
return (aps == null) ? 0 : aps.length;
}
/**
*
- * @param alignmentId
- * - if null, all sets are returned
+ * @param alignmentId - if null, all sets are returned
* @return all AlignmentPanels concerning the alignmentId sequence set
*/
- public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
- {
- if (Desktop.desktop == null)
- {
+ public static AlignmentPanel[] getAlignmentPanels(String alignmentId) {
+ if (Desktop.desktop == null) {
// no frames created and in headless mode
// TODO: verify that frames are recoverable when in headless mode
return null;
}
List<AlignmentPanel> aps = new ArrayList<>();
AlignFrame[] frames = getAlignFrames();
- if (frames == null)
- {
+ if (frames == null) {
return null;
}
- for (AlignFrame af : frames)
- {
- for (AlignmentPanel ap : af.alignPanels)
- {
- if (alignmentId == null
- || alignmentId.equals(ap.av.getSequenceSetId()))
- {
+ for (AlignFrame af : frames) {
+ for (AlignmentPanel ap : af.alignPanels) {
+ if (alignmentId == null || alignmentId.equals(ap.av.getSequenceSetId())) {
aps.add(ap);
}
}
}
- if (aps.size() == 0)
- {
+ if (aps.size() == 0) {
return null;
}
AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]);
/**
* get all the viewports on an alignment.
*
- * @param sequenceSetId
- * unique alignment id (may be null - all viewports returned in that
- * case)
+ * @param sequenceSetId unique alignment id (may be null - all viewports
+ * returned in that case)
* @return all viewports on the alignment bound to sequenceSetId
*/
- public static AlignmentViewport[] getViewports(String sequenceSetId)
- {
+ public static AlignmentViewport[] getViewports(String sequenceSetId) {
List<AlignmentViewport> viewp = new ArrayList<>();
- if (desktop != null)
- {
+ if (desktop != null) {
AlignFrame[] frames = Desktop.getAlignFrames();
- for (AlignFrame afr : frames)
- {
- if (sequenceSetId == null || afr.getViewport().getSequenceSetId()
- .equals(sequenceSetId))
- {
- if (afr.alignPanels != null)
- {
- for (AlignmentPanel ap : afr.alignPanels)
- {
- if (sequenceSetId == null
- || sequenceSetId.equals(ap.av.getSequenceSetId()))
- {
+ for (AlignFrame afr : frames) {
+ if (sequenceSetId == null || afr.getViewport().getSequenceSetId().equals(sequenceSetId)) {
+ if (afr.alignPanels != null) {
+ for (AlignmentPanel ap : afr.alignPanels) {
+ if (sequenceSetId == null || sequenceSetId.equals(ap.av.getSequenceSetId())) {
viewp.add(ap.av);
}
}
- }
- else
- {
+ } else {
viewp.add(afr.getViewport());
}
}
}
- if (viewp.size() > 0)
- {
+ if (viewp.size() > 0) {
return viewp.toArray(new AlignmentViewport[viewp.size()]);
}
}
*
* @param af
*/
- public static void explodeViews(AlignFrame af)
- {
+ public static void explodeViews(AlignFrame af) {
int size = af.alignPanels.size();
- if (size < 2)
- {
+ if (size < 2) {
return;
}
// FIXME: ideally should use UI interface API
- FeatureSettings viewFeatureSettings = (af.featureSettings != null
- && af.featureSettings.isOpen()) ? af.featureSettings : null;
+ FeatureSettings viewFeatureSettings = (af.featureSettings != null && af.featureSettings.isOpen())
+ ? af.featureSettings
+ : null;
Rectangle fsBounds = af.getFeatureSettingsGeometry();
- for (int i = 0; i < size; i++)
- {
+ for (int i = 0; i < size; i++) {
AlignmentPanel ap = af.alignPanels.get(i);
AlignFrame newaf = new AlignFrame(ap);
// transfer reference for existing feature settings to new alignFrame
- if (ap == af.alignPanel)
- {
- if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap)
- {
+ if (ap == af.alignPanel) {
+ if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap) {
newaf.featureSettings = viewFeatureSettings;
}
newaf.setFeatureSettingsGeometry(fsBounds);
}
/*
- * Restore the view's last exploded frame geometry if known. Multiple
- * views from one exploded frame share and restore the same (frame)
- * position and size.
+ * Restore the view's last exploded frame geometry if known. Multiple views from
+ * one exploded frame share and restore the same (frame) position and size.
*/
Rectangle geometry = ap.av.getExplodedGeometry();
- if (geometry != null)
- {
+ if (geometry != null) {
newaf.setBounds(geometry);
}
ap.av.setGatherViewsHere(false);
- addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
// and materialise a new feature settings dialog instance for the new
// alignframe
// (closes the old as if 'OK' was pressed)
- if (ap == af.alignPanel && newaf.featureSettings != null
- && newaf.featureSettings.isOpen()
- && af.alignPanel.getAlignViewport().isShowSequenceFeatures())
- {
+ if (ap == af.alignPanel && newaf.featureSettings != null && newaf.featureSettings.isOpen()
+ && af.alignPanel.getAlignViewport().isShowSequenceFeatures()) {
newaf.showFeatureSettingsUI();
}
}
/**
* Gather expanded views (separate AlignFrame's) with the same sequence set
- * identifier back in to this frame as additional views, and close the
- * expanded views. Note the expanded frames may themselves have multiple
- * views. We take the lot.
+ * identifier back in to this frame as additional views, and close the expanded
+ * views. Note the expanded frames may themselves have multiple views. We take
+ * the lot.
*
* @param source
*/
- public void gatherViews(AlignFrame source)
- {
+ public void gatherViews(AlignFrame source) {
source.viewport.setGatherViewsHere(true);
source.viewport.setExplodedGeometry(source.getBounds());
JInternalFrame[] frames = desktop.getAllFrames();
String viewId = source.viewport.getSequenceSetId();
- for (int t = 0; t < frames.length; t++)
- {
- if (frames[t] instanceof AlignFrame && frames[t] != source)
- {
+ for (int t = 0; t < frames.length; t++) {
+ if (frames[t] instanceof AlignFrame && frames[t] != source) {
AlignFrame af = (AlignFrame) frames[t];
boolean gatherThis = false;
- for (int a = 0; a < af.alignPanels.size(); a++)
- {
+ for (int a = 0; a < af.alignPanels.size(); a++) {
AlignmentPanel ap = af.alignPanels.get(a);
- if (viewId.equals(ap.av.getSequenceSetId()))
- {
+ if (viewId.equals(ap.av.getSequenceSetId())) {
gatherThis = true;
ap.av.setGatherViewsHere(false);
ap.av.setExplodedGeometry(af.getBounds());
}
}
- if (gatherThis)
- {
- if (af.featureSettings != null && af.featureSettings.isOpen())
- {
- if (source.featureSettings == null)
- {
+ if (gatherThis) {
+ if (af.featureSettings != null && af.featureSettings.isOpen()) {
+ if (source.featureSettings == null) {
// preserve the feature settings geometry for this frame
source.featureSettings = af.featureSettings;
- source.setFeatureSettingsGeometry(
- af.getFeatureSettingsGeometry());
- }
- else
- {
+ source.setFeatureSettingsGeometry(af.getFeatureSettingsGeometry());
+ } else {
// close it and forget
af.featureSettings.close();
}
}
// refresh the feature setting UI for the source frame if it exists
- if (source.featureSettings != null && source.featureSettings.isOpen())
- {
+ if (source.featureSettings != null && source.featureSettings.isOpen()) {
source.showFeatureSettingsUI();
}
+
}
- public JInternalFrame[] getAllFrames()
- {
+ public JInternalFrame[] getAllFrames() {
return desktop.getAllFrames();
}
*
* @param url
*/
- public void checkForQuestionnaire(String url)
- {
+ public void checkForQuestionnaire(String url) {
UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
// javax.swing.SwingUtilities.invokeLater(jvq);
new Thread(jvq).start();
}
- public void checkURLLinks()
- {
+ public void checkURLLinks() {
// Thread off the URL link checker
- addDialogThread(new Runnable()
- {
+ addDialogThread(new Runnable() {
@Override
- public void run()
- {
- if (Cache.getDefault("CHECKURLLINKS", true))
- {
+ public void run() {
+ if (Cache.getDefault("CHECKURLLINKS", true)) {
// check what the actual links are - if it's just the default don't
// bother with the warning
- List<String> links = Preferences.sequenceUrlLinks
- .getLinksForMenu();
+ List<String> links = Preferences.sequenceUrlLinks.getLinksForMenu();
// only need to check links if there is one with a
// SEQUENCE_ID which is not the default EMBL_EBI link
ListIterator<String> li = links.listIterator();
boolean check = false;
List<JLabel> urls = new ArrayList<>();
- while (li.hasNext())
- {
+ while (li.hasNext()) {
String link = li.next();
- if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID)
- && !UrlConstants.isDefaultString(link))
- {
+ if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID) && !UrlConstants.isDefaultString(link)) {
check = true;
int barPos = link.indexOf("|");
- String urlMsg = barPos == -1 ? link
- : link.substring(0, barPos) + ": "
- + link.substring(barPos + 1);
+ String urlMsg = barPos == -1 ? link : link.substring(0, barPos) + ": " + link.substring(barPos + 1);
urls.add(new JLabel(urlMsg));
}
}
- if (!check)
- {
+ if (!check) {
return;
}
JPanel msgPanel = new JPanel();
msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS));
msgPanel.add(Box.createVerticalGlue());
- JLabel msg = new JLabel(MessageManager
- .getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
- JLabel msg2 = new JLabel(MessageManager
- .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
+ JLabel msg = new JLabel(MessageManager.getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
+ JLabel msg2 = new JLabel(MessageManager.getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
msgPanel.add(msg);
- for (JLabel url : urls)
- {
+ for (JLabel url : urls) {
msgPanel.add(url);
}
msgPanel.add(msg2);
- final JCheckBox jcb = new JCheckBox(
- MessageManager.getString("label.do_not_display_again"));
- jcb.addActionListener(new ActionListener()
- {
+ final JCheckBox jcb = new JCheckBox(MessageManager.getString("label.do_not_display_again"));
+ jcb.addActionListener(new ActionListener() {
@Override
- public void actionPerformed(ActionEvent e)
- {
+ public void actionPerformed(ActionEvent e) {
// update Cache settings for "don't show this again"
boolean showWarningAgain = !jcb.isSelected();
- Cache.setProperty("CHECKURLLINKS",
- Boolean.valueOf(showWarningAgain).toString());
+ Cache.setProperty("CHECKURLLINKS", Boolean.valueOf(showWarningAgain).toString());
}
});
msgPanel.add(jcb);
JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
- MessageManager
- .getString("label.SEQUENCE_ID_no_longer_used"),
- JvOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.SEQUENCE_ID_no_longer_used"), JvOptionPane.WARNING_MESSAGE);
}
}
});
/**
* Proxy class for JDesktopPane which optionally displays the current memory
- * usage and highlights the desktop area with a red bar if free memory runs
- * low.
+ * usage and highlights the desktop area with a red bar if free memory runs low.
*
* @author AMW
*/
- public class MyDesktopPane extends JDesktopPane implements Runnable
- {
+ public class MyDesktopPane extends JDesktopPane implements Runnable {
private static final float ONE_MB = 1048576f;
boolean showMemoryUsage = false;
java.text.NumberFormat df;
- float maxMemory, allocatedMemory, freeMemory, totalFreeMemory,
- percentUsage;
+ float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, percentUsage;
- public MyDesktopPane(boolean showMemoryUsage)
- {
+ public MyDesktopPane(boolean showMemoryUsage) {
showMemoryUsage(showMemoryUsage);
}
- public void showMemoryUsage(boolean showMemory)
- {
+ public void showMemoryUsage(boolean showMemory) {
this.showMemoryUsage = showMemory;
- if (showMemory)
- {
+ if (showMemory) {
Thread worker = new Thread(this);
worker.start();
}
repaint();
}
- public boolean isShowMemoryUsage()
- {
+ public boolean isShowMemoryUsage() {
return showMemoryUsage;
}
@Override
- public void run()
- {
+ public void run() {
df = java.text.NumberFormat.getNumberInstance();
df.setMaximumFractionDigits(2);
runtime = Runtime.getRuntime();
- while (showMemoryUsage)
- {
- try
- {
+ while (showMemoryUsage) {
+ try {
maxMemory = runtime.maxMemory() / ONE_MB;
allocatedMemory = runtime.totalMemory() / ONE_MB;
freeMemory = runtime.freeMemory() / ONE_MB;
repaint();
// sleep after showing usage
Thread.sleep(3000);
- } catch (Exception ex)
- {
+ } catch (Exception ex) {
ex.printStackTrace();
}
}
}
@Override
- public void paintComponent(Graphics g)
- {
- if (showMemoryUsage && g != null && df != null)
- {
- if (percentUsage < 20)
- {
+ public void paintComponent(Graphics g) {
+ if (showMemoryUsage && g != null && df != null) {
+ if (percentUsage < 20) {
g.setColor(Color.red);
}
FontMetrics fm = g.getFontMetrics();
- if (fm != null)
- {
- g.drawString(MessageManager.formatMessage("label.memory_stats",
- new Object[]
- { df.format(totalFreeMemory), df.format(maxMemory),
- df.format(percentUsage) }),
- 10, getHeight() - fm.getHeight());
+ if (fm != null) {
+ g.drawString(
+ MessageManager.formatMessage("label.memory_stats",
+ new Object[] { df.format(totalFreeMemory), df.format(maxMemory), df.format(percentUsage) }),
+ 10, getHeight() - fm.getHeight());
}
}
*
* @return an array of AlignFrame, or null if none found
*/
- public static AlignFrame[] getAlignFrames()
- {
- if (Jalview.isHeadlessMode())
- {
+ public static AlignFrame[] getAlignFrames() {
+ if (Jalview.isHeadlessMode()) {
// Desktop.desktop is null in headless mode
return new AlignFrame[] { Jalview.currentAlignFrame };
}
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- if (frames == null)
- {
+ if (frames == null) {
return null;
}
List<AlignFrame> avp = new ArrayList<>();
// REVERSE ORDER
- for (int i = frames.length - 1; i > -1; i--)
- {
- if (frames[i] instanceof AlignFrame)
- {
+ for (int i = frames.length - 1; i > -1; i--) {
+ if (frames[i] instanceof AlignFrame) {
avp.add((AlignFrame) frames[i]);
- }
- else if (frames[i] instanceof SplitFrame)
- {
+ } else if (frames[i] instanceof SplitFrame) {
/*
* Also check for a split frame containing an AlignFrame
*/
GSplitFrame sf = (GSplitFrame) frames[i];
- if (sf.getTopFrame() instanceof AlignFrame)
- {
+ if (sf.getTopFrame() instanceof AlignFrame) {
avp.add((AlignFrame) sf.getTopFrame());
}
- if (sf.getBottomFrame() instanceof AlignFrame)
- {
+ if (sf.getBottomFrame() instanceof AlignFrame) {
avp.add((AlignFrame) sf.getBottomFrame());
}
}
}
- if (avp.size() == 0)
- {
+ if (avp.size() == 0) {
return null;
}
AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]);
*
* @return
*/
- public GStructureViewer[] getJmols()
- {
+ public GStructureViewer[] getJmols() {
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- if (frames == null)
- {
+ if (frames == null) {
return null;
}
List<GStructureViewer> avp = new ArrayList<>();
// REVERSE ORDER
- for (int i = frames.length - 1; i > -1; i--)
- {
- if (frames[i] instanceof AppJmol)
- {
+ for (int i = frames.length - 1; i > -1; i--) {
+ if (frames[i] instanceof AppJmol) {
GStructureViewer af = (GStructureViewer) frames[i];
avp.add(af);
}
}
- if (avp.size() == 0)
- {
+ if (avp.size() == 0) {
return null;
}
GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]);
* Add Groovy Support to Jalview
*/
@Override
- public void groovyShell_actionPerformed()
- {
- try
- {
+ public void groovyShell_actionPerformed() {
+ try {
openGroovyConsole();
- } catch (Exception ex)
- {
- Cache.log.error("Groovy Shell Creation failed.", ex);
+ } catch (Exception ex) {
+ jalview.bin.Console.error("Groovy Shell Creation failed.", ex);
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.couldnt_create_groovy_shell"),
- MessageManager.getString("label.groovy_support_failed"),
- JvOptionPane.ERROR_MESSAGE);
+ MessageManager.getString("label.couldnt_create_groovy_shell"),
+ MessageManager.getString("label.groovy_support_failed"), JvOptionPane.ERROR_MESSAGE);
}
}
/**
* Open the Groovy console
*/
- void openGroovyConsole()
- {
- if (groovyConsole == null)
- {
+ void openGroovyConsole() {
+ if (groovyConsole == null) {
groovyConsole = new groovy.ui.Console();
groovyConsole.setVariable("Jalview", this);
groovyConsole.run();
/*
* We allow only one console at a time, so that AlignFrame menu option
- * 'Calculate | Run Groovy script' is unambiguous.
- * Disable 'Groovy Console', and enable 'Run script', when the console is
- * opened, and the reverse when it is closed
+ * 'Calculate | Run Groovy script' is unambiguous. Disable 'Groovy Console', and
+ * enable 'Run script', when the console is opened, and the reverse when it is
+ * closed
*/
Window window = (Window) groovyConsole.getFrame();
- window.addWindowListener(new WindowAdapter()
- {
+ window.addWindowListener(new WindowAdapter() {
@Override
- public void windowClosed(WindowEvent e)
- {
+ public void windowClosed(WindowEvent e) {
/*
* rebind CMD-Q from Groovy Console to Jalview Quit
*/
((Window) groovyConsole.getFrame()).setVisible(true);
/*
- * if we got this far, enable 'Run Groovy' in AlignFrame menus
- * and disable opening a second console
+ * if we got this far, enable 'Run Groovy' in AlignFrame menus and disable
+ * opening a second console
*/
enableExecuteGroovy(true);
}
/**
- * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
- * binding when opened
- */
- protected void addQuitHandler()
- {
- getRootPane()
- .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
- KeyStroke
- .getKeyStroke(KeyEvent.VK_Q,
- jalview.util.ShortcutKeyMaskExWrapper
- .getMenuShortcutKeyMaskEx()),
- "Quit");
- getRootPane().getActionMap().put("Quit", new AbstractAction()
- {
+ * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this binding
+ * when opened
+ */
+ protected void addQuitHandler() {
+ getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
+ KeyStroke.getKeyStroke(KeyEvent.VK_Q, jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
+ "Quit");
+ getRootPane().getActionMap().put("Quit", new AbstractAction() {
@Override
- public void actionPerformed(ActionEvent e)
- {
+ public void actionPerformed(ActionEvent e) {
quit();
}
});
/**
* Enable or disable 'Run Groovy script' in AlignFrame calculate menus
*
- * @param enabled
- * true if Groovy console is open
+ * @param enabled true if Groovy console is open
*/
- public void enableExecuteGroovy(boolean enabled)
- {
+ public void enableExecuteGroovy(boolean enabled) {
/*
- * disable opening a second Groovy console
- * (or re-enable when the console is closed)
+ * disable opening a second Groovy console (or re-enable when the console is
+ * closed)
*/
groovyShell.setEnabled(!enabled);
AlignFrame[] alignFrames = getAlignFrames();
- if (alignFrames != null)
- {
- for (AlignFrame af : alignFrames)
- {
+ if (alignFrames != null) {
+ for (AlignFrame af : alignFrames) {
af.setGroovyEnabled(enabled);
}
}
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
@Override
- public void setProgressBar(String message, long id)
- {
- // Platform.timeCheck("Desktop " + message, Platform.TIME_MARK);
-
- if (progressBars == null)
- {
+ public void setProgressBar(String message, long id) {
+ if (progressBars == null) {
progressBars = new Hashtable<>();
progressBarHandlers = new Hashtable<>();
}
- if (progressBars.get(Long.valueOf(id)) != null)
- {
+ if (progressBars.get(Long.valueOf(id)) != null) {
JPanel panel = progressBars.remove(Long.valueOf(id));
- if (progressBarHandlers.contains(Long.valueOf(id)))
- {
+ if (progressBarHandlers.contains(Long.valueOf(id))) {
progressBarHandlers.remove(Long.valueOf(id));
}
removeProgressPanel(panel);
- }
- else
- {
+ } else {
progressBars.put(Long.valueOf(id), addProgressPanel(message));
}
}
* jalview.gui.IProgressIndicatorHandler)
*/
@Override
- public void registerHandler(final long id,
- final IProgressIndicatorHandler handler)
- {
- if (progressBarHandlers == null
- || !progressBars.containsKey(Long.valueOf(id)))
- {
- throw new Error(MessageManager.getString(
- "error.call_setprogressbar_before_registering_handler"));
+ public void registerHandler(final long id, final IProgressIndicatorHandler handler) {
+ if (progressBarHandlers == null || !progressBars.containsKey(Long.valueOf(id))) {
+ throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
}
progressBarHandlers.put(Long.valueOf(id), handler);
final JPanel progressPanel = progressBars.get(Long.valueOf(id));
- if (handler.canCancel())
- {
- JButton cancel = new JButton(
- MessageManager.getString("action.cancel"));
+ if (handler.canCancel()) {
+ JButton cancel = new JButton(MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
- cancel.addActionListener(new ActionListener()
- {
+ cancel.addActionListener(new ActionListener() {
@Override
- public void actionPerformed(ActionEvent e)
- {
+ public void actionPerformed(ActionEvent e) {
handler.cancelActivity(id);
- us.setProgressBar(MessageManager
- .formatMessage("label.cancelled_params", new Object[]
- { ((JLabel) progressPanel.getComponent(0)).getText() }),
- id);
+ us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
+ new Object[] { ((JLabel) progressPanel.getComponent(0)).getText() }), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
* @return true if any progress bars are still active
*/
@Override
- public boolean operationInProgress()
- {
- if (progressBars != null && progressBars.size() > 0)
- {
+ public boolean operationInProgress() {
+ if (progressBars != null && progressBars.size() > 0) {
return true;
}
return false;
}
/**
- * This will return the first AlignFrame holding the given viewport instance.
- * It will break if there are more than one AlignFrames viewing a particular
- * av.
+ * This will return the first AlignFrame holding the given viewport instance. It
+ * will break if there are more than one AlignFrames viewing a particular av.
*
* @param viewport
* @return alignFrame for viewport
*/
- public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
- {
- if (desktop != null)
- {
- AlignmentPanel[] aps = getAlignmentPanels(
- viewport.getSequenceSetId());
- for (int panel = 0; aps != null && panel < aps.length; panel++)
- {
- if (aps[panel] != null && aps[panel].av == viewport)
- {
+ public static AlignFrame getAlignFrameFor(AlignViewportI viewport) {
+ if (desktop != null) {
+ AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId());
+ for (int panel = 0; aps != null && panel < aps.length; panel++) {
+ if (aps[panel] != null && aps[panel].av == viewport) {
return aps[panel].alignFrame;
}
}
return null;
}
- public VamsasApplication getVamsasApplication()
- {
+ public VamsasApplication getVamsasApplication() {
// TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS
return null;
*
* @return inBatchMode
*/
- public boolean isInBatchMode()
- {
+ public boolean isInBatchMode() {
return inBatchMode;
}
*
* @param inBatchMode
*/
- public void setInBatchMode(boolean inBatchMode)
- {
+ public void setInBatchMode(boolean inBatchMode) {
this.inBatchMode = inBatchMode;
}
- public void startServiceDiscovery()
- {
+ /**
+ * start service discovery and wait till it is done
+ */
+ public void startServiceDiscovery() {
startServiceDiscovery(false);
}
- public void startServiceDiscovery(boolean blocking)
- {
+ /**
+ * start service discovery threads - blocking or non-blocking
+ *
+ * @param blocking
+ */
+ public void startServiceDiscovery(boolean blocking) {
+ startServiceDiscovery(blocking, false);
+ }
+
+ /**
+ * start service discovery threads
+ *
+ * @param blocking - false means call returns
+ * immediately
+ * @param ignore_SHOW_JWS2_SERVICES_preference - when true JABA services are
+ * discovered regardless of user's
+ * JWS2 discovery preference setting
+ */
+ public void startServiceDiscovery(boolean blocking, boolean ignore_SHOW_JWS2_SERVICES_preference) {
boolean alive = true;
Thread t0 = null, t1 = null, t2 = null;
// JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
- if (true)
- {
+ if (true) {
// todo: changesupport handlers need to be transferred
- if (discoverer == null)
- {
+ if (discoverer == null) {
discoverer = new jalview.ws.jws1.Discoverer();
// register PCS handler for desktop.
discoverer.addPropertyChangeListener(changeSupport);
(t0 = new Thread(discoverer)).start();
}
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
- {
- t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .startDiscoverer(changeSupport);
+ if (ignore_SHOW_JWS2_SERVICES_preference || Cache.getDefault("SHOW_JWS2_SERVICES", true)) {
+ t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(changeSupport);
}
Thread t3 = null;
{
// TODO: do rest service discovery
}
- if (blocking)
- {
- while (alive)
- {
- try
- {
+ if (blocking) {
+ while (alive) {
+ try {
Thread.sleep(15);
- } catch (Exception e)
- {
+ } catch (Exception e) {
}
- alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive())
- || (t3 != null && t3.isAlive())
- || (t0 != null && t0.isAlive());
+ alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive()) || (t3 != null && t3.isAlive())
+ || (t0 != null && t0.isAlive());
}
}
}
*
* @param evt
*/
- protected void JalviewServicesChanged(PropertyChangeEvent evt)
- {
- if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
- {
- final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .getErrorMessages();
- if (ermsg != null)
- {
- if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
- {
- if (serviceChangedDialog == null)
- {
+ protected void JalviewServicesChanged(PropertyChangeEvent evt) {
+ if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector) {
+ final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().getErrorMessages();
+ if (ermsg != null) {
+ if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true)) {
+ if (serviceChangedDialog == null) {
// only run if we aren't already displaying one of these.
- addDialogThread(serviceChangedDialog = new Runnable()
- {
+ addDialogThread(serviceChangedDialog = new Runnable() {
@Override
- public void run()
- {
+ public void run() {
/*
* JalviewDialog jd =new JalviewDialog() {
*
- * @Override protected void cancelPressed() { // TODO
- * Auto-generated method stub
+ * @Override protected void cancelPressed() { // TODO Auto-generated method stub
*
- * }@Override protected void okPressed() { // TODO
- * Auto-generated method stub
+ * }@Override protected void okPressed() { // TODO Auto-generated method stub
*
- * }@Override protected void raiseClosed() { // TODO
- * Auto-generated method stub
+ * }@Override protected void raiseClosed() { // TODO Auto-generated method stub
*
- * } }; jd.initDialogFrame(new
- * JLabel("<html><table width=\"450\"><tr><td>" + ermsg +
+ * } }; jd.initDialogFrame(new JLabel("<html><table width=\"450\"><tr><td>" +
+ * ermsg +
* "<br/>It may be that you have invalid JABA URLs in your web service preferences,"
* + " or mis-configured HTTP proxy settings.<br/>" +
- * "Check the <em>Connections</em> and <em>Web services</em> tab of the"
- * +
- * " Tools->Preferences dialog box to change them.</td></tr></table></html>"
- * ), true, true, "Web Service Configuration Problem", 450,
- * 400);
+ * "Check the <em>Connections</em> and <em>Web services</em> tab of the" +
+ * " Tools->Preferences dialog box to change them.</td></tr></table></html>" ),
+ * true, true, "Web Service Configuration Problem", 450, 400);
*
* jd.waitForInput();
*/
JvOptionPane.showConfirmDialog(Desktop.desktop,
- new JLabel("<html><table width=\"450\"><tr><td>"
- + ermsg + "</td></tr></table>"
- + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
- + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
- + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
- + " Tools->Preferences dialog box to change them.</p></html>"),
- "Web Service Configuration Problem",
- JvOptionPane.DEFAULT_OPTION,
- JvOptionPane.ERROR_MESSAGE);
+ new JLabel("<html><table width=\"450\"><tr><td>" + ermsg + "</td></tr></table>"
+ + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
+ + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
+ + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
+ + " Tools->Preferences dialog box to change them.</p></html>"),
+ "Web Service Configuration Problem", JvOptionPane.DEFAULT_OPTION, JvOptionPane.ERROR_MESSAGE);
serviceChangedDialog = null;
}
});
}
- }
- else
- {
- Cache.log.error(
- "Errors reported by JABA discovery service. Check web services preferences.\n"
- + ermsg);
+ } else {
+ jalview.bin.Console.error("Errors reported by JABA discovery service. Check web services preferences.\n" + ermsg);
}
}
}
*
* @param url
*/
- public static void showUrl(final String url)
- {
+ public static void showUrl(final String url) {
showUrl(url, Desktop.instance);
}
* Like showUrl but allows progress handler to be specified
*
* @param url
- * @param progress
- * (null) or object implementing IProgressIndicator
+ * @param progress (null) or object implementing IProgressIndicator
*/
- public static void showUrl(final String url,
- final IProgressIndicator progress)
- {
- new Thread(new Runnable()
- {
+ public static void showUrl(final String url, final IProgressIndicator progress) {
+ new Thread(new Runnable() {
@Override
- public void run()
- {
- try
- {
- if (progress != null)
- {
- progress.setProgressBar(MessageManager
- .formatMessage("status.opening_params", new Object[]
- { url }), this.hashCode());
+ public void run() {
+ try {
+ if (progress != null) {
+ progress.setProgressBar(MessageManager.formatMessage("status.opening_params", new Object[] { url }),
+ this.hashCode());
}
jalview.util.BrowserLauncher.openURL(url);
- } catch (Exception ex)
- {
+ } catch (Exception ex) {
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager
- .getString("label.web_browser_not_found_unix"),
- MessageManager.getString("label.web_browser_not_found"),
- JvOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"), JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
- if (progress != null)
- {
+ if (progress != null) {
progress.setProgressBar(null, this.hashCode());
}
}
public static WsParamSetManager wsparamManager = null;
- public static ParamManager getUserParameterStore()
- {
- if (wsparamManager == null)
- {
+ public static ParamManager getUserParameterStore() {
+ if (wsparamManager == null) {
wsparamManager = new WsParamSetManager();
}
return wsparamManager;
*
* @param e
*/
- public static void hyperlinkUpdate(HyperlinkEvent e)
- {
- if (e.getEventType() == EventType.ACTIVATED)
- {
+ public static void hyperlinkUpdate(HyperlinkEvent e) {
+ if (e.getEventType() == EventType.ACTIVATED) {
String url = null;
- try
- {
+ try {
url = e.getURL().toString();
Desktop.showUrl(url);
- } catch (Exception x)
- {
- if (url != null)
- {
- if (Cache.log != null)
- {
- Cache.log.error("Couldn't handle string " + url + " as a URL.");
- }
- else
- {
- System.err.println(
- "Couldn't handle string " + url + " as a URL.");
- }
+ } catch (Exception x) {
+ if (url != null) {
+ jalview.bin.Console.error("Couldn't handle string " + url + " as a URL.");
}
// ignore any exceptions due to dud links.
}
*
* @param prompter
*/
- public void addDialogThread(final Runnable prompter)
- {
- dialogExecutor.submit(new Runnable()
- {
+ public void addDialogThread(final Runnable prompter) {
+ dialogExecutor.submit(new Runnable() {
@Override
- public void run()
- {
- if (dialogPause)
- {
- try
- {
+ public void run() {
+ if (dialogPause) {
+ try {
block.acquire();
- } catch (InterruptedException x)
- {
+ } catch (InterruptedException x) {
}
}
- if (instance == null)
- {
+ if (instance == null) {
return;
}
- try
- {
+ try {
SwingUtilities.invokeAndWait(prompter);
- } catch (Exception q)
- {
- Cache.log.warn("Unexpected Exception in dialog thread.", q);
+ } catch (Exception q) {
+ jalview.bin.Console.warn("Unexpected Exception in dialog thread.", q);
}
}
});
}
- public void startDialogQueue()
- {
+ public void startDialogQueue() {
// set the flag so we don't pause waiting for another permit and semaphore
// the current task to begin
dialogPause = false;
* </pre>
*/
@Override
- protected void snapShotWindow_actionPerformed(ActionEvent e)
- {
+ protected void snapShotWindow_actionPerformed(ActionEvent e) {
// currently the menu option to do this is not shown
invalidate();
int width = getWidth();
int height = getHeight();
- File of = new File(
- "Jalview_snapshot_" + System.currentTimeMillis() + ".eps");
- ImageWriterI writer = new ImageWriterI()
- {
+ File of = new File("Jalview_snapshot_" + System.currentTimeMillis() + ".eps");
+ ImageWriterI writer = new ImageWriterI() {
@Override
- public void exportImage(Graphics g) throws Exception
- {
+ public void exportImage(Graphics g) throws Exception {
paintAll(g);
- Cache.log.info("Successfully written snapshot to file "
- + of.getAbsolutePath());
+ jalview.bin.Console.info("Successfully written snapshot to file " + of.getAbsolutePath());
}
};
String title = "View of desktop";
- ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS,
- title);
+ ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS, title);
exporter.doExport(of, this, width, height, title);
}
/**
* Explode the views in the given SplitFrame into separate SplitFrame windows.
- * This respects (remembers) any previous 'exploded geometry' i.e. the size
- * and location last time the view was expanded (if any). However it does not
+ * This respects (remembers) any previous 'exploded geometry' i.e. the size and
+ * location last time the view was expanded (if any). However it does not
* remember the split pane divider location - this is set to match the
* 'exploding' frame.
*
* @param sf
*/
- public void explodeViews(SplitFrame sf)
- {
+ public void explodeViews(SplitFrame sf) {
AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame();
AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame();
- List<? extends AlignmentViewPanel> topPanels = oldTopFrame
- .getAlignPanels();
- List<? extends AlignmentViewPanel> bottomPanels = oldBottomFrame
- .getAlignPanels();
+ List<? extends AlignmentViewPanel> topPanels = oldTopFrame.getAlignPanels();
+ List<? extends AlignmentViewPanel> bottomPanels = oldBottomFrame.getAlignPanels();
int viewCount = topPanels.size();
- if (viewCount < 2)
- {
+ if (viewCount < 2) {
return;
}
/*
- * Processing in reverse order works, forwards order leaves the first panels
- * not visible. I don't know why!
+ * Processing in reverse order works, forwards order leaves the first panels not
+ * visible. I don't know why!
*/
- for (int i = viewCount - 1; i >= 0; i--)
- {
+ for (int i = viewCount - 1; i >= 0; i--) {
/*
- * Make new top and bottom frames. These take over the respective
- * AlignmentPanel objects, including their AlignmentViewports, so the
- * cdna/protein relationships between the viewports is carried over to the
- * new split frames.
+ * Make new top and bottom frames. These take over the respective AlignmentPanel
+ * objects, including their AlignmentViewports, so the cdna/protein
+ * relationships between the viewports is carried over to the new split frames.
*
* explodedGeometry holds the (x, y) position of the previously exploded
* SplitFrame, and the (width, height) of the AlignFrame component
AlignFrame newTopFrame = new AlignFrame(topPanel);
newTopFrame.setSize(oldTopFrame.getSize());
newTopFrame.setVisible(true);
- Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
- .getExplodedGeometry();
- if (geometry != null)
- {
+ Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport()).getExplodedGeometry();
+ if (geometry != null) {
newTopFrame.setSize(geometry.getSize());
}
AlignFrame newBottomFrame = new AlignFrame(bottomPanel);
newBottomFrame.setSize(oldBottomFrame.getSize());
newBottomFrame.setVisible(true);
- geometry = ((AlignViewport) bottomPanel.getAlignViewport())
- .getExplodedGeometry();
- if (geometry != null)
- {
+ geometry = ((AlignViewport) bottomPanel.getAlignViewport()).getExplodedGeometry();
+ if (geometry != null) {
newBottomFrame.setSize(geometry.getSize());
}
topPanel.av.setGatherViewsHere(false);
bottomPanel.av.setGatherViewsHere(false);
- JInternalFrame splitFrame = new SplitFrame(newTopFrame,
- newBottomFrame);
- if (geometry != null)
- {
+ JInternalFrame splitFrame = new SplitFrame(newTopFrame, newBottomFrame);
+ if (geometry != null) {
splitFrame.setLocation(geometry.getLocation());
}
Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
}
/*
- * Clear references to the panels (now relocated in the new SplitFrames)
- * before closing the old SplitFrame.
+ * Clear references to the panels (now relocated in the new SplitFrames) before
+ * closing the old SplitFrame.
*/
topPanels.clear();
bottomPanels.clear();
*
* @param source
*/
- public void gatherViews(GSplitFrame source)
- {
+ public void gatherViews(GSplitFrame source) {
/*
* special handling of explodedGeometry for a view within a SplitFrame: - it
* holds the (x, y) position of the enclosing SplitFrame, and the (width,
*/
AlignFrame myTopFrame = (AlignFrame) source.getTopFrame();
AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame();
- myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
- source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
- myBottomFrame.viewport
- .setExplodedGeometry(new Rectangle(source.getX(), source.getY(),
- myBottomFrame.getWidth(), myBottomFrame.getHeight()));
+ myTopFrame.viewport.setExplodedGeometry(
+ new Rectangle(source.getX(), source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
+ myBottomFrame.viewport.setExplodedGeometry(
+ new Rectangle(source.getX(), source.getY(), myBottomFrame.getWidth(), myBottomFrame.getHeight()));
myTopFrame.viewport.setGatherViewsHere(true);
myBottomFrame.viewport.setGatherViewsHere(true);
String topViewId = myTopFrame.viewport.getSequenceSetId();
String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
JInternalFrame[] frames = desktop.getAllFrames();
- for (JInternalFrame frame : frames)
- {
- if (frame instanceof SplitFrame && frame != source)
- {
+ for (JInternalFrame frame : frames) {
+ if (frame instanceof SplitFrame && frame != source) {
SplitFrame sf = (SplitFrame) frame;
AlignFrame topFrame = (AlignFrame) sf.getTopFrame();
AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame();
boolean gatherThis = false;
- for (int a = 0; a < topFrame.alignPanels.size(); a++)
- {
+ for (int a = 0; a < topFrame.alignPanels.size(); a++) {
AlignmentPanel topPanel = topFrame.alignPanels.get(a);
AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a);
if (topViewId.equals(topPanel.av.getSequenceSetId())
- && bottomViewId.equals(bottomPanel.av.getSequenceSetId()))
- {
+ && bottomViewId.equals(bottomPanel.av.getSequenceSetId())) {
gatherThis = true;
topPanel.av.setGatherViewsHere(false);
bottomPanel.av.setGatherViewsHere(false);
- topPanel.av.setExplodedGeometry(
- new Rectangle(sf.getLocation(), topFrame.getSize()));
- bottomPanel.av.setExplodedGeometry(
- new Rectangle(sf.getLocation(), bottomFrame.getSize()));
+ topPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(), topFrame.getSize()));
+ bottomPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(), bottomFrame.getSize()));
myTopFrame.addAlignmentPanel(topPanel, false);
myBottomFrame.addAlignmentPanel(bottomPanel, false);
}
}
- if (gatherThis)
- {
+ if (gatherThis) {
topFrame.getAlignPanels().clear();
bottomFrame.getAlignPanels().clear();
sf.close();
myTopFrame.setDisplayedView(myTopFrame.alignPanel);
}
- public static groovy.ui.Console getGroovyConsole()
- {
+ public static groovy.ui.Console getGroovyConsole() {
return groovyConsole;
}
*
* TODO refactor to desktop utilities class
*
- * @param files
- * - Data source strings extracted from the drop event
- * @param protocols
- * - protocol for each data source extracted from the drop event
- * @param evt
- * - the drop event
- * @param t
- * - the payload from the drop event
+ * @param files - Data source strings extracted from the drop event
+ * @param protocols - protocol for each data source extracted from the drop
+ * event
+ * @param evt - the drop event
+ * @param t - the payload from the drop event
* @throws Exception
*/
- public static void transferFromDropTarget(List<Object> files,
- List<DataSourceType> protocols, DropTargetDropEvent evt,
- Transferable t) throws Exception
- {
-
- // BH 2018 changed List<String> to List<Object> to allow for File from
- // SwingJS
-
- // DataFlavor[] flavors = t.getTransferDataFlavors();
- // for (int i = 0; i < flavors.length; i++) {
- // if (flavors[i].isFlavorJavaFileListType()) {
- // evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- // List<File> list = (List<File>) t.getTransferData(flavors[i]);
- // for (int j = 0; j < list.size(); j++) {
- // File file = (File) list.get(j);
- // byte[] data = getDroppedFileBytes(file);
- // fileName.setText(file.getName() + " - " + data.length + " " +
- // evt.getLocation());
- // JTextArea target = (JTextArea) ((DropTarget)
- // evt.getSource()).getComponent();
- // target.setText(new String(data));
- // }
- // dtde.dropComplete(true);
- // return;
- // }
- //
-
- DataFlavor uriListFlavor = new DataFlavor(
- "text/uri-list;class=java.lang.String"), urlFlavour = null;
- try
- {
- urlFlavour = new DataFlavor(
- "application/x-java-url; class=java.net.URL");
- } catch (ClassNotFoundException cfe)
- {
- Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe);
+ public static void transferFromDropTarget(List<Object> files, List<DataSourceType> protocols, DropTargetDropEvent evt,
+ Transferable t) throws Exception {
+
+ DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String"), urlFlavour = null;
+ try {
+ urlFlavour = new DataFlavor("application/x-java-url; class=java.net.URL");
+ } catch (ClassNotFoundException cfe) {
+ jalview.bin.Console.debug("Couldn't instantiate the URL dataflavor.", cfe);
}
- if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour))
- {
+ if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour)) {
- try
- {
+ try {
java.net.URL url = (URL) t.getTransferData(urlFlavour);
// nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099
// means url may be null.
- if (url != null)
- {
+ if (url != null) {
protocols.add(DataSourceType.URL);
files.add(url.toString());
- Cache.log.debug("Drop handled as URL dataflavor "
- + files.get(files.size() - 1));
+ jalview.bin.Console.debug("Drop handled as URL dataflavor " + files.get(files.size() - 1));
return;
- }
- else
- {
- if (Platform.isAMacAndNotJS())
- {
- System.err.println(
- "Please ignore plist error - occurs due to problem with java 8 on OSX");
+ } else {
+ if (Platform.isAMacAndNotJS()) {
+ System.err.println("Please ignore plist error - occurs due to problem with java 8 on OSX");
}
}
- } catch (Throwable ex)
- {
- Cache.log.debug("URL drop handler failed.", ex);
+ } catch (Throwable ex) {
+ jalview.bin.Console.debug("URL drop handler failed.", ex);
}
}
- if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
- {
+ if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) {
// Works on Windows and MacOSX
- Cache.log.debug("Drop handled as javaFileListFlavor");
- for (Object file : (List) t
- .getTransferData(DataFlavor.javaFileListFlavor))
- {
+ jalview.bin.Console.debug("Drop handled as javaFileListFlavor");
+ for (Object file : (List) t.getTransferData(DataFlavor.javaFileListFlavor)) {
files.add(file);
protocols.add(DataSourceType.FILE);
}
- }
- else
- {
+ } else {
// Unix like behaviour
boolean added = false;
String data = null;
- if (t.isDataFlavorSupported(uriListFlavor))
- {
- Cache.log.debug("Drop handled as uriListFlavor");
+ if (t.isDataFlavorSupported(uriListFlavor)) {
+ jalview.bin.Console.debug("Drop handled as uriListFlavor");
// This is used by Unix drag system
data = (String) t.getTransferData(uriListFlavor);
}
- if (data == null)
- {
+ if (data == null) {
// fallback to text: workaround - on OSX where there's a JVM bug
- Cache.log.debug("standard URIListFlavor failed. Trying text");
+ jalview.bin.Console.debug("standard URIListFlavor failed. Trying text");
// try text fallback
- DataFlavor textDf = new DataFlavor(
- "text/plain;class=java.lang.String");
- if (t.isDataFlavorSupported(textDf))
- {
+ DataFlavor textDf = new DataFlavor("text/plain;class=java.lang.String");
+ if (t.isDataFlavorSupported(textDf)) {
data = (String) t.getTransferData(textDf);
}
- Cache.log.debug("Plain text drop content returned "
- + (data == null ? "Null - failed" : data));
+ jalview.bin.Console.debug("Plain text drop content returned " + (data == null ? "Null - failed" : data));
}
- if (data != null)
- {
- while (protocols.size() < files.size())
- {
- Cache.log.debug("Adding missing FILE protocol for "
- + files.get(protocols.size()));
+ if (data != null) {
+ while (protocols.size() < files.size()) {
+ jalview.bin.Console.debug("Adding missing FILE protocol for " + files.get(protocols.size()));
protocols.add(DataSourceType.FILE);
}
- for (java.util.StringTokenizer st = new java.util.StringTokenizer(
- data, "\r\n"); st.hasMoreTokens();)
- {
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(data, "\r\n"); st.hasMoreTokens();) {
added = true;
String s = st.nextToken();
- if (s.startsWith("#"))
- {
+ if (s.startsWith("#")) {
// the line is a comment (as per the RFC 2483)
continue;
}
java.net.URI uri = new java.net.URI(s);
- if (uri.getScheme().toLowerCase().startsWith("http"))
- {
+ if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http")) {
protocols.add(DataSourceType.URL);
files.add(uri.toString());
- }
- else
- {
+ } else {
// otherwise preserve old behaviour: catch all for file objects
java.io.File file = new java.io.File(uri);
protocols.add(DataSourceType.FILE);
}
}
- if (Cache.log.isDebugEnabled())
- {
- if (data == null || !added)
- {
+ if (jalview.bin.Console.isDebugEnabled()) {
+ if (data == null || !added) {
- if (t.getTransferDataFlavors() != null
- && t.getTransferDataFlavors().length > 0)
- {
- Cache.log.debug(
- "Couldn't resolve drop data. Here are the supported flavors:");
- for (DataFlavor fl : t.getTransferDataFlavors())
- {
- Cache.log.debug(
- "Supported transfer dataflavor: " + fl.toString());
+ if (t.getTransferDataFlavors() != null && t.getTransferDataFlavors().length > 0) {
+ jalview.bin.Console.debug("Couldn't resolve drop data. Here are the supported flavors:");
+ for (DataFlavor fl : t.getTransferDataFlavors()) {
+ jalview.bin.Console.debug("Supported transfer dataflavor: " + fl.toString());
Object df = t.getTransferData(fl);
- if (df != null)
- {
- Cache.log.debug("Retrieves: " + df);
- }
- else
- {
- Cache.log.debug("Retrieved nothing");
+ if (df != null) {
+ jalview.bin.Console.debug("Retrieves: " + df);
+ } else {
+ jalview.bin.Console.debug("Retrieved nothing");
}
}
- }
- else
- {
- Cache.log.debug("Couldn't resolve dataflavor for drop: "
- + t.toString());
+ } else {
+ jalview.bin.Console.debug("Couldn't resolve dataflavor for drop: " + t.toString());
}
}
}
}
- if (Platform.isWindowsAndNotJS())
- {
- Cache.log.debug("Scanning dropped content for Windows Link Files");
+ if (Platform.isWindowsAndNotJS()) {
+ jalview.bin.Console.debug("Scanning dropped content for Windows Link Files");
// resolve any .lnk files in the file drop
- for (int f = 0; f < files.size(); f++)
- {
- String source = files.get(f).toString().toLowerCase();
+ for (int f = 0; f < files.size(); f++) {
+ String source = files.get(f).toString().toLowerCase(Locale.ROOT);
if (protocols.get(f).equals(DataSourceType.FILE)
- && (source.endsWith(".lnk") || source.endsWith(".url")
- || source.endsWith(".site")))
- {
- try
- {
+ && (source.endsWith(".lnk") || source.endsWith(".url") || source.endsWith(".site"))) {
+ try {
Object obj = files.get(f);
- File lf = (obj instanceof File ? (File) obj
- : new File((String) obj));
+ File lf = (obj instanceof File ? (File) obj : new File((String) obj));
// process link file to get a URL
- Cache.log.debug("Found potential link file: " + lf);
+ jalview.bin.Console.debug("Found potential link file: " + lf);
WindowsShortcut wscfile = new WindowsShortcut(lf);
String fullname = wscfile.getRealFilename();
protocols.set(f, FormatAdapter.checkProtocol(fullname));
files.set(f, fullname);
- Cache.log.debug("Parsed real filename " + fullname
- + " to extract protocol: " + protocols.get(f));
- } catch (Exception ex)
- {
- Cache.log.error(
- "Couldn't parse " + files.get(f) + " as a link file.",
- ex);
+ jalview.bin.Console.debug("Parsed real filename " + fullname + " to extract protocol: " + protocols.get(f));
+ } catch (Exception ex) {
+ jalview.bin.Console.error("Couldn't parse " + files.get(f) + " as a link file.", ex);
}
}
}
* depending on the state of the controlling menu item
*/
@Override
- protected void showExperimental_actionPerformed(boolean selected)
- {
+ protected void showExperimental_actionPerformed(boolean selected) {
Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
}
/**
- * Answers a (possibly empty) list of any structure viewer frames (currently
- * for either Jmol or Chimera) which are currently open. This may optionally
- * be restricted to viewers of a specified class, or viewers linked to a
- * specified alignment panel.
+ * Answers a (possibly empty) list of any structure viewer frames (currently for
+ * either Jmol or Chimera) which are currently open. This may optionally be
+ * restricted to viewers of a specified class, or viewers linked to a specified
+ * alignment panel.
*
- * @param apanel
- * if not null, only return viewers linked to this panel
- * @param structureViewerClass
- * if not null, only return viewers of this class
+ * @param apanel if not null, only return viewers linked to this
+ * panel
+ * @param structureViewerClass if not null, only return viewers of this class
* @return
*/
- public List<StructureViewerBase> getStructureViewers(
- AlignmentPanel apanel,
- Class<? extends StructureViewerBase> structureViewerClass)
- {
+ public List<StructureViewerBase> getStructureViewers(AlignmentPanel apanel,
+ Class<? extends StructureViewerBase> structureViewerClass) {
List<StructureViewerBase> result = new ArrayList<>();
JInternalFrame[] frames = Desktop.instance.getAllFrames();
- for (JInternalFrame frame : frames)
- {
- if (frame instanceof StructureViewerBase)
- {
- if (structureViewerClass == null
- || structureViewerClass.isInstance(frame))
- {
- if (apanel == null
- || ((StructureViewerBase) frame).isLinkedWith(apanel))
- {
+ for (JInternalFrame frame : frames) {
+ if (frame instanceof StructureViewerBase) {
+ if (structureViewerClass == null || structureViewerClass.isInstance(frame)) {
+ if (apanel == null || ((StructureViewerBase) frame).isLinkedWith(apanel)) {
result.add((StructureViewerBase) frame);
}
}
private static boolean debugScaleMessageDone = false;
- public static void debugScaleMessage(Graphics g)
- {
- if (debugScaleMessageDone)
- {
+ public static void debugScaleMessage(Graphics g) {
+ if (debugScaleMessageDone) {
return;
}
// output used by tests to check HiDPI scaling settings in action
- try
- {
+ try {
Graphics2D gg = (Graphics2D) g;
- if (gg != null)
- {
+ if (gg != null) {
AffineTransform t = gg.getTransform();
double scaleX = t.getScaleX();
double scaleY = t.getScaleY();
- Cache.debug(debugScaleMessage + scaleX + " (X)");
- Cache.debug(debugScaleMessage + scaleY + " (Y)");
+ jalview.bin.Console.debug(debugScaleMessage + scaleX + " (X)");
+ jalview.bin.Console.debug(debugScaleMessage + scaleY + " (Y)");
debugScaleMessageDone = true;
+ } else {
+ jalview.bin.Console.debug("Desktop graphics null");
}
- else
- {
- Cache.debug("Desktop graphics null");
- }
- } catch (Exception e)
- {
- Cache.debug(Cache.getStackTraceString(e));
+ } catch (Exception e) {
+ jalview.bin.Console.debug(Cache.getStackTraceString(e));
}
}
}
*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
JPopupMenu men = new JPopupMenu(MessageManager
.formatMessage("label.settings_for_param", new String[]
{ type }));
- final FeatureColourI featureColour = (FeatureColourI) typeCol;
-
- /*
- * menu option to select (or deselect) variable colour
- */
- final JCheckBoxMenuItem variableColourCB = new JCheckBoxMenuItem(
- MessageManager.getString("label.variable_colour"));
- variableColourCB.setSelected(!featureColour.isSimpleColour());
- men.add(variableColourCB);
-
- /*
- * checkbox action listener doubles up as listener to OK
- * from the variable colour / filters dialog
- */
- variableColourCB.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (e.getSource() == variableColourCB)
- {
- // BH 2018 for JavaScript because this is a checkbox
- men.setVisible(true);
- men.setVisible(false);
- if (featureColour.isSimpleColour())
- {
- /*
- * toggle simple colour to variable colour - show dialog
- */
- FeatureTypeSettings fc = new FeatureTypeSettings(fr, type);
- fc.addActionListener(this);
- }
- else
- {
- /*
- * toggle variable to simple colour - show colour chooser
- */
- String title = MessageManager
- .formatMessage("label.select_colour_for", type);
- ColourChooserListener listener = new ColourChooserListener()
- {
- @Override
- public void colourSelected(Color c)
- {
- table.setValueAt(new FeatureColour(c), rowSelected,
- COLOUR_COLUMN);
- table.validate();
- updateFeatureRenderer(
- ((FeatureTableModel) table.getModel()).getData(),
- false);
- }
- };
- JalviewColourChooser.showColourChooser(FeatureSettings.this,
- title, featureColour.getMaxColour(), listener);
- }
- }
- else
- {
- if (e.getSource() instanceof FeatureTypeSettings)
- {
- /*
- * update after OK in feature colour dialog; the updated
- * colour will have already been set in the FeatureRenderer
- */
- FeatureColourI fci = fr.getFeatureColours().get(type);
- table.setValueAt(fci, rowSelected, COLOUR_COLUMN);
- // BH 2018 setting a table value does not invalidate it.
- // System.out.println("FeatureSettings is valied" +
- // table.validate();
- }
- }
- }
- });
-
- men.addSeparator();
JMenuItem scr = new JMenuItem(
MessageManager.getString("label.sort_by_score"));
String text = MessageManager.formatMessage("label.show_linked_features",
nucleotide
? MessageManager.getString("label.protein")
- .toLowerCase()
+ .toLowerCase(Locale.ROOT)
: "CDS");
showComplement = new JCheckBox(text);
showComplement.addActionListener(new ActionListener()
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.GraphLine;
import jalview.datamodel.features.FeatureAttributes;
import jalview.datamodel.features.FeatureAttributes.Datatype;
attName = (String) attCombo.getSelectedItem();
} catch (Exception e)
{
- Cache.log.error("Problem casting Combo box entry to String");
+ Console.error("Problem casting Combo box entry to String");
attName = attCombo.getSelectedItem().toString();
}
Condition cond = (Condition) condCombo.getSelectedItem();
*/
package jalview.gui;
-import jalview.api.AlignViewportI;
-import jalview.api.FinderI;
-import jalview.datamodel.SearchResultMatchI;
-import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GFinder;
-import jalview.util.MessageManager;
+import java.util.Locale;
import java.awt.Dimension;
-import java.awt.Graphics;
import java.awt.event.ActionEvent;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
import java.awt.event.KeyEvent;
import java.util.ArrayList;
import java.util.HashMap;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
+import jalview.api.AlignViewportI;
+import jalview.api.FinderI;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GFinder;
+import jalview.util.MessageManager;
+
/**
* Performs the menu option for searching the alignment, for the next or all
* matches. If matches are found, they are highlighted, and the user has the
private SearchResultsI searchResults;
+ /*
+ * true if Finder always acts on the same alignment,
+ * false if it acts on the alignment with focus
+ */
+ private boolean focusFixed;
+
/**
* Constructor given an associated alignment panel. Constructs and displays an
- * internal frame where the user can enter a search string.
+ * internal frame where the user can enter a search string. The Finder may
+ * have 'fixed focus' (always act the panel for which it is constructed), or
+ * not (acts on the alignment that has focus). An optional 'scope' may be
+ * added to be shown in the title of the Finder frame.
*
* @param alignPanel
+ * @param fixedFocus
+ * @param scope
*/
- public Finder(AlignmentPanel alignPanel)
+ public Finder(AlignmentPanel alignPanel, boolean fixedFocus, String scope)
{
av = alignPanel.getAlignViewport();
ap = alignPanel;
+ focusFixed = fixedFocus;
finders = new HashMap<>();
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- frame.addInternalFrameListener(
- new InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosing(InternalFrameEvent e)
- {
- closeAction();
- }
- });
+ frame.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosing(InternalFrameEvent e)
+ {
+ closeAction();
+ }
+ });
+ frame.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ /*
+ * ensure 'ignore hidden columns' is only enabled
+ * if the alignment with focus has hidden columns
+ */
+ getFocusedViewport();
+ }
+ });
+
addEscapeHandler();
- Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
- true, MY_WIDTH, MY_HEIGHT, true, true);
+ String title = MessageManager.getString("label.find");
+ if (scope != null)
+ {
+ title += " " + scope;
+ }
+ Desktop.addInternalFrame(frame, title, MY_WIDTH, MY_HEIGHT);
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
searchBox.getComponent().requestFocus();
}
/**
* if !focusfixed and not in a desktop environment, checks that av and ap are
* valid. Otherwise, gets the topmost alignment window and sets av and ap
- * accordingly. Also sets the 'ignore hidden' checkbox disabled if the viewport
- * has no hidden columns.
+ * accordingly. Also sets the 'ignore hidden' checkbox disabled if the
+ * viewport has no hidden columns.
*
* @return false if no alignment window was found
*/
boolean getFocusedViewport()
{
- if (Desktop.desktop == null)
+ if (focusFixed || Desktop.desktop == null)
{
if (ap != null && av != null)
{
+ ignoreHidden.setEnabled(av.hasHiddenColumns());
return true;
}
// we aren't in a desktop environment, so give up now.
if (doFindAll)
{
// then we report the matches that were found
- String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
- : "";
+ StringBuilder message = new StringBuilder();
+ if (idMatch.size() > 0)
+ {
+ message.append(idMatch.size()).append(" IDs");
+ }
if (searchResults != null)
{
if (idMatch.size() > 0 && searchResults.getCount() > 0)
{
- message += " and ";
+ message.append(" ").append(
+ MessageManager.getString("label.and").toLowerCase(Locale.ROOT))
+ .append(" ");
}
- message += searchResults.getCount()
- + " subsequence matches found.";
+ message.append(MessageManager.formatMessage(
+ "label.subsequence_matches_found",
+ searchResults.getCount()));
}
- JvOptionPane.showInternalMessageDialog(this, message, null,
- JvOptionPane.PLAIN_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(this, message.toString(),
+ null, JvOptionPane.INFORMATION_MESSAGE);
}
}
}
ap.alignFrame.requestFocus();
}
}
-
- @Override
- protected void paintComponent(Graphics g)
- {
- /*
- * enable 'hidden regions' option only if
- * 'top' viewport has hidden columns
- */
- getFocusedViewport();
- super.paintComponent(g);
- }
}
*/
package jalview.gui;
+import java.util.Locale;
+
import jalview.util.MessageManager;
import jalview.ws.seqfetcher.DbSourceProxy;
if (child.getUserObject() instanceof DbSourceProxy)
{
names[i] = ((DbSourceProxy) child.getUserObject()).getDbName()
- .toLowerCase();
+ .toLowerCase(Locale.ROOT);
}
else
{
- names[i] = ((String) child.getUserObject()).toLowerCase();
+ names[i] = ((String) child.getUserObject()).toLowerCase(Locale.ROOT);
sortTreeNodes(child);
}
}
*/
package jalview.gui;
+import jalview.bin.Console;
import jalview.util.MessageManager;
import java.awt.Component;
desktop = instance;
if (oomex != null)
{
- if (jalview.bin.Cache.log != null)
- {
- jalview.bin.Cache.log.error("Out of Memory when " + action,
+ Console.error("Out of Memory when " + action,
oomex);
- }
- else
- {
- System.err.println("Out of Memory when " + action);
- oomex.printStackTrace();
- }
}
javax.swing.SwingUtilities.invokeLater(this);
System.gc();
*/
package jalview.gui;
-import jalview.util.MessageManager;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.OptionI;
-import jalview.ws.params.ParameterI;
-import jalview.ws.params.ValueConstrainI;
-import jalview.ws.params.ValueConstrainI.ValueType;
-
import java.awt.BorderLayout;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.awt.event.MouseEvent;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.ValueConstrainI;
+import jalview.ws.params.ValueConstrainI.ValueType;
import net.miginfocom.swing.MigLayout;
/**
JLabel optlabel = new JLabel();
- JComboBox val = new JComboBox();
+ JComboBox<String> val = new JComboBox<>();
public OptionBox(OptionI opt)
{
}
}
add(enabled, BorderLayout.NORTH);
- for (Object str : opt.getPossibleValues())
+ for (String str : opt.getPossibleValues())
{
val.addItem(str);
}
{
if (choice)
{
- choicebox = new JComboBox();
+ choicebox = new JComboBox<>();
choicebox.addActionListener(this);
controlPanel.add(choicebox, BorderLayout.CENTER);
}
{
}
});
+ valueField.addFocusListener(new FocusAdapter() {
+
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ actionPerformed(null);
+ }
+
+ });
valueField.setPreferredSize(new Dimension(60, 25));
+ valueField.setText(parm.getValue());
slider = makeSlider(parm.getValidValue());
+ updateSliderFromValueField();
slider.addChangeListener(this);
controlPanel.add(slider, BorderLayout.WEST);
import jalview.api.AlignViewportI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
// JAL-2647 disabled after load from project (until save to project done)
if (getPcaModel().getInputData() == null)
{
- Cache.log.info(
+ Console.info(
"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.event.ActionEvent;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
urlLink = new UrlLink(link);
} catch (Exception foo)
{
- Cache.log.error("Exception for URLLink '" + link + "'", foo);
+ Console.error("Exception for URLLink '" + link + "'", foo);
continue;
}
if (!urlLink.isValid())
{
- Cache.log.error(urlLink.getInvalidMessage());
+ Console.error(urlLink.getInvalidMessage());
continue;
}
/*
* show local rather than linked feature coordinates
*/
- int[] beginRange = mf.getMappedPositions(start, start);
- start = beginRange[0];
- int[] endRange = mf.getMappedPositions(end, end);
- end = endRange[endRange.length - 1];
+ int[] localRange = mf.getMappedPositions(start, end);
+ if (localRange == null)
+ {
+ // e.g. variant extending to stop codon so not mappable
+ return;
+ }
+ start = localRange[0];
+ end = localRange[localRange.length - 1];
}
StringBuilder desc = new StringBuilder();
desc.append(sf.getType()).append(" ").append(String.valueOf(start));
for (int d = 0; d < nd; d++)
{
DBRefEntry e = dbr.get(d);
- String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+ String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT);
Object[] sarray = commonDbrefs.get(src);
if (sarray == null)
{
urlLink = new GroupUrlLink(link);
} catch (Exception foo)
{
- Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
+ Console.error("Exception for GroupURLLink '" + link + "'", foo);
continue;
}
if (!urlLink.isValid())
{
- Cache.log.error(urlLink.getInvalidMessage());
+ Console.error(urlLink.getInvalidMessage());
continue;
}
final String label = urlLink.getLabel();
boolean usingNames = false;
// Now see which parts of the group apply for this URL
String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
- Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
+ Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT));
String[] seqstr, ids; // input to makeUrl
if (idset != null)
{
import java.io.File;
import java.util.ArrayList;
import java.util.List;
+import java.util.concurrent.CompletableFuture;
import javax.help.HelpSetException;
import javax.swing.JComboBox;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.bin.MemorySetting;
import jalview.ext.pymol.PymolManager;
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
/**
* Holds name and link separated with | character. Sequence IDS and Sequences
- * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
- * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
- * for first and second token specified after a pipe character at end |,|.
- * (TODO: proper escape for using | to separate ids or sequences
+ * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and $SEQUENCES$
+ * or $SEQUENCES=/.possible | chars ./=$ and separation character for first and
+ * second token specified after a pipe character at end |,|. (TODO: proper
+ * escape for using | to separate ids or sequences
*/
public static List<String> groupURLLinks;
public static void openPreferences()
{
- openPreferences(0, null);
+ openPreferences(null, null);
}
- public static void openPreferences(int selectTab, String message)
+ public static void openPreferences(TabRef selectTab, String message)
{
Preferences p = getInstance();
- p.selectTab(selectTab);
- p.setMessage(message);
+ if (selectTab != null)
+ p.selectTab(selectTab, message);
p.frame.show();
p.frame.moveToFront();
p.frame.grabFocus();
}
+ public void selectTab(TabRef selectTab, String message)
+ {
+ this.selectTab(selectTab);
+ if (message != null)
+ this.setMessage(message);
+ this.frame.show();
+ }
+
/**
* Creates a new Preferences object.
*/
startupCheckbox
.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org", "http://www.jalview.org")
- + "/examples/exampleFile_2_3.jar"));
+ Cache.getDefault("www.jalview.org", "https://www.jalview.org")
+ + "/examples/exampleFile_2_7.jvp"));
/*
* Set Colours tab defaults
/*
* Set Structure tab defaults
*/
- final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
+ final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, true);
structFromPdb.setSelected(structSelected);
- useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
- useRnaView.setEnabled(structSelected);
- addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
+ addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, true));
addSecondaryStructure.setEnabled(structSelected);
- addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
+ addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true));
addTempFactor.setEnabled(structSelected);
/*
}
} catch (IllegalArgumentException e)
{
- Cache.log.error("Unknown structure viewer type: " + viewerType
+ Console.error("Unknown structure viewer type: " + viewerType
+ ", defaulting to Jmol");
type = ViewerType.JMOL;
}
{
if (validateViewerPath())
{
- Cache.setProperty(
- structViewer.getSelectedItem().equals(
- ViewerType.CHIMERAX.name()) ? CHIMERAX_PATH
- : CHIMERA_PATH,
- structureViewerPath.getText());
+ String path = structureViewerPath.getText();
+ try {
+ ViewerType type = ViewerType.valueOf(viewerType);
+ switch (type)
+ {
+ case JMOL:
+ break;
+ case CHIMERA:
+ Cache.setProperty(CHIMERA_PATH, path);
+ break;
+ case CHIMERAX:
+ Cache.setProperty(CHIMERAX_PATH, path);
+ break;
+ case PYMOL:
+ Cache.setProperty(PYMOL_PATH, path);
+ break;
+ }
+ } catch (IllegalArgumentException x)
+ {
+ Console.error("Failed to set path - unknown viewer type",x);
+ }
}
}
});
proxyType.setSelected(customProxy.getModel(), true);
break;
default:
- Cache.log.warn(
+ Console.warn(
"Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
+ proxyTypeString);
}
* Set Backups tab defaults
*/
loadLastSavedBackupsOptions();
+
+ /*
+ * Set Startup tab defaults
+ */
+
}
/**
Boolean.toString(addTempFactor.isSelected()));
Cache.applicationProperties.setProperty(ADD_SS_ANN,
Boolean.toString(addSecondaryStructure.isSelected()));
- Cache.applicationProperties.setProperty(USE_RNAVIEW,
- Boolean.toString(useRnaView.isSelected()));
Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
Boolean.toString(structFromPdb.isSelected()));
String viewer = structViewer.getSelectedItem().toString();
Cache.applicationProperties.setProperty(
BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
+ /*
+ * Save Memory Settings
+ */
+ Cache.applicationProperties.setProperty(
+ MemorySetting.CUSTOMISED_SETTINGS,
+ Boolean.toString(customiseMemorySetting.isSelected()));
+ Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMPC,
+ Integer.toString(jvmMemoryPercentSlider.getValue()));
+ Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMMAX,
+ jvmMemoryMaxTextField.getText());
+
+ /*
+ * save and close Preferences
+ */
+
Cache.saveProperties();
Desktop.instance.doConfigureStructurePrefs();
try
}
/**
- * Do any necessary validation before saving settings. Return focus to the
- * first tab which fails validation.
+ * Do any necessary validation before saving settings. Return focus to the first
+ * tab which fails validation.
*
* @return
*/
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
@Override
public void cancel_actionPerformed(ActionEvent e)
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
@Override
public void annotations_actionPerformed(ActionEvent e)
if (index == -1)
{
// button no longer enabled if row is not selected
- Cache.log.debug("Edit with no row selected in linkUrlTable");
+ Console.debug("Edit with no row selected in linkUrlTable");
return;
}
if (index == -1)
{
// button no longer enabled if row is not selected
- Cache.log.debug("Delete with no row selected in linkUrlTable");
+ Console.debug("Delete with no row selected in linkUrlTable");
return;
}
else
}
/**
- * Returns true if structure viewer path is to a valid executable, else shows
- * an error dialog. Does nothing if the path is empty, as is the case for Jmol
+ * Returns true if structure viewer path is to a valid executable, else shows an
+ * error dialog. Does nothing if the path is empty, as is the case for Jmol
* (built in to Jalview) or when Jalview is left to try default paths.
*/
private boolean validateViewerPath()
}
/**
- * If Chimera or ChimeraX or Pymol is selected, check it can be found on
- * default or user-specified path, if not show a warning/help dialog
+ * If Chimera or ChimeraX or Pymol is selected, check it can be found on default
+ * or user-specified path, if not show a warning/help dialog
*/
@Override
protected void structureViewer_actionPerformed(String selectedItem)
MessageManager.getString("label.viewer_missing")),
"", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
null, options, options[0]);
+
if (showHelp == JvOptionPane.NO_OPTION)
{
+ this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
try
{
Help.showHelpWindow(HelpId.StructureViewer);
e.printStackTrace();
}
}
+ else if (showHelp == JvOptionPane.OK_OPTION)
+ {
+ this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
+ CompletableFuture<Void> cf = CompletableFuture.runAsync(() -> {
+ try
+ {
+ for (int i = 0; i < 3; i++)
+ {
+ structureViewerPath.setBackground(Color.PINK);
+ Thread.sleep(500);
+ structureViewerPath.setBackground(Color.WHITE);
+ Thread.sleep(500);
+ }
+ } catch (InterruptedException e)
+ {
+ }
+ });
+ }
}
}
package jalview.gui;
import jalview.bin.Cache;
+import jalview.bin.Console;
import java.awt.Component;
* @param desktop
* - where the dialog box will be shown
* @param property
- * - boolean property in jalview.bin.Cache
+ * - boolean property in Cache
* @param dialogTitle
* - title of prompt box
* @param dialogText
return;
}
// First - check to see if wee have an old questionnaire/response id pair.
- String lastq = jalview.bin.Cache.getProperty(property);
+ String lastq = Cache.getProperty(property);
if (lastq == null)
{
raiseDialog();
- Cache.log.debug("Got user response.");
+ Console.debug("Got user response.");
}
- lastq = jalview.bin.Cache.getProperty(property);
+ lastq = Cache.getProperty(property);
String extype = "";
Exception e = null;
if (lastq == null)
// report any exceptions
if (e != null)
{
- Cache.log.warn("Unexpected exception when executing the " + extype
+ Console.warn("Unexpected exception when executing the " + extype
+ " runnable for property " + property, e);
}
}
*/
private void raiseDialog()
{
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Prompting user for " + dialogTitle
+ Console.debug("Prompting user for " + dialogTitle
+ " for Cache property " + property);
}
try
JvOptionPane.QUESTION_MESSAGE);
// and finish parsing the result
- jalview.bin.Cache.log.debug("Got response : " + reply);
+ Console.debug("Got response : " + reply);
if (reply == JvOptionPane.YES_OPTION)
{
- jalview.bin.Cache.setProperty(property, "true");
+ Cache.setProperty(property, "true");
}
else if (reply == JvOptionPane.NO_OPTION)
{
if (removeifunset)
{
- jalview.bin.Cache.removeProperty(property);
+ Cache.removeProperty(property);
}
else
{
- jalview.bin.Cache.setProperty(property, "false");
+ Cache.setProperty(property, "false");
}
}
else
{
- jalview.bin.Cache.log.debug("User cancelled setting " + property);
+ Console.debug("User cancelled setting " + property);
return;
}
// verify the property is set for debugging
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("User set property to "
- + jalview.bin.Cache.getProperty(property));
+ Console.debug("User set property to "
+ + Cache.getProperty(property));
}
} catch (Exception e)
{
- jalview.bin.Cache.log.warn(
+ Console.warn(
"Unexpected exception when prompting user for yes/no setting for property "
+ property,
e);
import java.util.Map;
import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.pymol.PymolCommands;
public void highlightAtoms(List<AtomSpec> atoms)
{
/*
- * https://pymolwiki.org/index.php/Label#examples
+ * https://pymolwiki.org/index.php/indicate#examples
*/
StringBuilder sb = new StringBuilder();
for (AtomSpec atom : atoms)
{
// todo promote to StructureCommandsI.showLabel()
- // todo handle CA|P correctly
String modelId = getModelIdForFile(atom.getPdbFile());
- sb.append(String.format(" %s//%s/%d/CA", modelId,
+ sb.append(String.format(" %s//%s/%d/*", modelId,
atom.getChain(),
atom.getPdbResNum()));
}
{
return;
}
- StructureCommandI command = new StructureCommand("label", labelSpec, LABEL_FORMAT);
+ StructureCommandI command = new StructureCommand("indicate", labelSpec);
executeCommand(command, false);
- /*
- * and remove the label(s) previously shown
- */
- if (lastLabelSpec != null)
- {
- command = new StructureCommand("label", lastLabelSpec, "");
- executeCommand(command, false);
- }
-
lastLabelSpec = labelSpec;
}
}
else
{
- Cache.log.error("Failed to launch PyMOL!");
+ Console.error("Failed to launch PyMOL!");
}
return pymol != null;
}
* a second parameter sets the pdbid as the loaded PyMOL object name
*/
String pdbId = pe.getId();
+ try {
+ String safePDBId = java.net.URLEncoder.encode(pdbId,"UTF-8");
+ pdbId = safePDBId.replace('%', '_');
+ pdbId = pdbId.replace("-", "__");
+ char fc = pdbId.charAt(0);
+ // put an 's' before any numerics
+ if (fc>='0' && fc<='9')
+ {
+ pdbId = 's'+pdbId;
+ }
+// pdbId.replace('-', 0)
+ } catch (Exception x)
+ {
+ Console.error("Unxpected encoding exception for '"+pdbId+"'",x);
+ }
cmd.addParameter(pdbId);
executeCommand(cmd, false);
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
initPymol();
} catch (Exception ex)
{
- Cache.log.error("Couldn't open PyMOL viewer!", ex);
+ Console.error("Couldn't open PyMOL viewer!", ex);
}
}
int num = -1;
binding.stashFoundChains(pdb, pe.getFile());
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Couldn't open " + pe.getFile() + " in Chimera viewer!",
ex);
} finally
{
- // Cache.log.debug("File locations are " + files);
+ // Cache.debug("File locations are " + files);
}
}
}
boolean opened = binding.openSession(pymolSessionFile);
if (!opened)
{
- Cache.log.error(
+ Console.error(
"An error occurred opening PyMOL session file "
+ pymolSessionFile);
}
{
return "PyMOL";
}
-
+ JMenuItem writeFeatures = null;
@Override
protected void initMenus()
{
savemenu.setVisible(false); // not yet implemented
viewMenu.add(fitToWindow);
- JMenuItem writeFeatures = new JMenuItem(
+ writeFeatures = new JMenuItem(
MessageManager.getString("label.create_viewer_attributes"));
writeFeatures.setToolTipText(MessageManager
.getString("label.create_viewer_attributes_tip"));
});
viewerActionMenu.add(writeFeatures);
}
+
+ @Override
+ protected void buildActionMenu()
+ {
+ super.buildActionMenu();
+ viewerActionMenu.add(writeFeatures);
+ }
protected void sendFeaturesToPymol()
{
int count = binding.sendFeaturesToViewer(getAlignmentPanel());
statusBar.setText(
- MessageManager.formatMessage("label.attributes_set", count));
+ MessageManager.formatMessage("label.attributes_set", count, getViewerName()));
}
}
}
else if (evt.getKeyChar() == 's')
{
- // Cache.log.warn("DEBUG: Rectangle selection");
+ // Cache.warn("DEBUG: Rectangle selection");
// todo not yet enabled as rectx2, recty2 are always -1
// need to set them in mouseDragged; JAL-1124
// if ((rectx2 != -1) && (recty2 != -1))
import javax.swing.ToolTipManager;
import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
void moveCursor(int dx, int dy)
{
- seqCanvas.cursorX += dx;
- seqCanvas.cursorY += dy;
-
+ moveCursor(dx, dy,false);
+ }
+ void moveCursor(int dx, int dy, boolean nextWord)
+ {
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
+ if (nextWord)
{
- int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
-
- if (!hidden.isVisible(seqCanvas.cursorX))
- {
- int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
- int[] region = hidden.getRegionWithEdgeAtRes(visx);
-
- if (region != null) // just in case
+ int maxHeight=av.getAlignment().getHeight();
+ SequenceI seqAtRow = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+ // look for next gap or residue
+ boolean isGap = Comparison.isGap(seqAtRow.getCharAt(seqCanvas.cursorX));
+ int p = seqCanvas.cursorX,lastP,r=seqCanvas.cursorY,lastR;
+ do
+ {
+ lastP = p;
+ lastR = r;
+ if (dy != 0)
{
- if (dx == 1)
+ r += dy;
+ if (r < 0)
{
- // moving right
- seqCanvas.cursorX = region[1] + 1;
+ r = 0;
}
- else if (dx == -1)
+ if (r >= maxHeight)
{
- // moving left
- seqCanvas.cursorX = region[0] - 1;
+ r = maxHeight - 1;
}
+ seqAtRow = av.getAlignment().getSequenceAt(r);
}
- seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
- }
+ p = nextVisible(hidden, maxWidth, p, dx);
+ } while ((dx != 0 ? p != lastP : r != lastR)
+ && isGap == Comparison.isGap(seqAtRow.getCharAt(p)));
+ seqCanvas.cursorX=p;
+ seqCanvas.cursorY=r;
+ } else {
+ int maxWidth = av.getAlignment().getWidth();
+ seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX, dx);
+ seqCanvas.cursorY += dy;
+ }
+ scrollToVisible(false);
+ }
- if (seqCanvas.cursorX >= maxWidth
- || !hidden.isVisible(seqCanvas.cursorX))
+ private int nextVisible(HiddenColumns hidden,int maxWidth, int original, int dx)
+ {
+ int newCursorX=original+dx;
+ if (av.hasHiddenColumns() && !hidden.isVisible(newCursorX))
+ {
+ int visx = hidden.absoluteToVisibleColumn(newCursorX - dx);
+ int[] region = hidden.getRegionWithEdgeAtRes(visx);
+
+ if (region != null) // just in case
{
- seqCanvas.cursorX = original;
+ if (dx == 1)
+ {
+ // moving right
+ newCursorX = region[1] + 1;
+ }
+ else if (dx == -1)
+ {
+ // moving left
+ newCursorX = region[0] - 1;
+ }
}
}
-
- scrollToVisible(false);
+ newCursorX = (newCursorX < 0) ? 0 : newCursorX;
+ if (newCursorX >= maxWidth
+ || !hidden.isVisible(newCursorX))
+ {
+ newCursorX = original;
+ }
+ return newCursorX;
}
-
/**
* Scroll to make the cursor visible in the viewport.
*
{
if (av.getAlignment() == null)
{
- Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
+ Console.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
+ " ViewId=" + av.getViewId()
+ " 's alignment is NULL! returning immediately.");
return;
*/
package jalview.gui;
-import jalview.api.FeatureSettingsModelI;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.SequenceI;
-import jalview.fts.core.GFTSPanel;
-import jalview.fts.service.pdb.PDBFTSPanel;
-import jalview.fts.service.uniprot.UniprotFTSPanel;
-import jalview.io.FileFormatI;
-import jalview.io.gff.SequenceOntologyI;
-import jalview.util.DBRefUtils;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
import java.awt.BorderLayout;
import java.awt.Font;
import java.awt.event.ActionEvent;
import javax.swing.JTextArea;
import javax.swing.SwingConstants;
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
+import jalview.fts.core.GFTSPanel;
+import jalview.fts.service.pdb.PDBFTSPanel;
+import jalview.fts.service.threedbeacons.TDBeaconsFTSPanel;
+import jalview.fts.service.uniprot.UniprotFTSPanel;
+import jalview.io.FileFormatI;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
/**
* A panel where the use may choose a database source, and enter one or more
* accessions, to retrieve entries from the database.
*/
public class SequenceFetcher extends JPanel implements Runnable
{
+ private class StringPair
+ {
+ private String key;
+
+ private String display;
+
+ public StringPair(String s1, String s2)
+ {
+ key = s1;
+ display = s2;
+ }
+
+ public StringPair(String s)
+ {
+ this(s, s);
+ }
+
+ public String getKey()
+ {
+ return key;
+ }
+
+ public String getDisplay()
+ {
+ return display;
+ }
+
+ @Override
+ public String toString()
+ {
+ return display;
+ }
+
+ public boolean equals(StringPair other)
+ {
+ return other.key == this.key;
+ }
+ }
+
private static jalview.ws.SequenceFetcher sfetch = null;
JLabel exampleAccession;
- JComboBox<String> database;
+ JComboBox<StringPair> database;
JCheckBox replacePunctuation;
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, getFrameTitle(), true, 400,
- Platform.isAMacAndNotJS() ? 240 : 180);
+ Desktop.addInternalFrame(frame, getFrameTitle(), true, 400,
+ Platform.isAMacAndNotJS() ? 240 : 180);
}
private String getFrameTitle()
database = new JComboBox<>();
database.setFont(JvSwingUtils.getLabelFont());
- database.setPrototypeDisplayValue("ENSEMBLGENOMES ");
+ StringPair instructionItem = new StringPair(
+ MessageManager.getString("action.select_ddbb"));
+ database.setPrototypeDisplayValue(instructionItem);
String[] sources = new jalview.ws.SequenceFetcher().getSupportedDb();
Arrays.sort(sources, String.CASE_INSENSITIVE_ORDER);
- database.addItem(MessageManager.getString("action.select_ddbb"));
+ database.addItem(instructionItem);
for (String source : sources)
{
- database.addItem(source);
+ List<DbSourceProxy> slist = sfetch.getSourceProxy(source);
+ if (slist.size() == 1 && slist.get(0) != null)
+ {
+ database.addItem(new StringPair(source, slist.get(0).getDbName()));
+ }
+ else
+ {
+ database.addItem(new StringPair(source));
+ }
}
- database.setSelectedItem(selectedDb);
+ setDatabaseSelectedItem(selectedDb);
if (database.getSelectedIndex() == -1)
{
database.setSelectedIndex(0);
@Override
public void actionPerformed(ActionEvent e)
{
- String currentSelection = (String) database.getSelectedItem();
+ String currentSelection = ((StringPair) database.getSelectedItem())
+ .getKey();
updateExampleQuery(currentSelection);
if ("pdb".equalsIgnoreCase(currentSelection))
frame.dispose();
new UniprotFTSPanel(SequenceFetcher.this);
}
+ else if ("3d-beacons".equalsIgnoreCase(currentSelection))
+ {
+ frame.dispose();
+ new TDBeaconsFTSPanel(SequenceFetcher.this);
+ }
else
{
otherSourceAction();
this.add(databasePanel, BorderLayout.NORTH);
}
+ private void setDatabaseSelectedItem(String db)
+ {
+ for (int i = 0; i < database.getItemCount(); i++)
+ {
+ StringPair sp = database.getItemAt(i);
+ if (sp != null && db != null && db.equals(sp.getKey()))
+ {
+ database.setSelectedIndex(i);
+ return;
+ }
+ }
+ }
+
/**
* Answers a semi-colon-delimited string with the example query or queries for
* the selected database
*/
protected void example_actionPerformed()
{
- String eq = getExampleQueries((String) database.getSelectedItem());
+ String eq = getExampleQueries(
+ ((StringPair) database.getSelectedItem()).getKey());
textArea.setText(eq);
repaint();
}
text = text.replace(",", ";");
}
text = text.replaceAll("(\\s|[; ])+", ";");
- if (!t0.equals(text))
+ if (!t0.equals(text))
{
- textArea.setText(text);
+ textArea.setText(text);
}
if (text.isEmpty())
{
List<String> presultTitle = new ArrayList<>();
List<AlignmentI> presult = new ArrayList<>();
List<AlignmentI> aresult = new ArrayList<>();
- List<DbSourceProxy> sources = sfetch
- .getSourceProxy((String) database.getSelectedItem());
+ List<DbSourceProxy> sources = sfetch.getSourceProxy(
+ ((StringPair) database.getSelectedItem()).getKey());
Iterator<DbSourceProxy> proxies = sources.iterator();
String[] qries = textArea.getText().trim().split(";");
List<String> nextFetch = Arrays.asList(qries);
} catch (Exception e)
{
showErrorMessage("Error retrieving " + textArea.getText() + " from "
- + database.getSelectedItem());
+ + ((StringPair) database.getSelectedItem()).getDisplay());
// error
// +="Couldn't retrieve sequences from "+database.getSelectedItem();
System.err.println("Retrieval failed for source ='"
- + database.getSelectedItem() + "' and query\n'"
- + textArea.getText() + "'\n");
+ + ((StringPair) database.getSelectedItem()).getDisplay()
+ + "' and query\n'" + textArea.getText() + "'\n");
e.printStackTrace();
} catch (OutOfMemoryError e)
{
showErrorMessage("Out of Memory when retrieving "
- + textArea.getText() + " from " + database.getSelectedItem()
+ + textArea.getText() + " from "
+ + ((StringPair) database.getSelectedItem()).getDisplay()
+ "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
e.printStackTrace();
} catch (Error e)
{
showErrorMessage("Serious Error retrieving " + textArea.getText()
- + " from " + database.getSelectedItem());
+ + " from "
+ + ((StringPair) database.getSelectedItem()).getDisplay());
e.printStackTrace();
}
} catch (OutOfMemoryError oome)
{
new OOMWarning("fetching " + multiacc + " from "
- + database.getSelectedItem(), oome, this);
+ + ((StringPair) database.getSelectedItem()).getDisplay(),
+ oome, this);
}
}
}
} catch (Exception e)
{
- Cache.log.info("Error retrieving " + accession + " from "
+ Console.info("Error retrieving " + accession + " from "
+ proxy.getDbName(), e);
}
return success;
for (String q : queries)
{
- // BH 2019.01.25 dbr is never used.
-// DBRefEntry dbr = new DBRefEntry();
-// dbr.setSource(proxy.getDbSource());
-// dbr.setVersion(null);
+ // BH 2019.01.25 dbr is never used.
+ // DBRefEntry dbr = new DBRefEntry();
+ // dbr.setSource(proxy.getDbSource());
+ // dbr.setVersion(null);
String accId = proxy.getAccessionIdFromQuery(q);
-// dbr.setAccessionId(accId);
+ // dbr.setAccessionId(accId);
boolean rfound = false;
for (int r = 0, nr = rs.length; r < nr; r++)
{
*/
public String getDefaultRetrievalTitle()
{
- return "Retrieved from " + database.getSelectedItem();
+ return "Retrieved from "
+ + ((StringPair) database.getSelectedItem()).getDisplay();
}
- AlignmentI parseResult(AlignmentI al, String title,
+ /**
+ * constructs an alignment frame given the data and metadata
+ *
+ * @param al
+ * @param title
+ * @param currentFileFormat
+ * @param preferredFeatureColours
+ * @return the alignment
+ */
+ public AlignmentI parseResult(AlignmentI al, String title,
FileFormatI currentFileFormat,
FeatureSettingsModelI preferredFeatureColours)
{
}
}
- if (preferredFeatureColours != null)
- {
- af.getViewport().applyFeaturesStyle(preferredFeatureColours);
- }
+ af.getViewport().applyFeaturesStyle(preferredFeatureColours);
if (Cache.getDefault("HIDE_INTRONS", true))
{
af.hideFeatureColumns(SequenceOntologyI.EXON, false);
public class Slider extends JSlider
{
/*
+ * the number of nominal positions the slider represents
+ * (higher number = more fine-grained positioning)
+ */
+ private static final int SCALE_TICKS = 1000;
+
+ /*
* 'true' value corresponding to zero on the slider
*/
private float trueMin;
trueMin = min;
trueMax = max;
setMinimum(0);
- sliderScaleFactor = 100f / (max - min);
+ sliderScaleFactor = SCALE_TICKS / (max - min);
int sliderMax = (int) ((max - min) * sliderScaleFactor);
setMaximum(sliderMax);
setSliderValue(value);
if (c != null && c instanceof AlignFrame)
{
AlignFrame af = (AlignFrame) c;
- new Finder(af.alignPanel);
+ boolean dna = af.getViewport().getAlignment().isNucleotide();
+ String scope = MessageManager.getString("label.in") + " "
+ + (dna ? MessageManager.getString("label.nucleotide")
+ : MessageManager.getString("label.protein"));
+ new Finder(af.alignPanel, true, scope);
}
}
};
package jalview.gui;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Locale;
+import java.util.concurrent.Executors;
+
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+import javax.swing.JTable;
+import javax.swing.SwingUtilities;
+import javax.swing.table.AbstractTableModel;
+
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.fts.api.FTSData;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSDataColumnPreferences;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.fts.service.threedbeacons.TDB_FTSData;
+import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
+import jalview.gui.structurechooser.StructureChooserQuerySource;
+import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
import jalview.io.DataSourceType;
+import jalview.jbgui.FilterOption;
import jalview.jbgui.GStructureChooser;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.ws.DBRefFetcher;
+import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.seqfetcher.DbSourceProxy;
import jalview.ws.sifts.SiftsSettings;
-import java.awt.event.ItemEvent;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Objects;
-import java.util.Set;
-import java.util.Vector;
-
-import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
-import javax.swing.JLabel;
-import javax.swing.JTable;
-import javax.swing.SwingUtilities;
-import javax.swing.table.AbstractTableModel;
-
/**
* Provides the behaviors for the Structure chooser Panel
*
{
private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
- private static int MAX_QLENGTH = 7820;
-
private SequenceI selectedSequence;
private SequenceI[] selectedSequences;
private Collection<FTSData> discoveredStructuresSet;
- private FTSRestRequest lastPdbRequest;
+ private StructureChooserQuerySource data;
- private FTSRestClientI pdbRestClient;
+ @Override
+ protected FTSDataColumnPreferences getFTSDocFieldPrefs()
+ {
+ return data.getDocFieldPrefs();
+ }
private String selectedPdbFileName;
private boolean cachedPDBExists;
+ private Collection<FTSData> lastDiscoveredStructuresSet;
+
+ private boolean canQueryTDB = false;
+
+ private boolean notQueriedTDBYet = true;
+
+ List<SequenceI> seqsWithoutSourceDBRef = null;
+
private static StructureViewer lastTargetedView = null;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
{
+ // which FTS engine to use
+ data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
+ initDialog();
+
this.ap = ap;
this.selectedSequence = selectedSeq;
this.selectedSequences = selectedSeqs;
this.progressIndicator = (ap == null) ? null : ap.alignFrame;
init();
+
}
/**
+ * sets canQueryTDB if protein sequences without a canonical uniprot ref or at
+ * least one structure are discovered.
+ */
+ private void populateSeqsWithoutSourceDBRef()
+ {
+ seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+ boolean needCanonical = false;
+ for (SequenceI seq : selectedSequences)
+ {
+ if (seq.isProtein())
+ {
+ int dbRef = ThreeDBStructureChooserQuerySource
+ .checkUniprotRefs(seq.getDBRefs());
+ if (dbRef < 0)
+ {
+ if (dbRef == -1)
+ {
+ // need to retrieve canonicals
+ needCanonical = true;
+ seqsWithoutSourceDBRef.add(seq);
+ }
+ else
+ {
+ // could be a sequence with pdb ref
+ if (seq.getAllPDBEntries() == null
+ || seq.getAllPDBEntries().size() == 0)
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ }
+ }
+ }
+ }
+ }
+ // retrieve database refs for protein sequences
+ if (!seqsWithoutSourceDBRef.isEmpty())
+ {
+ canQueryTDB = true;
+ if (needCanonical)
+ {
+ // triggers display of the 'Query TDB' button
+ notQueriedTDBYet = true;
+ }
+ }
+ };
+
+ /**
* Initializes parameters used by the Structure Chooser Panel
*/
protected void init()
}
chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
+ btn_queryTDB.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ promptForTDBFetch(false);
+ }
+ });
+
+ Executors.defaultThreadFactory().newThread(new Runnable()
+ {
+ public void run()
+ {
+ populateSeqsWithoutSourceDBRef();
+ initialStructureDiscovery();
+ }
+
+ }).start();
+
+ }
+
+ // called by init
+ private void initialStructureDiscovery()
+ {
+ // check which FTS engine to use
+ data = StructureChooserQuerySource.getQuerySourceFor(selectedSequences);
// ensure a filter option is in force for search
populateFilterComboBox(true, cachedPDBExists);
- Thread discoverPDBStructuresThread = new Thread(new Runnable()
+
+ // looks for any existing structures already loaded
+ // for the sequences (the cached ones)
+ // then queries the StructureChooserQuerySource to
+ // discover more structures.
+ //
+ // Possible optimisation is to only begin querying
+ // the structure chooser if there are no cached structures.
+
+ long startTime = System.currentTimeMillis();
+ updateProgressIndicator(
+ MessageManager.getString("status.loading_cached_pdb_entries"),
+ startTime);
+ loadLocalCachedPDBEntries();
+ updateProgressIndicator(null, startTime);
+ updateProgressIndicator(
+ MessageManager.getString("status.searching_for_pdb_structures"),
+ startTime);
+ fetchStructuresMetaData();
+ // revise filter options if no results were found
+ populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
+ discoverStructureViews();
+ updateProgressIndicator(null, startTime);
+ mainFrame.setVisible(true);
+ updateCurrentView();
+ }
+
+ /**
+ * raises dialog for Uniprot fetch followed by 3D beacons search
+ * @param ignoreGui - when true, don't ask, just fetch
+ */
+ public void promptForTDBFetch(boolean ignoreGui)
+ {
+ final long progressId = System.currentTimeMillis();
+
+ // final action after prompting and discovering db refs
+ final Runnable strucDiscovery = new Runnable()
{
@Override
public void run()
{
- long startTime = System.currentTimeMillis();
- updateProgressIndicator(MessageManager
- .getString("status.loading_cached_pdb_entries"), startTime);
- loadLocalCachedPDBEntries();
- updateProgressIndicator(null, startTime);
- updateProgressIndicator(MessageManager.getString(
- "status.searching_for_pdb_structures"), startTime);
- fetchStructuresMetaData();
- // revise filter options if no results were found
- populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
- discoverStructureViews();
- updateProgressIndicator(null, startTime);
- mainFrame.setVisible(true);
- updateCurrentView();
+ mainFrame.setEnabled(false);
+ cmb_filterOption.setEnabled(false);
+ progressBar.setProgressBar(MessageManager.getString("status.searching_3d_beacons"), progressId);
+ // TODO: warn if no accessions discovered
+ populateSeqsWithoutSourceDBRef();
+ // redo initial discovery - this time with 3d beacons
+ // Executors.
+ previousWantedFields=null;
+ lastSelected=(FilterOption) cmb_filterOption.getSelectedItem();
+ cmb_filterOption.setSelectedItem(null);
+ cachedPDBExists=false; // reset to initial
+ initialStructureDiscovery();
+ if (!isStructuresDiscovered())
+ {
+ progressBar.setProgressBar(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"), progressId);
+ btn_queryTDB.setToolTipText(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"));
+ btn_queryTDB.setEnabled(false);
+ } else {
+ cmb_filterOption.setSelectedIndex(0); // select 'best'
+ btn_queryTDB.setVisible(false);
+ progressBar.setProgressBar(null, progressId);
+ }
+ mainFrame.setEnabled(true);
+ cmb_filterOption.setEnabled(true);
}
- });
- discoverPDBStructuresThread.start();
+ };
+
+ final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI()
+ {
+
+ @Override
+ public void finished()
+ {
+ // filter has been selected, so we set flag to remove ourselves
+ notQueriedTDBYet = false;
+ // new thread to discover structures - via 3d beacons
+ Executors.defaultThreadFactory().newThread(strucDiscovery).start();
+
+ }
+ };
+
+ // fetch db refs if OK pressed
+ final Runnable discoverCanonicalDBrefs = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ populateSeqsWithoutSourceDBRef();
+
+ final int y = seqsWithoutSourceDBRef.size();
+ if (y > 0)
+ {
+ final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
+ .toArray(new SequenceI[y]);
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef,
+ progressBar, new DbSourceProxy[]
+ { new jalview.ws.dbsources.Uniprot() }, null, false);
+ dbRefFetcher.addListener(afterDbRefFetch);
+ // ideally this would also gracefully run with callbacks
+ dbRefFetcher.fetchDBRefs(true);
+ } else {
+ // call finished action directly
+ afterDbRefFetch.finished();
+ }
+ }
+
+ };
+ final Runnable revertview = new Runnable() {
+ public void run() {
+ if (lastSelected!=null) {
+ cmb_filterOption.setSelectedItem(lastSelected);
+ }
+ };
+ };
+ if (ignoreGui)
+ {
+ Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs).start();
+ return;
+ }
+ // need cancel and no to result in the discoverPDB action - mocked is
+ // 'cancel' TODO: mock should be OK
+ JvOptionPane.newOptionDialog(this)
+ .setResponseHandler(JvOptionPane.OK_OPTION,
+ discoverCanonicalDBrefs)
+ .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
+ .setResponseHandler(JvOptionPane.NO_OPTION, revertview)
+ .showDialog(
+ MessageManager.formatMessage(
+ "label.fetch_references_for_3dbeacons",
+ seqsWithoutSourceDBRef.size()),
+ MessageManager
+ .getString("label.3dbeacons"),
+ JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE,
+ null, new Object[]
+ { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") },
+ MessageManager.getString("action.ok"));
}
/**
if (view.isLinkedWith(ap))
{
- targetView.insertItemAt(viewHandler,
- linkedViewsAt++);
+ targetView.insertItemAt(viewHandler, linkedViewsAt++);
}
else
{
void fetchStructuresMetaData()
{
long startTime = System.currentTimeMillis();
- pdbRestClient = PDBFTSRestClient.getInstance();
- Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+ Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
.getStructureSummaryFields();
discoveredStructuresSet = new LinkedHashSet<>();
HashSet<String> errors = new HashSet<>();
+
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+
for (SequenceI seq : selectedSequences)
{
- FTSRestRequest pdbRequest = new FTSRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(500);
- pdbRequest.setFieldToSearchBy("(");
- FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
- .getSelectedItem());
- pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
- !chk_invertFilter.isSelected());
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setAssociatedSequence(seq);
+
FTSRestResponse resultList;
try
{
- resultList = pdbRestClient.executeRequest(pdbRequest);
+ resultList = data.fetchStructuresMetaData(seq, wantedFields,
+ selectedFilterOpt, !chk_invertFilter.isSelected());
+ // null response means the FTSengine didn't yield a query for this
+ // consider designing a special exception if we really wanted to be
+ // OOCrazy
+ if (resultList == null)
+ {
+ continue;
+ }
} catch (Exception e)
{
e.printStackTrace();
errors.add(e.getMessage());
continue;
}
- lastPdbRequest = pdbRequest;
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
- getResultTable().setModel(FTSRestResponse
- .getTableModel(lastPdbRequest, discoveredStructuresSet));
+ getResultTable()
+ .setModel(data.getTableModel(discoveredStructuresSet));
+
noOfStructuresFound = discoveredStructuresSet.size();
+ lastDiscoveredStructuresSet = discoveredStructuresSet;
mainFrame.setTitle(MessageManager.formatMessage(
"label.structure_chooser_no_of_structures",
noOfStructuresFound, totalTime));
}
/**
- * Builds a query string for a given sequences using its DBRef entries
- *
- * @param seq
- * the sequences to build a query for
- * @return the built query string
- */
-
- static String buildQuery(SequenceI seq)
- {
- boolean isPDBRefsFound = false;
- boolean isUniProtRefsFound = false;
- StringBuilder queryBuilder = new StringBuilder();
- Set<String> seqRefs = new LinkedHashSet<>();
-
- /*
- * note PDBs as DBRefEntry so they are not duplicated in query
- */
- Set<String> pdbids = new HashSet<>();
-
- if (seq.getAllPDBEntries() != null
- && queryBuilder.length() < MAX_QLENGTH)
- {
- for (PDBEntry entry : seq.getAllPDBEntries())
- {
- if (isValidSeqName(entry.getId()))
- {
- String id = entry.getId().toLowerCase();
- queryBuilder.append("pdb_id:").append(id).append(" OR ");
- isPDBRefsFound = true;
- pdbids.add(id);
- }
- }
- }
-
- List<DBRefEntry> refs = seq.getDBRefs();
- if (refs != null && refs.size() != 0)
- {
- for (int ib = 0, nb = refs.size(); ib < nb; ib++)
- {
- DBRefEntry dbRef = refs.get(ib);
- if (isValidSeqName(getDBRefId(dbRef))
- && queryBuilder.length() < MAX_QLENGTH)
- {
- if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
- {
- queryBuilder.append("uniprot_accession:")
- .append(getDBRefId(dbRef)).append(" OR ");
- queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
- .append(" OR ");
- isUniProtRefsFound = true;
- }
- else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
- {
-
- String id = getDBRefId(dbRef).toLowerCase();
- if (!pdbids.contains(id))
- {
- queryBuilder.append("pdb_id:").append(id).append(" OR ");
- isPDBRefsFound = true;
- pdbids.add(id);
- }
- }
- else
- {
- seqRefs.add(getDBRefId(dbRef));
- }
- }
- }
- }
-
- if (!isPDBRefsFound && !isUniProtRefsFound)
- {
- String seqName = seq.getName();
- seqName = sanitizeSeqName(seqName);
- String[] names = seqName.toLowerCase().split("\\|");
- for (String name : names)
- {
- // System.out.println("Found name : " + name);
- name.trim();
- if (isValidSeqName(name))
- {
- seqRefs.add(name);
- }
- }
-
- for (String seqRef : seqRefs)
- {
- queryBuilder.append("text:").append(seqRef).append(" OR ");
- }
- }
-
- int endIndex = queryBuilder.lastIndexOf(" OR ");
- if (queryBuilder.toString().length() < 6)
- {
- return null;
- }
- String query = queryBuilder.toString().substring(0, endIndex);
- return query;
- }
-
- /**
- * Remove the following special characters from input string +, -, &, !, (, ),
- * {, }, [, ], ^, ", ~, *, ?, :, \
- *
- * @param seqName
- * @return
- */
- static String sanitizeSeqName(String seqName)
- {
- Objects.requireNonNull(seqName);
- return seqName.replaceAll("\\[\\d*\\]", "")
- .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
- }
-
- /**
- * Ensures sequence ref names are not less than 3 characters and does not
- * contain a database name
- *
- * @param seqName
- * @return
- */
- static boolean isValidSeqName(String seqName)
- {
- // System.out.println("seqName : " + seqName);
- String ignoreList = "pdb,uniprot,swiss-prot";
- if (seqName.length() < 3)
- {
- return false;
- }
- if (seqName.contains(":"))
- {
- return false;
- }
- seqName = seqName.toLowerCase();
- for (String ignoredEntry : ignoreList.split(","))
- {
- if (seqName.contains(ignoredEntry))
- {
- return false;
- }
- }
- return true;
- }
-
- static String getDBRefId(DBRefEntry dbRef)
- {
- String ref = dbRef.getAccessionId().replaceAll("GO:", "");
- return ref;
- }
-
- /**
* Filters a given list of discovered structures based on supplied argument
*
* @param fieldToFilterBy
{
Thread filterThread = new Thread(new Runnable()
{
+
@Override
public void run()
{
long startTime = System.currentTimeMillis();
- pdbRestClient = PDBFTSRestClient.getInstance();
lbl_loading.setVisible(true);
- Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+ Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
.getStructureSummaryFields();
Collection<FTSData> filteredResponse = new HashSet<>();
HashSet<String> errors = new HashSet<>();
for (SequenceI seq : selectedSequences)
{
- FTSRestRequest pdbRequest = new FTSRestRequest();
- if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
- {
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(");
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setAssociatedSequence(seq);
- pdbRequest.setFacet(true);
- pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
- pdbRequest.setFacetPivotMinCount(1);
- }
- else
- {
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(");
- pdbRequest.setFieldToSortBy(fieldToFilterBy,
- !chk_invertFilter.isSelected());
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setAssociatedSequence(seq);
- }
+
FTSRestResponse resultList;
try
{
- resultList = pdbRestClient.executeRequest(pdbRequest);
+ resultList = data.selectFirstRankedQuery(seq,
+ discoveredStructuresSet, wantedFields, fieldToFilterBy,
+ !chk_invertFilter.isSelected());
+
} catch (Exception e)
{
e.printStackTrace();
errors.add(e.getMessage());
continue;
}
- lastPdbRequest = pdbRequest;
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
- getResultTable().setModel(FTSRestResponse
- .getTableModel(lastPdbRequest, reorderedStructuresSet));
+ getResultTable()
+ .setModel(data.getTableModel(reorderedStructuresSet));
FTSRestResponse.configureTableColumn(getResultTable(),
wantedFields, tempUserPrefs);
@Override
protected void pdbFromFile_actionPerformed()
{
- // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and StructureChooser
+ // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and
+ // StructureChooser
// works
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(
MessageManager.formatMessage("label.select_pdb_file_for",
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
selectedPdbFileName = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
validateSelections();
}
}
protected void populateFilterComboBox(boolean haveData,
boolean cachedPDBExist)
{
+ populateFilterComboBox(haveData, cachedPDBExist, null);
+ }
+
+ /**
+ * Populates the filter combo-box options dynamically depending on discovered
+ * structures
+ */
+ protected void populateFilterComboBox(boolean haveData,
+ boolean cachedPDBExist, FilterOption lastSel)
+ {
+
/*
* temporarily suspend the change listener behaviour
*/
cmb_filterOption.removeItemListener(this);
-
+ int selSet = -1;
cmb_filterOption.removeAllItems();
if (haveData)
{
- cmb_filterOption.addItem(new FilterOption(
- MessageManager.getString("label.best_quality"),
- "overall_quality", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption(
- MessageManager.getString("label.best_resolution"),
- "resolution", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption(
- MessageManager.getString("label.most_protein_chain"),
- "number_of_protein_chains", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption(
- MessageManager.getString("label.most_bound_molecules"),
- "number_of_bound_molecules", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption(
- MessageManager.getString("label.most_polymer_residues"),
- "number_of_polymer_residues", VIEWS_FILTER, true));
+ List<FilterOption> filters = data
+ .getAvailableFilterOptions(VIEWS_FILTER);
+ data.updateAvailableFilterOptions(VIEWS_FILTER, filters,
+ lastDiscoveredStructuresSet);
+ int p = 0;
+ for (FilterOption filter : filters)
+ {
+ if (lastSel != null && filter.equals(lastSel))
+ {
+ selSet = p;
+ }
+ p++;
+ cmb_filterOption.addItem(filter);
+ }
}
+
cmb_filterOption.addItem(
new FilterOption(MessageManager.getString("label.enter_pdb_id"),
- "-", VIEWS_ENTER_ID, false));
+ "-", VIEWS_ENTER_ID, false, null));
cmb_filterOption.addItem(
new FilterOption(MessageManager.getString("label.from_file"),
- "-", VIEWS_FROM_FILE, false));
+ "-", VIEWS_FROM_FILE, false, null));
+ if (canQueryTDB && notQueriedTDBYet)
+ {
+ btn_queryTDB.setVisible(true);
+ }
if (cachedPDBExist)
{
FilterOption cachedOption = new FilterOption(
- MessageManager.getString("label.cached_structures"),
- "-", VIEWS_LOCAL_PDB, false);
+ MessageManager.getString("label.cached_structures"), "-",
+ VIEWS_LOCAL_PDB, false, null);
cmb_filterOption.addItem(cachedOption);
- cmb_filterOption.setSelectedItem(cachedOption);
+ if (selSet == -1)
+ {
+ cmb_filterOption.setSelectedItem(cachedOption);
+ }
+ }
+ if (selSet > -1)
+ {
+ cmb_filterOption.setSelectedIndex(selSet);
}
-
cmb_filterOption.addItemListener(this);
}
{
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
+
+ if (lastSelected == selectedFilterOpt)
+ {
+ // don't need to do anything, probably
+ return;
+ }
+ // otherwise, record selection
+ // and update the layout and dialog accordingly
+ lastSelected = selectedFilterOpt;
+
layout_switchableViews.show(pnl_switchableViews,
selectedFilterOpt.getView());
String filterTitle = mainFrame.getTitle();
mainFrame.setTitle(frameTitle);
chk_invertFilter.setVisible(false);
+
if (selectedFilterOpt.getView() == VIEWS_FILTER)
{
mainFrame.setTitle(filterTitle);
- chk_invertFilter.setVisible(true);
- filterResultSet(selectedFilterOpt.getValue());
+ // TDB Query has no invert as yet
+ chk_invertFilter.setVisible(selectedFilterOpt
+ .getQuerySource() instanceof PDBStructureChooserQuerySource);
+
+ if (data != selectedFilterOpt.getQuerySource()
+ || data.needsRefetch(selectedFilterOpt))
+ {
+ data = selectedFilterOpt.getQuerySource();
+ // rebuild the views completely, since prefs will also change
+ tabRefresh();
+ return;
+ }
+ else
+ {
+ filterResultSet(selectedFilterOpt.getValue());
+ }
}
else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
|| selectedFilterOpt.getView() == VIEWS_FROM_FILE)
.setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
}
+ @Override
+ protected boolean showPopupFor(int selectedRow, int x, int y)
+ {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+
+ if (currentView == VIEWS_FILTER && data instanceof ThreeDBStructureChooserQuerySource)
+ {
+
+ TDB_FTSData row=((ThreeDBStructureChooserQuerySource)data).getFTSDataFor(getResultTable(), selectedRow, discoveredStructuresSet);
+ String pageUrl = row.getModelViewUrl();
+ JPopupMenu popup = new JPopupMenu("3D Beacons");
+ JMenuItem viewUrl = new JMenuItem("View model web page");
+ viewUrl.addActionListener(
+ new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ Desktop.showUrl(pageUrl);
+ }
+ }
+ );
+ popup.add(viewUrl);
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() { popup.show(getResultTable(), x, y); }
+ });
+ return true;
+ }
+ // event not handled by us
+ return false;
+ }
/**
* Validates inputs from the Manual PDB entry panel
*/
{
validateSelections();
}
-
+ private FilterOption lastSelected=null;
/**
* Handles the state change event for the 'filter' combo-box and 'invert'
* check-box
}
return found;
}
-
+
/**
* Handles the 'New View' action
*/
if (currentView == VIEWS_FILTER)
{
- int pdbIdColIndex = restable.getColumn("PDB Id")
- .getModelIndex();
- int refSeqColIndex = restable.getColumn("Ref Sequence")
- .getModelIndex();
int[] selectedRows = restable.getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
List<SequenceI> selectedSeqsToView = new ArrayList<>();
- for (int row : selectedRows)
- {
- String pdbIdStr = restable
- .getValueAt(row, pdbIdColIndex).toString();
- SequenceI selectedSeq = (SequenceI) restable
- .getValueAt(row, refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
- PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
- if (pdbEntry == null)
- {
- pdbEntry = getFindEntry(pdbIdStr,
- selectedSeq.getAllPDBEntries());
- }
+ pdbEntriesToView = data.collectSelectedRows(restable,
+ selectedRows, selectedSeqsToView);
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
- selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
- }
- pdbEntriesToView[count++] = pdbEntry;
- }
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
List<SequenceI> selectedSeqsToView = new ArrayList<>();
for (int row : selectedRows)
{
- PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
- pdbIdColIndex);
+ PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb
+ .getModel()).getPDBEntryAt(row).getPdbEntry();
+
pdbEntriesToView[count++] = pdbEntry;
SequenceI selectedSeq = (SequenceI) tbl_local_pdb
.getValueAt(row, refSeqColIndex);
if (pdbIdStr.split(":").length > 1)
{
pdbEntry.setId(pdbIdStr.split(":")[0]);
- pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
+ pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
}
else
{
DataSourceType.FILE, selectedSequence, true,
Desktop.instance);
- sViewer = launchStructureViewer(
- ssm, new PDBEntry[]
- { fileEntry }, ap,
- new SequenceI[]
+ sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
+ ap, new SequenceI[]
{ selectedSequence });
}
SwingUtilities.invokeLater(new Runnable()
}
}
- private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
- {
- Objects.requireNonNull(id);
- Objects.requireNonNull(pdbEntries);
- PDBEntry foundEntry = null;
- for (PDBEntry entry : pdbEntries)
- {
- if (entry.getId().equalsIgnoreCase(id))
- {
- return entry;
- }
- }
- return foundEntry;
- }
-
/**
* Answers a structure viewer (new or existing) configured to superimpose
* added structures or not according to the user's choice
* @param ssm
* @return
*/
- StructureViewer getTargetedStructureViewer(
- StructureSelectionManager ssm)
+ StructureViewer getTargetedStructureViewer(StructureSelectionManager ssm)
{
Object sv = targetView.getSelectedItem();
* @return
*/
private StructureViewer launchStructureViewer(
- StructureSelectionManager ssm,
- final PDBEntry[] pdbEntriesToView,
+ StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
final AlignmentPanel alignPanel, SequenceI[] sequences)
{
long progressId = sequences.hashCode();
}
if (pdbEntriesToView.length > 1)
{
- setProgressBar(MessageManager.getString(
- "status.fetching_3d_structures_for_selected_entries"),
+ setProgressBar(
+ MessageManager.getString(
+ "status.fetching_3d_structures_for_selected_entries"),
progressId);
theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
}
{
setProgressBar(MessageManager.formatMessage(
"status.fetching_3d_structures_for",
- pdbEntriesToView[0].getId()),progressId);
+ pdbEntriesToView[0].getId()), progressId);
theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
}
setProgressBar(null, progressId);
&& !discoveredStructuresSet.isEmpty();
}
- protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes this.
+ protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes
+ // this.
// Doing a search for "1" or "1c" is valuable?
// Those work but are enormously slow.
protected void txt_search_ActionPerformed()
{
String text = txt_search.getText().trim();
- if (text.length() >= PDB_ID_MIN)
- new Thread()
- {
-
- @Override
- public void run()
+ if (text.length() >= PDB_ID_MIN)
+ new Thread()
{
- errorWarning.setLength(0);
- isValidPBDEntry = false;
- if (text.length() > 0)
+
+ @Override
+ public void run()
{
- String searchTerm = text.toLowerCase();
- searchTerm = searchTerm.split(":")[0];
- // System.out.println(">>>>> search term : " + searchTerm);
- List<FTSDataColumnI> wantedFields = new ArrayList<>();
- FTSRestRequest pdbRequest = new FTSRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(pdb_id:");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setSearchTerm(searchTerm + ")");
- pdbRequest.setAssociatedSequence(selectedSequence);
- pdbRestClient = PDBFTSRestClient.getInstance();
- wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
- FTSRestResponse resultList;
- try
+ errorWarning.setLength(0);
+ isValidPBDEntry = false;
+ if (text.length() > 0)
{
- resultList = pdbRestClient.executeRequest(pdbRequest);
- } catch (Exception e)
- {
- errorWarning.append(e.getMessage());
- return;
- } finally
- {
- validateSelections();
- }
- if (resultList.getSearchSummary() != null
- && resultList.getSearchSummary().size() > 0)
- {
- isValidPBDEntry = true;
+ // TODO move this pdb id search into the PDB specific
+ // FTSSearchEngine
+ // for moment, it will work fine as is because it is self-contained
+ String searchTerm = text.toLowerCase(Locale.ROOT);
+ searchTerm = searchTerm.split(":")[0];
+ // System.out.println(">>>>> search term : " + searchTerm);
+ List<FTSDataColumnI> wantedFields = new ArrayList<>();
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(pdb_id:");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setSearchTerm(searchTerm + ")");
+ pdbRequest.setAssociatedSequence(selectedSequence);
+ FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance();
+ wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
+ FTSRestResponse resultList;
+ try
+ {
+ resultList = pdbRestClient.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ errorWarning.append(e.getMessage());
+ return;
+ } finally
+ {
+ validateSelections();
+ }
+ if (resultList.getSearchSummary() != null
+ && resultList.getSearchSummary().size() > 0)
+ {
+ isValidPBDEntry = true;
+ }
}
+ validateSelections();
}
- validateSelections();
- }
- }.start();
+ }.start();
}
@Override
public void run()
{
fetchStructuresMetaData();
+ // populateFilterComboBox(true, cachedPDBExists);
+
filterResultSet(
((FilterOption) cmb_filterOption.getSelectedItem())
.getValue());
value = entry.getSequence();
break;
case 1:
- value = entry.getPdbEntry();
+ value = entry.getQualifiedId();
break;
case 2:
value = entry.getPdbEntry().getChainCode() == null ? "_"
this.pdbEntry = pdbEntry;
}
+ public String getQualifiedId()
+ {
+ if (pdbEntry.hasProvider())
+ {
+ return pdbEntry.getProvider() + ":" + pdbEntry.getId();
+ }
+ return pdbEntry.toString();
+ }
+
public SequenceI getSequence()
{
return sequence;
{
return sViewer == null ? null : sViewer.sview;
}
+
+ @Override
+ protected void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs)
+ {
+ data.setDocFieldPrefs(newPrefs);
+
+ }
+
+ /**
+ *
+ * @return true when all initialisation threads have finished and dialog is
+ * visible
+ */
+ public boolean isDialogVisible()
+ {
+ return mainFrame != null && data != null && cmb_filterOption != null
+ && mainFrame.isVisible()
+ && cmb_filterOption.getSelectedItem() != null;
+ }
+ /**
+ *
+ * @return true if the 3D-Beacons query button will/has been displayed
+ */
+ public boolean isCanQueryTDB() {
+ return canQueryTDB;
+ }
+
+ public boolean isNotQueriedTDBYet()
+ {
+ return notQueriedTDBYet;
+ }
}
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
return sv;
}
+
@Override
public String toString()
{
}
return "New View";
}
- public ViewerType getViewerType()
+ /**
+ *
+ * @return ViewerType for currently configured structure viewer
+ */
+ public static ViewerType getViewerType()
{
String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
ViewerType.JMOL.name());
}
else
{
- Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
+ Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
}
return sview;
}
}
else
{
- Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
+ Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
}
return sview;
}
viewer = new PymolViewer(viewerData, alignPanel, sessionFile, vid);
break;
default:
- Cache.log.error(UNKNOWN_VIEWER_TYPE + type.toString());
+ Console.error(UNKNOWN_VIEWER_TYPE + type.toString());
}
return viewer;
}
+
public boolean isBusy()
{
if (sview != null)
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import jalview.ws.dbsources.EBIAlfaFold;
import jalview.ws.dbsources.Pdb;
+import jalview.ws.utils.UrlDownloadClient;
/**
* Base class with common functionality for JMol, Chimera or other structure
{
alignAddedStructures = alignAdded;
}
+
+ /**
+ * called by the binding model to indicate when adding structures is happening or has been completed
+ * @param addingStructures
+ */
+ public synchronized void setAddingStructures(boolean addingStructures)
+ {
+ this.addingStructures = addingStructures;
+ }
/**
*
_alignwith.add(ap);
}
;
+ // TODO: refactor to allow concrete classes to register buttons for adding
+ // here
+ // currently have to override to add buttons back in after they are cleared
+ // in this loop
for (Component c : viewerActionMenu.getMenuComponents())
{
if (c != alignStructs)
{
sp.append("'" + alignPanel.getViewName() + "' ");
}
- Cache.log.info("Couldn't align structures with the " + sp.toString()
+ Console.info("Couldn't align structures with the " + sp.toString()
+ "associated alignment panels.", e);
}
return reply;
progressBar = pi;
}
- protected void setProgressMessage(String message, long id)
+ public void setProgressMessage(String message, long id)
{
if (progressBar != null)
{
{
if (afclient.isValidReference(pdbid))
{
- pdbseq = afclient.getSequenceRecords(pdbid);
+ pdbseq = afclient.getSequenceRecords(pdbid,processingEntry.getRetrievalUrl());
} else {
- pdbseq = pdbclient.getSequenceRecords(pdbid);
+ if (processingEntry.hasRetrievalUrl())
+ {
+ String safePDBId = java.net.URLEncoder.encode(pdbid,"UTF-8").replace("%","__");
+
+ // retrieve from URL to new local tmpfile
+ File tmpFile = File.createTempFile(safePDBId,
+ "." + (PDBEntry.Type.MMCIF.toString().equals(
+ processingEntry.getType().toString()) ? "cif"
+ : "pdb"));
+ String fromUrl = processingEntry.getRetrievalUrl();
+ UrlDownloadClient.download(fromUrl, tmpFile);
+
+ // may not need this check ?
+ String file = tmpFile.getAbsolutePath();
+ if (file != null)
+ {
+ pdbseq = EBIAlfaFold.importDownloadedStructureFromUrl(fromUrl,tmpFile,pdbid,null,null,null);
+ }
+ } else {
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
+ }
}
} catch (Exception e)
{
*/
public File saveSession()
{
- // TODO: a wait loop to ensure the file is written fully before returning?
- return getBinding() == null ? null : getBinding().saveSession();
+ if (getBinding() == null) { return null;}
+ File session = getBinding().saveSession();
+ long l = session.length();
+ int wait=50;
+ do {
+ try {
+ Thread.sleep(5);
+ } catch (InterruptedException e) {
+ }
+ long nextl = session.length();
+ if (nextl!=l)
+ {
+ wait = 50;
+ l=nextl;
+ }
+ } while (--wait>0);
+ return session;
}
/**
+ ex.getMessage());
}
}
-
+ @Override
+ public boolean hasViewerActionsMenu()
+ {
+ return viewerActionMenu != null && viewerActionMenu.isEnabled()
+ && viewerActionMenu.getItemCount() > 0
+ && viewerActionMenu.isVisible();
+ }
}
*/
package jalview.gui;
+import java.util.Locale;
+
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AverageDistanceTree;
import jalview.analysis.NJTree;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import jalview.datamodel.Alignment;
{
// TODO: JAL-3048 save newick file for Jalview-JS
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_tree_as_newick"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ Cache.setProperty("LAST_DIRECTORY",
chooser.getSelectedFile().getParent());
try
AlignmentView originalData = tree.getOriginalData();
if (originalData == null)
{
- jalview.bin.Cache.log.info(
+ Console.info(
"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
String tree = MessageManager.getString("label.tree");
ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
tree);
- exporter.doExport(null, this, width, height, tree.toLowerCase());
+ exporter.doExport(null, this, width, height, tree.toLowerCase(Locale.ROOT));
}
/**
// search dbrefs, features and annotation
List<DBRefEntry> refs = jalview.util.DBRefUtils
.selectRefs(sq.getDBRefs(), new String[]
- { labelClass.toUpperCase() });
+ { labelClass.toUpperCase(Locale.ROOT) });
if (refs != null)
{
for (int i = 0, ni = refs.size(); i < ni; i++)
* i18n description of Neighbour Joining or Average Distance method
*/
String treecalcnm = MessageManager
- .getString("label.tree_calc_" + treeType.toLowerCase());
+ .getString("label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
/*
* short score model name (long description can be too long)
*/
package jalview.gui;
+import java.util.Locale;
+
import jalview.bin.Cache;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
{
int row = i / cols + 1;
int index = (row * cols) + i;
- JButton button = makeButton(ResidueProperties.aa[i].toLowerCase(),
- ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
+ JButton button = makeButton(ResidueProperties.aa[i].toLowerCase(Locale.ROOT),
+ ResidueProperties.aa[i].toLowerCase(Locale.ROOT), lowerCaseButtons, i);
buttonPanel.add(button, index);
}
*/
package jalview.gui;
+import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.util.MessageManager;
import java.io.BufferedReader;
{
if (url.indexOf("questionnaire.pl") == -1)
{
- jalview.bin.Cache.log.error("'" + url
+ Console.error("'" + url
+ "' is an Invalid URL for the checkForQuestionnaire() method.\n"
+ "This argument is only for questionnaires derived from jalview's questionnaire.pl cgi interface.");
}
private boolean checkresponse(URL qurl) throws Exception
{
- jalview.bin.Cache.log.debug("Checking Response for : " + qurl);
+ Console.debug("Checking Response for : " + qurl);
boolean prompt = false;
// see if we have already responsed to this questionnaire or get a new
// qid/rid pair
try
{
// First - check to see if wee have an old questionnaire/response id pair.
- String lastq = jalview.bin.Cache.getProperty("QUESTIONNAIRE");
+ String lastq = Cache.getProperty("QUESTIONNAIRE");
if (lastq == null)
{
prompt = checkresponse(new URL(url
if (qid != null && rid != null)
{
// Update our local property cache with latest qid and rid
- jalview.bin.Cache.setProperty("QUESTIONNAIRE", qid + ":" + rid);
+ Cache.setProperty("QUESTIONNAIRE", qid + ":" + rid);
}
if (prompt)
{
String qurl = url + (url.indexOf('?') > -1 ? "&" : "?") + "qid="
+ qid + "&rid=" + rid;
- jalview.bin.Cache.log
- .info("Prompting user for questionnaire at " + qurl);
+ Console.info("Prompting user for questionnaire at " + qurl);
int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.getString("label.jalview_new_questionnaire"),
MessageManager.getString("label.jalview_user_survey"),
if (reply == JvOptionPane.YES_OPTION)
{
- jalview.bin.Cache.log.debug("Opening " + qurl);
+ Console.debug("Opening " + qurl);
jalview.util.BrowserLauncher.openURL(qurl);
}
}
} catch (Exception e)
{
- jalview.bin.Cache.log
- .warn("When trying to access questionnaire URL " + url, e);
+ Console.warn("When trying to access questionnaire URL " + url, e);
}
}
package jalview.gui;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
} catch (Exception e)
{
- jalview.bin.Cache.log.error("Couldn't instantiate vamsas client !",
+ Console.error("Couldn't instantiate vamsas client !",
e);
return false;
}
}
} catch (Error e)
{
- Cache.log.warn(
+ Console.warn(
"Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
e);
} catch (Exception e)
{
- Cache.log.warn(
+ Console.warn(
"Probable VAMSAS client incompatibility - carrying on regardless",
e);
}
private ClientHandle getJalviewHandle()
{
return new ClientHandle("jalview.bin.Jalview",
- jalview.bin.Cache.getProperty("VERSION"));
+ Cache.getProperty("VERSION"));
}
/**
addStoreDocumentHandler();
startSession();
inInitialUpdate = true;
- Cache.log.debug(
+ Console.debug(
"Jalview loading the Vamsas Session for the first time.");
dealWithDocumentUpdate(false); // we don't push an update out to the
inInitialUpdate = false;
// document yet.
- Cache.log.debug("... finished update for the first time.");
+ Console.debug("... finished update for the first time.");
}
/**
}
} catch (Exception e)
{
- Cache.log.warn(
+ Console.warn(
"Exception whilst refreshing jalview windows after a vamsas document update.",
e);
}
@Override
public void run()
{
- Cache.log.info("Jalview updating to the Vamsas Session.");
+ Console.info("Jalview updating to the Vamsas Session.");
dealWithDocumentUpdate(true);
- Cache.log.info("Jalview finished updating to the Vamsas Session.");
+ Console.info("Jalview finished updating to the Vamsas Session.");
}
});
{
throw new Error("Jalview not connected to Vamsas session");
}
- Cache.log.info("Jalview disconnecting from the Vamsas Session.");
+ Console.info("Jalview disconnecting from the Vamsas Session.");
try
{
if (joinedSession)
boolean ourprompt = this.promptUser;
this.promptUser = promptUser;
vclient.finalizeClient();
- Cache.log.info("Jalview has left the session.");
+ Console.info("Jalview has left the session.");
this.promptUser = ourprompt; // restore default value
}
else
{
- Cache.log.warn(
+ Console.warn(
"JV Client leaving a session that's its not joined yet.");
}
joinedSession = false;
vobj2jv = null;
} catch (Exception e)
{
- Cache.log.error("Vamsas Session finalization threw exceptions!", e);
+ Console.error("Vamsas Session finalization threw exceptions!", e);
}
}
public void updateJalview(IClientDocument cdoc)
{
- Cache.log.debug("Jalview updating from sesion document ..");
+ Console.debug("Jalview updating from sesion document ..");
ensureJvVamsas();
VamsasAppDatastore vds = new VamsasAppDatastore(cdoc, vobj2jv, jv2vobj,
baseProvEntry(), alRedoState);
vds.updateToJalview();
} catch (Exception e)
{
- Cache.log.error("Failed to update Jalview from vamsas document.", e);
+ Console.error("Failed to update Jalview from vamsas document.", e);
}
try
{
}
} catch (Exception e)
{
- Cache.log.error(
+ Console.error(
"Exception when updating Jalview settings from Appdata.", e);
}
- Cache.log.debug(".. finished updating from sesion document.");
+ Console.debug(".. finished updating from sesion document.");
}
} catch (Exception e)
{
errorsDuringUpdate = true;
- Cache.log.error("Exception synchronizing " + af.getTitle()
+ Console.error("Exception synchronizing " + af.getTitle()
+ " "
+ (af.getViewport().getViewName() == null ? ""
: " view " + af.getViewport().getViewName())
}
} catch (Exception e)
{
- Cache.log.error("Exception synchronizing Views to Document :", e);
+ Console.error("Exception synchronizing Views to Document :", e);
errorsDuringUpdate = true;
}
}
} catch (Exception e)
{
- Cache.log.error("Client Appdata Write exception", e);
+ Console.error("Client Appdata Write exception", e);
errorsDuringAppUpdate = true;
}
vds.clearSkipList();
{
int storedviews = 0;
// called by update handler for document update.
- Cache.log.debug("Updating jalview from changed vamsas document.");
+ Console.debug("Updating jalview from changed vamsas document.");
disableGui(true);
try
{
long time = System.currentTimeMillis();
IClientDocument cdoc = vclient.getClientDocument();
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug("Time taken to get ClientDocument = "
+ Console.debug("Time taken to get ClientDocument = "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
if (fromJalview)
{
storedviews += updateVamsasDocument(cdoc);
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Time taken to update Vamsas Document from jalview\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
cdoc.setVamsasRoots(cdoc.getVamsasRoots());
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug("Time taken to set Document Roots\t\t= "
+ Console.debug("Time taken to set Document Roots\t\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
else
{
updateJalview(cdoc);
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Time taken to update Jalview from vamsas document Roots\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
vclient.updateDocument(cdoc);
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug("Time taken to update Session Document\t= "
+ Console.debug("Time taken to update Session Document\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
recover_objectMappingBackup();
storedviews = 0;
}
- Cache.log.debug("Finished updating from document change.");
+ Console.debug("Finished updating from document change.");
disableGui(false);
return storedviews;
}
@Override
public void propertyChange(PropertyChangeEvent evt)
{
- Cache.log.debug("Dealing with document update event.");
+ Console.debug("Dealing with document update event.");
client.dealWithDocumentUpdate(false);
- Cache.log.debug("finished dealing with event.");
+ Console.debug("finished dealing with event.");
}
});
- Cache.log.debug("Added Jalview handler for vamsas document updates.");
+ Console.debug("Added Jalview handler for vamsas document updates.");
}
private void addStoreDocumentHandler()
{
if (client.promptUser)
{
- Cache.log.debug(
+ Console.debug(
"Asking user if the vamsas session should be stored.");
int reply = JvOptionPane.showInternalConfirmDialog(
Desktop.desktop,
if (reply == JvOptionPane.YES_OPTION)
{
- Cache.log.debug("Prompting for vamsas store filename.");
+ Console.debug("Prompting for vamsas store filename.");
Desktop.instance.vamsasSave_actionPerformed(null);
- Cache.log
- .debug("Finished attempt at storing document.");
+ Console.debug("Finished attempt at storing document.");
}
- Cache.log.debug(
+ Console.debug(
"finished dealing with REQUESTTOCLOSE event.");
}
else
{
- Cache.log.debug(
+ Console.debug(
"Ignoring store document request (promptUser==false)");
}
}
});
- Cache.log.debug("Added Jalview handler for vamsas document updates.");
+ Console.debug("Added Jalview handler for vamsas document updates.");
}
public void disableGui(boolean b)
} catch (Exception e)
{
// Complain to GUI
- Cache.log.error("Failed to join vamsas session.", e);
+ Console.error("Failed to join vamsas session.", e);
vclient = null;
}
try
{
return;
}
- // if (Cache.log.isDebugEnabled())
+ // if (Cache.isDebugEnabled())
// {
- // Cache.log.debug("Received MouseOverMessage "+mm.getVorbaID()+"
+ // Cache.debug("Received MouseOverMessage "+mm.getVorbaID()+"
// "+mm.getPosition());
// }
Object jvobj = vobj2jv.get(mm.getVorbaID());
if (jvobj != null && jvobj instanceof SequenceI)
{
last = mstring;
- // Cache.log.debug("Handling Mouse over "+mm.getVorbaID()+"
+ // Cache.debug("Handling Mouse over "+mm.getVorbaID()+"
// bound to "+jvobj+" at "+mm.getPosition());
// position is character position in aligned sequence
ssm.mouseOverVamsasSequence((SequenceI) jvobj,
if (v != null)
{
// this should really be a trace message.
- // Cache.log.debug("Mouse over " + v.getId() + " bound to "
+ // Cache.debug("Mouse over " + v.getId() + " bound to "
// + seq + " at " + index);
last = seq;
i = index;
{
if (vobj2jv == null)
{
- Cache.log.warn(
+ Console.warn(
"Selection listener still active for dead session.");
// not in a session.
return;
if (sm != null)
{
sm.validate(); // debug
- Cache.log.debug("Selection Message\n" + sm.getRawMessage());
+ Console.debug("Selection Message\n" + sm.getRawMessage());
pm.sendMessage(sm);
}
}
ssm.addSelectionListener(selecter);
} catch (Exception e)
{
- Cache.log.error("Failed to init Vamsas Picking", e);
+ Console.error("Failed to init Vamsas Picking", e);
}
}
}
import jalview.api.AlignmentViewPanel;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.awt.Component;
import java.awt.event.ActionEvent;
}
}
});
+ final ViewSelectionMenu us=this;
checkBox.addMouseListener(new MouseAdapter()
{
@Override
{
try
{
- ap.setSelected(false);
} catch (Exception ex)
{
}
{
try
{
- ap.setSelected(true);
+ ap.setAlignFrameView();
} catch (Exception ex)
{
}
*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
{
return null;
}
- String lowertxt = text.toLowerCase();
+ String lowertxt = text.toLowerCase(Locale.ROOT);
int htmlpos = leaveFirst ? -1 : lowertxt.indexOf("<body");
int htmlend = leaveLast ? -1 : lowertxt.indexOf("</body");
{
return "";
}
- String lowertxt = text.toLowerCase();
+ String lowertxt = text.toLowerCase(Locale.ROOT);
int htmlpos = lowertxt.indexOf("<body");
int htmlend = lowertxt.indexOf("</body");
int doctype = lowertxt.indexOf("<!doctype");
*/
package jalview.gui;
-import jalview.gui.OptsAndParamsPage.OptionBox;
-import jalview.gui.OptsAndParamsPage.ParamBox;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.JabaPreset;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.OptionI;
-import jalview.ws.params.ParamDatastoreI;
-import jalview.ws.params.ParameterI;
-import jalview.ws.params.WsParamSetI;
-
import java.awt.BorderLayout;
import java.awt.Component;
import java.awt.Dimension;
import compbio.metadata.Preset;
import compbio.metadata.PresetManager;
import compbio.metadata.RunnerConfig;
+import jalview.bin.Console;
+import jalview.gui.OptsAndParamsPage.OptionBox;
+import jalview.gui.OptsAndParamsPage.ParamBox;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.JabaPreset;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.WsParamSetI;
import net.miginfocom.swing.MigLayout;
/**
if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
{
final String setname = (String) setName.getSelectedItem();
- System.out.println("Item state changed for " + setname
- + " (handling ? " + !settingDialog + ")");
+ if (Console.isDebugEnabled())
+ {
+ Console.debug("Item state changed for " + setname
+ + " (handling ? " + !settingDialog + ")");
+ }
if (settingDialog)
{
// ignore event
package jalview.gui;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.util.MessageManager;
}
} catch (IOException e)
{
- Cache.log.info("Failed to parse parameter file " + pfile
+ Console.info("Failed to parse parameter file " + pfile
+ " (Check that all JALVIEW_WSPARAMFILES entries are valid!)",
e);
}
{
if (filename != null && !((outfile = new File(filename)).canWrite()))
{
- Cache.log.warn("Can't write to " + filename
+ Console.warn("Can't write to " + filename
+ " - Prompting for new file to write to.");
filename = null;
}
}
if (outfile != null)
{
- String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES",
+ String paramFiles = Cache.getDefault("WS_PARAM_FILES",
filename);
if (paramFiles.indexOf(filename) == -1)
{
parameterSet.setSourceFile(filename);
} catch (Exception e)
{
- Cache.log.error("Couldn't write parameter file to " + outfile, e);
+ Console.error("Couldn't write parameter file to " + outfile, e);
}
}
}
/*
*
- * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ * JalviewFileChooser chooser = new JalviewFileChooser(Cache
* .getProperty("LAST_DIRECTORY"), new String[] { "jc" }, new String[] {
* "Jalview User Colours" }, "Jalview User Colours"); chooser.setFileView(new
* jalview.io.JalviewFileView());
* int value = chooser.showOpenDialog(this);
*
* if (value == JalviewFileChooser.APPROVE_OPTION) { File choice =
- * chooser.getSelectedFile(); jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- * choice.getParent()); String defaultColours = jalview.bin.Cache.getDefault(
+ * chooser.getSelectedFile(); Cache.setProperty("LAST_DIRECTORY",
+ * choice.getParent()); String defaultColours = Cache.getDefault(
* "USER_DEFINED_COLOURS", choice.getPath()); if
* (defaultColours.indexOf(choice.getPath()) == -1) { defaultColours =
* defaultColours.concat("|") .concat(choice.getPath()); } (non-Javadoc)
{
return;
}
- String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES", "");
+ String paramFiles = Cache.getDefault("WS_PARAM_FILES", "");
if (paramFiles.indexOf(filename) > -1)
{
String nparamFiles = new String();
nparamFiles = nparamFiles.concat("|").concat(fl);
}
}
- jalview.bin.Cache.setProperty("WS_PARAM_FILES", nparamFiles);
+ Cache.setProperty("WS_PARAM_FILES", nparamFiles);
}
try
}
} catch (Exception e)
{
- Cache.log.error(
+ Console.error(
"Exception when trying to delete webservice user preset: ",
e);
}
--- /dev/null
+package jalview.gui.structurechooser;
+
+import java.util.Locale;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+
+import javax.swing.JTable;
+import javax.swing.table.TableModel;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSDataColumnPreferences;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.jbgui.FilterOption;
+import jalview.util.MessageManager;
+
+/**
+ * logic for querying the PDBe API for structures of sequences
+ *
+ * @author jprocter
+ */
+public class PDBStructureChooserQuerySource
+ extends StructureChooserQuerySource
+{
+
+ private static int MAX_QLENGTH = 7820;
+
+ protected FTSRestRequest lastPdbRequest;
+
+ protected FTSRestClientI pdbRestClient;
+
+ public PDBStructureChooserQuerySource()
+ {
+ pdbRestClient = PDBFTSRestClient.getInstance();
+ docFieldPrefs = new FTSDataColumnPreferences(
+ PreferenceSource.STRUCTURE_CHOOSER,
+ PDBFTSRestClient.getInstance());
+
+ }
+
+
+ /**
+ * Builds a query string for a given sequences using its DBRef entries
+ *
+ * @param seq
+ * the sequences to build a query for
+ * @return the built query string
+ */
+
+ public String buildQuery(SequenceI seq)
+ {
+ boolean isPDBRefsFound = false;
+ boolean isUniProtRefsFound = false;
+ StringBuilder queryBuilder = new StringBuilder();
+ Set<String> seqRefs = new LinkedHashSet<>();
+
+ /*
+ * note PDBs as DBRefEntry so they are not duplicated in query
+ */
+ Set<String> pdbids = new HashSet<>();
+
+ if (seq.getAllPDBEntries() != null
+ && queryBuilder.length() < MAX_QLENGTH)
+ {
+ for (PDBEntry entry : seq.getAllPDBEntries())
+ {
+ if (isValidSeqName(entry.getId()))
+ {
+ String id = entry.getId().toLowerCase(Locale.ROOT);
+ queryBuilder.append("pdb_id:").append(id).append(" OR ");
+ isPDBRefsFound = true;
+ pdbids.add(id);
+ }
+ }
+ }
+
+ List<DBRefEntry> refs = seq.getDBRefs();
+ if (refs != null && refs.size() != 0)
+ {
+ for (int ib = 0, nb = refs.size(); ib < nb; ib++)
+ {
+ DBRefEntry dbRef = refs.get(ib);
+ if (isValidSeqName(getDBRefId(dbRef))
+ && queryBuilder.length() < MAX_QLENGTH)
+ {
+ if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+ {
+ queryBuilder.append("uniprot_accession:")
+ .append(getDBRefId(dbRef)).append(" OR ");
+ queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
+ .append(" OR ");
+ isUniProtRefsFound = true;
+ }
+ else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
+ {
+
+ String id = getDBRefId(dbRef).toLowerCase(Locale.ROOT);
+ if (!pdbids.contains(id))
+ {
+ queryBuilder.append("pdb_id:").append(id).append(" OR ");
+ isPDBRefsFound = true;
+ pdbids.add(id);
+ }
+ }
+ else
+ {
+ seqRefs.add(getDBRefId(dbRef));
+ }
+ }
+ }
+ }
+
+ if (!isPDBRefsFound && !isUniProtRefsFound)
+ {
+ String seqName = seq.getName();
+ seqName = sanitizeSeqName(seqName);
+ String[] names = seqName.toLowerCase(Locale.ROOT).split("\\|");
+ for (String name : names)
+ {
+ // System.out.println("Found name : " + name);
+ name.trim();
+ if (isValidSeqName(name))
+ {
+ seqRefs.add(name);
+ }
+ }
+
+ for (String seqRef : seqRefs)
+ {
+ queryBuilder.append("text:").append(seqRef).append(" OR ");
+ }
+ }
+
+ int endIndex = queryBuilder.lastIndexOf(" OR ");
+ if (queryBuilder.toString().length() < 6)
+ {
+ return null;
+ }
+ String query = queryBuilder.toString().substring(0, endIndex);
+ return query;
+ }
+
+ /**
+ * Remove the following special characters from input string +, -, &, !, (, ),
+ * {, }, [, ], ^, ", ~, *, ?, :, \
+ *
+ * @param seqName
+ * @return
+ */
+ public static String sanitizeSeqName(String seqName)
+ {
+ Objects.requireNonNull(seqName);
+ return seqName.replaceAll("\\[\\d*\\]", "")
+ .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
+ }
+
+ /**
+ * Ensures sequence ref names are not less than 3 characters and does not
+ * contain a database name
+ *
+ * @param seqName
+ * @return
+ */
+ static boolean isValidSeqName(String seqName)
+ {
+ // System.out.println("seqName : " + seqName);
+ String ignoreList = "pdb,uniprot,swiss-prot";
+ if (seqName.length() < 3)
+ {
+ return false;
+ }
+ if (seqName.contains(":"))
+ {
+ return false;
+ }
+ seqName = seqName.toLowerCase(Locale.ROOT);
+ for (String ignoredEntry : ignoreList.split(","))
+ {
+ if (seqName.contains(ignoredEntry))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ static String getDBRefId(DBRefEntry dbRef)
+ {
+ String ref = dbRef.getAccessionId().replaceAll("GO:", "");
+ return ref;
+ }
+
+ /**
+ * FTSRestClient specific query builder to recover associated structure data
+ * records for a sequence
+ *
+ * @param seq
+ * - seq to generate a query for
+ * @param wantedFields
+ * - fields to retrieve
+ * @param selectedFilterOpt
+ * - criterion for ranking results (e.g. resolution)
+ * @param b
+ * - sort ascending or descending
+ * @return
+ * @throws Exception
+ */
+ public FTSRestResponse fetchStructuresMetaData(SequenceI seq,
+ Collection<FTSDataColumnI> wantedFields,
+ FilterOption selectedFilterOpt, boolean b) throws Exception
+ {
+ FTSRestResponse resultList;
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(500);
+ pdbRequest.setFieldToSearchBy("(");
+ pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(), b);
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setAssociatedSequence(seq);
+ resultList = pdbRestClient.executeRequest(pdbRequest);
+
+ lastPdbRequest = pdbRequest;
+ return resultList;
+ }
+ public List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER)
+ {
+ List<FilterOption> filters = new ArrayList<FilterOption>();
+ filters.add(new FilterOption("PDBe "+
+ MessageManager.getString("label.best_quality"),
+ "overall_quality", VIEWS_FILTER, false,this));
+ filters.add(new FilterOption("PDBe "+
+ MessageManager.getString("label.best_resolution"),
+ "resolution", VIEWS_FILTER, false,this));
+ filters.add(new FilterOption("PDBe "+
+ MessageManager.getString("label.most_protein_chain"),
+ "number_of_protein_chains", VIEWS_FILTER, false,this));
+ filters.add(new FilterOption("PDBe "+
+ MessageManager.getString("label.most_bound_molecules"),
+ "number_of_bound_molecules", VIEWS_FILTER, false,this));
+ filters.add(new FilterOption("PDBe "+
+ MessageManager.getString("label.most_polymer_residues"),
+ "number_of_polymer_residues", VIEWS_FILTER, true,this));
+
+ return filters;
+ }
+
+ @Override
+ public boolean needsRefetch(FilterOption selectedFilterOpt)
+ {
+ // PDBe queries never need a refetch first
+ return false;
+ }
+
+ /**
+ * FTSRestClient specific query builder to pick top ranked entry from a
+ * fetchStructuresMetaData query
+ *
+ * @param seq
+ * - seq to generate a query for
+ * @param wantedFields
+ * - fields to retrieve
+ * @param selectedFilterOpt
+ * - criterion for ranking results (e.g. resolution)
+ * @param b
+ * - sort ascending or descending
+ * @return
+ * @throws Exception
+ */
+ public FTSRestResponse selectFirstRankedQuery(SequenceI seq, Collection<FTSData> collectedResults,
+ Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
+ boolean b) throws Exception
+ {
+
+ FTSRestResponse resultList;
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
+ {
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(");
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setAssociatedSequence(seq);
+ pdbRequest.setFacet(true);
+ pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
+ pdbRequest.setFacetPivotMinCount(1);
+ }
+ else
+ {
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(");
+ pdbRequest.setFieldToSortBy(fieldToFilterBy, b);
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setAssociatedSequence(seq);
+ }
+ resultList = pdbRestClient.executeRequest(pdbRequest);
+
+ lastPdbRequest = pdbRequest;
+ return resultList;
+ }
+
+
+ @Override
+ public PDBEntry[] collectSelectedRows(JTable restable, int[] selectedRows,
+ List<SequenceI> selectedSeqsToView)
+ {
+ int refSeqColIndex = restable.getColumn("Ref Sequence")
+ .getModelIndex();
+
+ PDBEntry[] pdbEntriesToView=new PDBEntry[selectedRows.length];
+ int count = 0;
+ int idColumnIndex=-1;
+ boolean fromTDB=true;
+ idColumnIndex = restable.getColumn("PDB Id").getModelIndex();
+
+ for (int row : selectedRows)
+ {
+
+ String pdbIdStr = restable.getValueAt(row,idColumnIndex)
+ .toString();
+ SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
+ refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
+ PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
+ if (pdbEntry == null)
+ {
+ pdbEntry = getFindEntry(pdbIdStr,
+ selectedSeq.getAllPDBEntries());
+ }
+
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType(PDBEntry.Type.MMCIF);
+ selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
+ }
+ pdbEntriesToView[count++] = pdbEntry;
+ }
+ return pdbEntriesToView;
+ }
+
+
+ @Override
+ protected FTSRestRequest getLastFTSRequest()
+ {
+ return lastPdbRequest;
+ }
+
+
+ public FTSRestResponse executePDBFTSRestRequest(FTSRestRequest pdbRequest) throws Exception
+ {
+ return pdbRestClient.executeRequest(pdbRequest);
+ }
+
+}
\ No newline at end of file
--- /dev/null
+package jalview.gui.structurechooser;
+
+import java.util.Locale;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Objects;
+import java.util.Vector;
+
+import javax.swing.JTable;
+import javax.swing.table.TableModel;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSDataColumnPreferences;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.jbgui.FilterOption;
+
+/**
+ * logic for querying sources of structural data for structures of sequences
+ *
+ * @author jprocter
+ *
+ * @param <T>
+ */
+public abstract class StructureChooserQuerySource
+{
+
+ protected FTSDataColumnPreferences docFieldPrefs;
+
+ /**
+ * max length of a GET URL (probably :( )
+ */
+ protected static int MAX_QLENGTH = 7820;
+
+ public StructureChooserQuerySource()
+ {
+ }
+
+ public static StructureChooserQuerySource getPDBfts()
+ {
+ return new PDBStructureChooserQuerySource();
+ }
+
+ public static StructureChooserQuerySource getTDBfts()
+ {
+ return new ThreeDBStructureChooserQuerySource();
+ }
+
+ public FTSDataColumnPreferences getDocFieldPrefs()
+ {
+ return docFieldPrefs;
+ }
+
+ public void setDocFieldPrefs(FTSDataColumnPreferences docFieldPrefs)
+ {
+ this.docFieldPrefs = docFieldPrefs;
+ }
+
+ public FTSDataColumnPreferences getInitialFieldPreferences()
+ {
+ return docFieldPrefs;
+ }
+
+ /**
+ * Builds a query string for a given sequences using its DBRef entries
+ *
+ * @param seq
+ * the sequences to build a query for
+ * @return the built query string
+ */
+
+ public abstract String buildQuery(SequenceI seq);
+
+ /**
+ * Remove the following special characters from input string +, -, &, !, (, ),
+ * {, }, [, ], ^, ", ~, *, ?, :, \
+ *
+ * @param seqName
+ * @return
+ */
+ public static String sanitizeSeqName(String seqName)
+ {
+ Objects.requireNonNull(seqName);
+ return seqName.replaceAll("\\[\\d*\\]", "")
+ .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
+ }
+
+ /**
+ * Ensures sequence ref names are not less than 3 characters and does not
+ * contain a database name
+ *
+ * @param seqName
+ * @return
+ */
+ static boolean isValidSeqName(String seqName)
+ {
+ // System.out.println("seqName : " + seqName);
+ String ignoreList = "pdb,uniprot,swiss-prot";
+ if (seqName.length() < 3)
+ {
+ return false;
+ }
+ if (seqName.contains(":"))
+ {
+ return false;
+ }
+ seqName = seqName.toLowerCase(Locale.ROOT);
+ for (String ignoredEntry : ignoreList.split(","))
+ {
+ if (seqName.contains(ignoredEntry))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ static String getDBRefId(DBRefEntry dbRef)
+ {
+ String ref = dbRef.getAccessionId().replaceAll("GO:", "");
+ return ref;
+ }
+
+ static PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
+ {
+ Objects.requireNonNull(id);
+ Objects.requireNonNull(pdbEntries);
+ PDBEntry foundEntry = null;
+ for (PDBEntry entry : pdbEntries)
+ {
+ if (entry.getId().equalsIgnoreCase(id))
+ {
+ return entry;
+ }
+ }
+ return foundEntry;
+ }
+
+ /**
+ * FTSRestClient specific query builder to recover associated structure data
+ * records for a sequence
+ *
+ * @param seq
+ * - seq to generate a query for
+ * @param wantedFields
+ * - fields to retrieve
+ * @param selectedFilterOpt
+ * - criterion for ranking results (e.g. resolution)
+ * @param b
+ * - sort ascending or descending
+ * @return
+ * @throws Exception
+ */
+ public abstract FTSRestResponse fetchStructuresMetaData(SequenceI seq,
+ Collection<FTSDataColumnI> wantedFields,
+ FilterOption selectedFilterOpt, boolean b) throws Exception;
+
+ /**
+ * FTSRestClient specific query builder to pick top ranked entry from a
+ * fetchStructuresMetaData query
+ *
+ * @param seq
+ * - seq to generate a query for
+ * @param discoveredStructuresSet
+ * - existing set of entries - allows client side selection
+ * @param wantedFields
+ * - fields to retrieve
+ * @param selectedFilterOpt
+ * - criterion for ranking results (e.g. resolution)
+ * @param b
+ * - sort ascending or descending
+ * @return
+ * @throws Exception
+ */
+ public abstract FTSRestResponse selectFirstRankedQuery(SequenceI seq,
+ Collection<FTSData> discoveredStructuresSet,
+ Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
+ boolean b) throws Exception;
+
+ /**
+ *
+ * @param discoveredStructuresSet
+ * @return the table model for the given result set for this engine
+ */
+ public TableModel getTableModel(
+ Collection<FTSData> discoveredStructuresSet)
+ {
+ return FTSRestResponse.getTableModel(getLastFTSRequest(),
+ discoveredStructuresSet);
+ }
+
+ protected abstract FTSRestRequest getLastFTSRequest();
+
+ public abstract PDBEntry[] collectSelectedRows(JTable restable,
+ int[] selectedRows, List<SequenceI> selectedSeqsToView);
+
+ /**
+ * @param VIEWS_FILTER
+ * - a String key that can be used by the caller to tag the returned
+ * filter options to distinguish them in a collection
+ * @return list of FilterOption - convention is that the last one in the list
+ * will be constructed with 'addSeparator==true'
+ */
+ public abstract List<FilterOption> getAvailableFilterOptions(
+ String VIEWS_FILTER);
+
+ /**
+ * construct a structure chooser query source for the given set of sequences
+ *
+ * @param selectedSeqs
+ * @return PDBe or 3DB query source
+ */
+ public static StructureChooserQuerySource getQuerySourceFor(
+ SequenceI[] selectedSeqs)
+ {
+ ThreeDBStructureChooserQuerySource tdbSource = new ThreeDBStructureChooserQuerySource();
+ boolean hasUniprot = false, hasCanonical = false;
+ boolean hasNA = false, hasProtein = false;
+ int protWithoutUni = 0;
+ int protWithoutCanon = 0;
+ for (SequenceI seq : selectedSeqs)
+ {
+ hasNA |= !seq.isProtein();
+ hasProtein |= seq.isProtein();
+ if (seq.isProtein())
+ {
+ int refsAvailable = ThreeDBStructureChooserQuerySource
+ .checkUniprotRefs(seq.getDBRefs());
+ if (refsAvailable > -2)
+ {
+ if (refsAvailable > -1)
+ {
+ hasCanonical = true;
+ } else {
+ protWithoutCanon++;
+ }
+ hasUniprot = true;
+ } else {
+ protWithoutUni++;
+
+ }
+ }
+ }
+ //
+ // logic: all canonicals - no fetchdb
+ // some uniprot no canonicals: defer to PDB, user can optionally fetch
+ //
+ if (hasProtein && hasCanonical && !hasNA && protWithoutCanon == 0 && protWithoutUni == 0)
+
+ {
+ return tdbSource;
+ }
+ return new PDBStructureChooserQuerySource();
+ }
+
+ /**
+ * some filter options may mean the original query needs to be executed again.
+ *
+ * @param selectedFilterOpt
+ * @return true if the fetchStructuresMetadata method needs to be called again
+ */
+ public abstract boolean needsRefetch(FilterOption selectedFilterOpt);
+
+ public void updateAvailableFilterOptions(String VIEWS_FILTER,
+ List<FilterOption> xtantOptions, Collection<FTSData> lastFTSData)
+ {
+ // TODO Auto-generated method stub
+
+ }
+}
\ No newline at end of file
--- /dev/null
+package jalview.gui.structurechooser;
+
+import java.util.Locale;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.core.FTSRestRequest;
+
+public class TDBResultAnalyser
+{
+
+ /**
+ * model categories - update as needed. warnings output if unknown types
+ * encountered.
+ *
+ * Order denotes 'trust'
+ */
+ private static List<String> EXP_CATEGORIES = Arrays
+ .asList(new String[]
+ { "EXPERIMENTALLY DETERMINED", "DEEP-LEARNING", "TEMPLATE-BASED",
+ "AB-INITIO", "CONFORMATIONAL ENSEMBLE" });
+
+ private SequenceI seq;
+
+ private Collection<FTSData> collectedResults;
+
+ private FTSRestRequest lastTdbRequest;
+
+ private int idx_ups;
+
+ private int idx_upe;
+
+ private int idx_mcat;
+
+ private int idx_mqual;
+
+ private int idx_resol;
+
+ /**
+ * selection model
+ */
+ private String filter = null;
+
+ /**
+ * limit to particular source
+ */
+ private String sourceFilter = null;
+
+ private int idx_mprov;
+
+ public TDBResultAnalyser(SequenceI seq,
+ Collection<FTSData> collectedResults,
+ FTSRestRequest lastTdbRequest, String fieldToFilterBy,
+ String string)
+ {
+ this.seq = seq;
+ this.collectedResults = collectedResults;
+ this.lastTdbRequest = lastTdbRequest;
+ this.filter = fieldToFilterBy;
+ this.sourceFilter = string;
+ idx_ups = lastTdbRequest.getFieldIndex("Uniprot Start");
+ idx_upe = lastTdbRequest.getFieldIndex("Uniprot End");
+ idx_mcat = lastTdbRequest.getFieldIndex("Model Category");
+ idx_mprov = lastTdbRequest.getFieldIndex("Provider");
+ idx_mqual = lastTdbRequest.getFieldIndex("Confidence");
+ idx_resol = lastTdbRequest.getFieldIndex("Resolution");
+ }
+
+ /**
+ * maintain and resolve categories to 'trust order' TODO: change the trust
+ * scheme to something comprehensible.
+ *
+ * @param cat
+ * @return 0 for null cat, less than zero for others
+ */
+ public final int scoreCategory(String cat)
+ {
+ if (cat == null)
+ {
+ return 0;
+ }
+ String upper_cat = cat.toUpperCase(Locale.ROOT);
+ int idx = EXP_CATEGORIES.indexOf(upper_cat);
+ if (idx == -1)
+ {
+ System.out.println("Unknown category: '" + cat + "'");
+ EXP_CATEGORIES.add(upper_cat);
+ idx = EXP_CATEGORIES.size() - 1;
+ }
+ return -EXP_CATEGORIES.size() - idx;
+ }
+
+ /**
+ * sorts records discovered by 3D beacons and excludes any that don't
+ * intersect with the sequence's start/end rage
+ *
+ * @return
+ */
+ public List<FTSData> getFilteredResponse()
+ {
+ List<FTSData> filteredResponse = new ArrayList<FTSData>();
+
+ // ignore anything outside the sequence region
+ for (FTSData row : collectedResults)
+ {
+ int up_s = (Integer) row.getSummaryData()[idx_ups];
+ int up_e = (Integer) row.getSummaryData()[idx_upe];
+ String provider = (String) row.getSummaryData()[idx_mprov];
+ String mcat = (String) row.getSummaryData()[idx_mcat];
+ // this makes sure all new categories are in the score array.
+ int scorecat = scoreCategory(mcat);
+ if (sourceFilter == null || sourceFilter.equals(provider))
+ {
+ if (seq == row.getSummaryData()[0] && up_e > seq.getStart()
+ && up_s < seq.getEnd())
+ {
+ filteredResponse.add(row);
+ }
+ }
+ }
+ // sort according to decreasing length,
+ // increasing start
+ Collections.sort(filteredResponse, new Comparator<FTSData>()
+ {
+ @Override
+ public int compare(FTSData o1, FTSData o2)
+ {
+ Object[] o1data = o1.getSummaryData();
+ Object[] o2data = o2.getSummaryData();
+ int o1_s = (Integer) o1data[idx_ups];
+ int o1_e = (Integer) o1data[idx_upe];
+ int o1_cat = scoreCategory((String) o1data[idx_mcat]);
+ String o1_prov= ((String) o1data[idx_mprov]).toUpperCase(Locale.ROOT);
+ int o2_s = (Integer) o2data[idx_ups];
+ int o2_e = (Integer) o2data[idx_upe];
+ int o2_cat = scoreCategory((String) o2data[idx_mcat]);
+ String o2_prov= ((String) o2data[idx_mprov]).toUpperCase(Locale.ROOT);
+
+
+ if (o1_cat == o2_cat)
+ {
+ if (o1_s == o2_s)
+ {
+ int o1_xtent = o1_e - o1_s;
+ int o2_xtent = o2_e - o2_s;
+ if (o1_xtent == o2_xtent)
+ {
+ if (o1_cat == scoreCategory(EXP_CATEGORIES.get(0)))
+ {
+ if (o1_prov.equals(o2_prov)) {
+ if ("PDBE".equals(o1_prov)) {
+ if (eitherNull(idx_resol,o1data,o2data))
+ {
+ return nonNullFirst(idx_resol,o1data,o2data);
+ }
+ // experimental structures, so rank on quality
+ double o1_res = (Double) o1data[idx_resol];
+ double o2_res = (Double) o2data[idx_resol];
+ return (o2_res < o1_res) ? 1 : (o2_res == o1_res) ? 0 : -1;
+ } else {
+ return 0; // no change in order
+ }
+ } else {
+ // PDBe always ranked above all other experimentally determined categories
+ return "PDBE".equals(o1_prov) ? -1 : "PDBE".equals(o2_prov) ? 1 : 0;
+ }
+ }
+ else
+ {
+ if (eitherNull(idx_mqual,o1data, o2data)) {
+ return nonNullFirst(idx_mqual, o1data, o2data);
+ }
+ // models, so rank on qmean - b
+ double o1_mq = (Double) o1data[idx_mqual];
+ double o2_mq = (Double) o2data[idx_mqual];
+ return (o2_mq < o1_mq) ? 1 : (o2_mq == o1_mq) ? 0 : -1;
+ }
+ }
+ else
+ {
+ return o1_xtent - o2_xtent;
+ }
+ }
+ else
+ {
+ return o1_s - o2_s;
+ }
+ }
+ else
+ {
+ return o2_cat - o1_cat;
+ }
+ }
+
+ private int nonNullFirst(int idx_resol, Object[] o1data,
+ Object[] o2data)
+ {
+ return o1data[idx_resol] == o2data[idx_resol] ? 0: o1data[idx_resol] != null ? -1 : 1;
+ }
+
+ private boolean eitherNull(int idx_resol, Object[] o1data,
+ Object[] o2data)
+ {
+ return (o1data[idx_resol] == null || o2data[idx_resol]==null);
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ return super.equals(obj);
+ }
+ });
+ return filteredResponse;
+ }
+
+ /**
+ * return list of structures to be marked as selected for this sequence
+ * according to given criteria
+ *
+ * @param filteredStructures
+ * - sorted, filtered structures from getFilteredResponse
+ *
+ */
+ public List<FTSData> selectStructures(List<FTSData> filteredStructures)
+ {
+ List<FTSData> selected = new ArrayList<FTSData>();
+ BitSet cover = new BitSet();
+ cover.set(seq.getStart(), seq.getEnd());
+ // walk down the list of structures, selecting some to add to selected
+ // TODO: could do simple DP - double loop to select largest number of
+ // structures covering largest number of sites
+ for (FTSData structure : filteredStructures)
+ {
+ Object[] odata = structure.getSummaryData();
+ int o1_s = (Integer) odata[idx_ups];
+ int o1_e = (Integer) odata[idx_upe];
+ int o1_cat = scoreCategory((String) odata[idx_mcat]);
+ BitSet scover = new BitSet();
+ // measure intersection
+ scover.set(o1_s, o1_e);
+ scover.and(cover);
+ if (scover.cardinality() > 4)
+ {
+ selected.add(structure);
+ // clear the range covered by this structure
+ cover.andNot(scover);
+ }
+ }
+ if (selected.size()==0)
+ {
+ return selected;
+ }
+ // final step is to sort on length - this might help the superposition
+ // process
+ Collections.sort(selected, new Comparator<FTSData>()
+ {
+ @Override
+ public int compare(FTSData o1, FTSData o2)
+ {
+ Object[] o1data = o1.getSummaryData();
+ Object[] o2data = o2.getSummaryData();
+ int o1_xt = ((Integer) o1data[idx_upe])
+ - ((Integer) o1data[idx_ups]);
+ int o1_cat = scoreCategory((String) o1data[idx_mcat]);
+ int o2_xt = ((Integer) o2data[idx_upe] - (Integer) o2data[idx_ups]);
+ int o2_cat = scoreCategory((String) o2data[idx_mcat]);
+ return o2_xt - o1_xt;
+ }
+ });
+ if (filter.equals(
+ ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE))
+ {
+ return selected.subList(0, 1);
+ }
+ return selected;
+ }
+
+}
--- /dev/null
+package jalview.gui.structurechooser;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Locale;
+import java.util.Set;
+
+import javax.swing.JTable;
+
+import jalview.bin.Console;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSDataColumnPreferences;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.threedbeacons.TDB_FTSData;
+import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
+import jalview.jbgui.FilterOption;
+
+/**
+ * logic for querying the 3DBeacons API for structures of sequences
+ *
+ * @author jprocter
+ */
+public class ThreeDBStructureChooserQuerySource
+ extends StructureChooserQuerySource
+{
+
+ private Set<String> tdBeaconsFilters = null, defaultFilters = null;
+
+ public static final String FILTER_TDBEACONS_COVERAGE = "3d_beacons_coverage";
+
+ public static final String FILTER_FIRST_BEST_COVERAGE = "3d_beacons_first_best_coverage";
+
+ private static final String FILTER_SOURCE_PREFIX = "only_";
+
+ protected FTSRestRequest lastTdbRequest;
+
+ protected FTSRestClientI tdbRestClient;
+
+ private FTSRestRequest lastPdbRequest;
+
+ public ThreeDBStructureChooserQuerySource()
+ {
+ defaultFilters = new LinkedHashSet<String>();
+ defaultFilters.add(FILTER_TDBEACONS_COVERAGE);
+ defaultFilters.add(FILTER_FIRST_BEST_COVERAGE);
+
+ tdbRestClient = TDBeaconsFTSRestClient.getInstance();
+ docFieldPrefs = new FTSDataColumnPreferences(
+ PreferenceSource.STRUCTURE_CHOOSER,
+ TDBeaconsFTSRestClient.getInstance());
+ }
+
+ /**
+ * Builds a query string for a given sequences using its DBRef entries 3d
+ * Beacons is only useful for uniprot IDs
+ *
+ * @param seq
+ * the sequences to build a query for
+ * @return the built query string
+ */
+
+ public String buildQuery(SequenceI seq)
+ {
+ List<DBRefEntry> refs = seq.getDBRefs();
+ int ib = checkUniprotRefs(refs);
+ if (ib > -1)
+ {
+ return getDBRefId(refs.get(ib));
+ }
+ return null;
+ }
+
+ /**
+ * Searches DBRefEntry for uniprot refs
+ *
+ * @param seq
+ * @return -2 if no uniprot refs, -1 if no canonical ref., otherwise index of
+ * Uniprot canonical DBRefEntry
+ */
+ public static int checkUniprotRefs(List<DBRefEntry> refs)
+ {
+ boolean hasUniprot = false;
+ if (refs != null && refs.size() != 0)
+ {
+ for (int ib = 0, nb = refs.size(); ib < nb; ib++)
+ {
+ DBRefEntry dbRef = refs.get(ib);
+ if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+ {
+ hasUniprot = true;
+ if (dbRef.isCanonical())
+ {
+ return ib;
+ }
+ }
+ }
+ }
+ return hasUniprot ? -1 : -2;
+ }
+
+ /**
+ * Ensures sequence ref names are not less than 3 characters and does not
+ * contain a database name
+ *
+ * @param seqName
+ * @return
+ */
+ static boolean isValidSeqName(String seqName)
+ {
+ String ignoreList = "pdb,uniprot,swiss-prot";
+ if (seqName.length() < 3)
+ {
+ return false;
+ }
+ if (seqName.contains(":"))
+ {
+ return false;
+ }
+ seqName = seqName.toLowerCase(Locale.ROOT);
+ for (String ignoredEntry : ignoreList.split(","))
+ {
+ if (seqName.contains(ignoredEntry))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ static String getDBRefId(DBRefEntry dbRef)
+ {
+ String ref = dbRef.getAccessionId().replaceAll("GO:", "");
+ return ref;
+ }
+
+ /**
+ * FTSRestClient specific query builder to recover associated structure data
+ * records for a sequence
+ *
+ * @param seq
+ * - seq to generate a query for
+ * @param wantedFields
+ * - fields to retrieve
+ * @param selectedFilterOpt
+ * - criterion for ranking results (e.g. resolution)
+ * @param b
+ * - sort ascending or descending
+ * @return
+ * @throws Exception
+ */
+ public FTSRestResponse fetchStructuresMetaData(SequenceI seq,
+ Collection<FTSDataColumnI> wantedFields,
+ FilterOption selectedFilterOpt, boolean b) throws Exception
+ {
+ FTSRestResponse resultList;
+ if (selectedFilterOpt != null
+ && tdBeaconsFilter(selectedFilterOpt.getValue()))
+ {
+ FTSRestRequest tdbRequest = getTDBeaconsRequest(seq, wantedFields);
+ resultList = tdbRestClient.executeRequest(tdbRequest);
+
+ lastTdbRequest = tdbRequest;
+ if (resultList != null)
+ { // Query the PDB and add additional metadata
+ FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(
+ getPDBQuerySource(), resultList);
+
+ resultList = joinResponses(resultList, pdbResponse);
+ }
+ return resultList;
+ }
+ // use the PDBFTS directly
+ resultList = getPDBQuerySource().fetchStructuresMetaData(seq,
+ wantedFields, selectedFilterOpt, b);
+ lastTdbRequest = getPDBQuerySource().lastPdbRequest;
+ lastPdbRequest = lastTdbRequest; // both queries the same - indicates we
+ // rank using PDBe
+ return resultList;
+
+ }
+
+ PDBStructureChooserQuerySource pdbQuerySource = null;
+
+ private PDBStructureChooserQuerySource getPDBQuerySource()
+ {
+ if (pdbQuerySource == null)
+ {
+ pdbQuerySource = new PDBStructureChooserQuerySource();
+ }
+ return pdbQuerySource;
+ }
+
+ private FTSRestRequest getTDBeaconsRequest(SequenceI seq,
+ Collection<FTSDataColumnI> wantedFields)
+ {
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(500);
+ pdbRequest.setWantedFields(wantedFields);
+ String query = buildQuery(seq);
+ if (query == null)
+ {
+ return null;
+ }
+ pdbRequest.setSearchTerm(query + ".json");
+ pdbRequest.setAssociatedSequence(seq);
+ return pdbRequest;
+ }
+
+ @Override
+ public List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER)
+ {
+ List<FilterOption> filters = getPDBQuerySource()
+ .getAvailableFilterOptions(VIEWS_FILTER);
+ tdBeaconsFilters = new LinkedHashSet<String>();
+ tdBeaconsFilters.addAll(defaultFilters);
+ filters.add(0, new FilterOption("Best 3D-Beacons Coverage",
+ FILTER_FIRST_BEST_COVERAGE, VIEWS_FILTER, false, this));
+ filters.add(1, new FilterOption("Multiple 3D-Beacons Coverage",
+ FILTER_TDBEACONS_COVERAGE, VIEWS_FILTER, true, this));
+
+ return filters;
+ }
+
+ @Override
+ public void updateAvailableFilterOptions(String VIEWS_FILTER,
+ List<FilterOption> xtantOptions, Collection<FTSData> tdbEntries)
+ {
+ if (tdbEntries != null && lastTdbRequest != null)
+ {
+ boolean hasPDBe = false;
+ for (FTSData _row : tdbEntries)
+ {
+ // tdb returns custom object
+ TDB_FTSData row = (TDB_FTSData) _row;
+ String provider = (String) row.getProvider();
+ FilterOption providerOpt = new FilterOption(
+ "3DB Provider - " + provider,
+ FILTER_SOURCE_PREFIX + provider, VIEWS_FILTER, false, this);
+ if (!xtantOptions.contains(providerOpt))
+ {
+ xtantOptions.add(1, providerOpt);
+ tdBeaconsFilters.add(FILTER_SOURCE_PREFIX + provider);
+ if ("PDBe".equalsIgnoreCase(provider))
+ {
+ hasPDBe = true;
+ }
+ }
+ }
+ if (!hasPDBe)
+ {
+ // remove the PDBe options from the available filters
+ int op = 0;
+ while (op < xtantOptions.size())
+ {
+ FilterOption filter = xtantOptions.get(op);
+ if (filter
+ .getQuerySource() instanceof PDBStructureChooserQuerySource)
+ {
+ xtantOptions.remove(op);
+ }
+ else
+ {
+ op++;
+ }
+ }
+ }
+ }
+
+ }
+
+ private boolean tdBeaconsFilter(String fieldToFilterBy)
+ {
+ return tdBeaconsFilters != null
+ && tdBeaconsFilters.contains(fieldToFilterBy);
+ }
+
+ private String remove_prefix(String fieldToFilterBy)
+ {
+ if (tdBeaconsFilters != null
+ && tdBeaconsFilters.contains(fieldToFilterBy)
+ && !defaultFilters.contains(fieldToFilterBy))
+ {
+ return fieldToFilterBy.substring(FILTER_SOURCE_PREFIX.length());
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ @Override
+ public boolean needsRefetch(FilterOption selectedFilterOpt)
+ {
+ return selectedFilterOpt == null
+ || !tdBeaconsFilter(selectedFilterOpt.getValue())
+ && lastPdbRequest != lastTdbRequest;
+ }
+
+ /**
+ * FTSRestClient specific query builder to pick top ranked entry from a
+ * fetchStructuresMetaData query
+ *
+ * @param seq
+ * - seq to generate a query for
+ * @param wantedFields
+ * - fields to retrieve
+ * @param selectedFilterOpt
+ * - criterion for ranking results (e.g. resolution)
+ * @param b
+ * - sort ascending or descending
+ * @return
+ * @throws Exception
+ */
+ public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
+ Collection<FTSData> collectedResults,
+ Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
+ boolean b) throws Exception
+ {
+ if (fieldToFilterBy != null && tdBeaconsFilter(fieldToFilterBy))
+ {
+ TDBResultAnalyser analyser = new TDBResultAnalyser(seq,
+ collectedResults, lastTdbRequest, fieldToFilterBy,
+ remove_prefix(fieldToFilterBy));
+
+ FTSRestResponse resultList = new FTSRestResponse();
+
+ List<FTSData> filteredResponse = analyser.getFilteredResponse();
+
+ List<FTSData> selectedStructures = analyser
+ .selectStructures(filteredResponse);
+ resultList.setNumberOfItemsFound(selectedStructures.size());
+ resultList.setSearchSummary(selectedStructures);
+ return resultList;
+ }
+ // Fall back to PDBe rankings
+ return getPDBQuerySource().selectFirstRankedQuery(seq, collectedResults,
+ wantedFields, fieldToFilterBy, b);
+ }
+
+ @Override
+ public PDBEntry[] collectSelectedRows(JTable restable, int[] selectedRows,
+ List<SequenceI> selectedSeqsToView)
+ {
+ int refSeqColIndex = restable.getColumn("Ref Sequence").getModelIndex();
+
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ int idColumnIndex = restable.getColumn("Model id").getModelIndex();
+ int urlColumnIndex = restable.getColumn("Url").getModelIndex();
+ int typeColumnIndex = restable.getColumn("Provider").getModelIndex();
+ int humanUrl = restable.getColumn("Page URL").getModelIndex();
+ int modelformat = restable.getColumn("Model Format").getModelIndex();
+ final int up_start_idx = restable.getColumn("Uniprot Start")
+ .getModelIndex();
+ final int up_end_idx = restable.getColumn("Uniprot End")
+ .getModelIndex();
+ int i = 0;
+
+ // bleugh!
+ Integer[] sellist = new Integer[selectedRows.length];
+ for (Integer row : selectedRows)
+ {
+ sellist[i++] = row;
+ }
+ // Sort rows by coverage
+ Arrays.sort(sellist, new Comparator<Integer>()
+ {
+ @Override
+ public int compare(Integer o1, Integer o2)
+ {
+ int o1_xt = ((Integer) restable.getValueAt(o1, up_end_idx))
+ - (Integer) restable.getValueAt(o1, up_start_idx);
+ int o2_xt = ((Integer) restable.getValueAt(o2, up_end_idx))
+ - (Integer) restable.getValueAt(o2, up_start_idx);
+ return o2_xt - o1_xt;
+ }
+ });
+
+ for (int row : sellist)
+ {
+ // unique id - could be a horrible hash
+
+ String pdbIdStr = restable.getValueAt(row, idColumnIndex).toString();
+ String urlStr = restable.getValueAt(row, urlColumnIndex).toString();
+ String typeColumn = restable.getValueAt(row, typeColumnIndex)
+ .toString();
+ String modelPage = humanUrl < 1 ? null
+ : (String) restable.getValueAt(row, humanUrl);
+ String strucFormat = restable.getValueAt(row, modelformat).toString();
+
+ SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
+ refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
+ PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
+ if (pdbEntry == null)
+ {
+ pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries());
+ }
+
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setAuthoritative(true);
+ try
+ {
+ pdbEntry.setType(PDBEntry.Type.valueOf(strucFormat));
+ } catch (Exception q)
+ {
+ Console.warn("Unknown filetype for 3D Beacons Model from: "
+ + strucFormat + " - " + pdbIdStr + " - " + modelPage);
+ }
+
+ if (!"PDBe".equalsIgnoreCase(typeColumn))
+ {
+ pdbEntry.setRetrievalUrl(urlStr);
+ }
+ pdbEntry.setProvider(typeColumn);
+ pdbEntry.setProviderPage(modelPage);
+ selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
+ }
+ pdbEntriesToView[count++] = pdbEntry;
+ }
+ return pdbEntriesToView;
+ }
+
+ @Override
+ protected FTSRestRequest getLastFTSRequest()
+ {
+ return lastTdbRequest;
+ }
+
+ /**
+ * generate a query for PDBFTS to retrieve structure metadata
+ *
+ * @param ftsRestRequest
+ * @param upResponse
+ * @return
+ */
+
+ public String buildPDBFTSQueryFor(FTSRestResponse upResponse)
+ {
+ Set<String> pdbIds = new HashSet<String>();
+ int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
+ int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
+ for (FTSData row : upResponse.getSearchSummary())
+ {
+ String id = (String) row.getSummaryData()[idx_modelId];
+ String provider = (String) row.getSummaryData()[idx_provider];
+ if ("PDBe".equalsIgnoreCase(provider))
+ {
+ pdbIds.add(id);
+ }
+ }
+ return String.join(" OR ", pdbIds).toString();
+ }
+
+ /**
+ * query PDBe for structure metadata
+ *
+ * @param pdbquery
+ * @param upResponse
+ * @return FTSRestResponse via PDBStructureChooserQuerySource
+ */
+ public FTSRestResponse fetchStructuresMetaDataFor(
+ PDBStructureChooserQuerySource pdbquery,
+ FTSRestResponse upResponse) throws Exception
+ {
+
+ String pdb_Query = buildPDBFTSQueryFor(upResponse);
+ if (pdb_Query.length() == 0)
+ {
+ return null;
+ }
+ FTSRestResponse resultList;
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(500);
+ pdbRequest.setFieldToSearchBy("(");
+ // pdbRequest.setFieldToSortBy("pdb_id");
+ pdbRequest.setWantedFields(
+ pdbquery.getDocFieldPrefs().getStructureSummaryFields());
+ pdbRequest.setSearchTerm(pdb_Query + ")");
+
+ resultList = pdbquery.executePDBFTSRestRequest(pdbRequest);
+
+ lastPdbRequest = pdbRequest;
+ return resultList;
+ }
+
+ public FTSRestResponse joinResponses(FTSRestResponse upResponse,
+ FTSRestResponse pdbResponse)
+ {
+ boolean hasPdbResp = lastPdbRequest != null;
+
+ int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
+ // join on
+ int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
+ int pdbIdx = hasPdbResp ? lastPdbRequest.getFieldIndex("PDB Id") : -1;
+ int pdbTitle_idx = hasPdbResp ? lastPdbRequest.getFieldIndex("Title")
+ : -1;
+ int tdbTitle_idx = getLastFTSRequest().getFieldIndex("Title");
+
+ for (final FTSData row : upResponse.getSearchSummary())
+ {
+ String id = (String) row.getSummaryData()[idx_modelId];
+ String provider = (String) row.getSummaryData()[idx_provider];
+ if ("PDBe".equalsIgnoreCase(provider))
+ {
+ if (!hasPdbResp)
+ {
+ System.out.println(
+ "Warning: seems like we couldn't get to the PDBe search interface.");
+ }
+ else
+ {
+ for (final FTSData pdbrow : pdbResponse.getSearchSummary())
+ {
+ String pdbid = (String) pdbrow.getSummaryData()[pdbIdx];
+ if (id.equalsIgnoreCase(pdbid))
+ {
+ row.getSummaryData()[tdbTitle_idx] = pdbrow
+ .getSummaryData()[pdbTitle_idx];
+ }
+ }
+ }
+
+ }
+ else
+ {
+ row.getSummaryData()[tdbTitle_idx] = "Model from TDB";
+ }
+ }
+ return upResponse;
+ }
+
+ public TDB_FTSData getFTSDataFor(JTable restable, int selectedRow,
+ Collection<FTSData> discoveredStructuresSet)
+ {
+ int idColumnIndex = restable.getColumn("Model id").getModelIndex();
+
+ String modelId = (String) restable.getValueAt(selectedRow,
+ idColumnIndex);
+ for (FTSData row : discoveredStructuresSet)
+ {
+ if (row instanceof TDB_FTSData
+ && ((TDB_FTSData) row).getModelId().equals(modelId))
+ {
+ return ((TDB_FTSData) row);
+ }
+ }
+ return null;
+ }
+
+}
\ No newline at end of file
*/
package jalview.io;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-
import java.io.IOException;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.List;
import java.util.Vector;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
/**
* DOCUMENT ME!
*
private boolean parseImmediately = true;
+ private boolean dataClosed = false;
+
/**
* @return if doParse() was called at construction time
*/
public AlignFile(boolean parseImmediately, FileParse source)
throws IOException
{
+ this(parseImmediately, source, true);
+ }
+
+ public AlignFile(boolean parseImmediately, FileParse source,
+ boolean closeData) throws IOException
+ {
super(source);
initData();
if (parseImmediately)
{
- doParse();
+ doParse(closeData);
}
}
*/
public void doParse() throws IOException
{
+ doParse(true);
+ }
+
+ public void doParse(boolean closeData) throws IOException
+ {
if (parseCalled)
{
throw new IOException(
}
parseCalled = true;
parse();
+ if (closeData && !dataClosed)
+ {
+ dataIn.close();
+ dataClosed = true;
+ }
}
/**
import java.util.ArrayList;
import java.util.BitSet;
import java.util.Enumeration;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
if (rowset != null && rowset.size() > 0)
{
AlignmentAnnotation alan = null;
- for (int elm = 0, elmSize = rowset
- .size(); elm < elmSize; elm++)
+ for (int elm = 0,
+ elmSize = rowset.size(); elm < elmSize; elm++)
{
alan = (AlignmentAnnotation) rowset.elementAt(elm);
alan.groupRef = theGroup;
}
String name = st.nextToken();
- SequenceGroup sg = null;
- for (SequenceGroup _sg : al.getGroups())
+
+ Map<String, String> properties = new HashMap<>();
+ while (st.hasMoreTokens())
{
- if ((sg = _sg).getName().equals(name))
- {
- break;
- }
- else
+ String keyValue = st.nextToken();
+ String key = keyValue.substring(0, keyValue.indexOf("="));
+ String value = keyValue.substring(keyValue.indexOf("=") + 1);
+ properties.put(key, value);
+ }
+
+ for (SequenceGroup sg : al.getGroups())
+ {
+ if (sg.getName().equals(name))
{
- sg = null;
+ addProperties(sg, properties, al);
}
}
+ }
- if (sg != null)
+ /**
+ * Helper method that applies any specified properties to a SequenceGroup
+ *
+ * @param sg
+ * @param properties
+ * @param al
+ */
+ private void addProperties(SequenceGroup sg,
+ Map<String, String> properties, AlignmentI al)
+ {
+ ColourSchemeI def = sg.getColourScheme();
+ for (String key : properties.keySet())
{
- String keyValue, key, value;
- ColourSchemeI def = sg.getColourScheme();
- while (st.hasMoreTokens())
+ String value = properties.get(key);
+ if (key.equalsIgnoreCase("description"))
{
- keyValue = st.nextToken();
- key = keyValue.substring(0, keyValue.indexOf("="));
- value = keyValue.substring(keyValue.indexOf("=") + 1);
-
- if (key.equalsIgnoreCase("description"))
- {
- sg.setDescription(value);
- }
- else if (key.equalsIgnoreCase("colour"))
- {
- // TODO need to notify colourscheme of view reference once it is
- // available
- sg.cs.setColourScheme(
- ColourSchemeProperty.getColourScheme(null, al, value));
- }
- else if (key.equalsIgnoreCase("pidThreshold"))
- {
- sg.cs.setThreshold(Integer.parseInt(value), true);
+ sg.setDescription(value);
+ }
+ else if (key.equalsIgnoreCase("colour"))
+ {
+ // TODO need to notify colourscheme of view reference once it is
+ // available
+ sg.cs.setColourScheme(
+ ColourSchemeProperty.getColourScheme(null, al, value));
+ }
+ else if (key.equalsIgnoreCase("pidThreshold"))
+ {
+ sg.cs.setThreshold(Integer.parseInt(value), true);
- }
- else if (key.equalsIgnoreCase("consThreshold"))
- {
- sg.cs.setConservationInc(Integer.parseInt(value));
- Conservation c = new Conservation("Group", sg.getSequences(null),
- sg.getStartRes(), sg.getEndRes() + 1);
+ }
+ else if (key.equalsIgnoreCase("consThreshold"))
+ {
+ sg.cs.setConservationInc(Integer.parseInt(value));
+ Conservation c = new Conservation("Group", sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes() + 1);
- c.calculate();
- c.verdict(false, 25); // TODO: refer to conservation percent threshold
+ c.calculate();
+ c.verdict(false, 25); // TODO: refer to conservation percent threshold
- sg.cs.setConservation(c);
+ sg.cs.setConservation(c);
- }
- else if (key.equalsIgnoreCase("outlineColour"))
- {
- sg.setOutlineColour(ColorUtils.parseColourString(value));
- }
- else if (key.equalsIgnoreCase("displayBoxes"))
- {
- sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());
- }
- else if (key.equalsIgnoreCase("showUnconserved"))
- {
- sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());
- }
- else if (key.equalsIgnoreCase("displayText"))
- {
- sg.setDisplayText(Boolean.valueOf(value).booleanValue());
- }
- else if (key.equalsIgnoreCase("colourText"))
- {
- sg.setColourText(Boolean.valueOf(value).booleanValue());
- }
- else if (key.equalsIgnoreCase("textCol1"))
- {
- sg.textColour = ColorUtils.parseColourString(value);
- }
- else if (key.equalsIgnoreCase("textCol2"))
- {
- sg.textColour2 = ColorUtils.parseColourString(value);
- }
- else if (key.equalsIgnoreCase("textColThreshold"))
- {
- sg.thresholdTextColour = Integer.parseInt(value);
- }
- else if (key.equalsIgnoreCase("idColour"))
- {
- Color idColour = ColorUtils.parseColourString(value);
- sg.setIdColour(idColour == null ? Color.black : idColour);
- }
- else if (key.equalsIgnoreCase("hide"))
- {
- // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
- sg.setHidereps(true);
- }
- else if (key.equalsIgnoreCase("hidecols"))
- {
- // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
- sg.setHideCols(true);
- }
- sg.recalcConservation();
}
- if (sg.getColourScheme() == null)
+ else if (key.equalsIgnoreCase("outlineColour"))
{
- sg.setColourScheme(def);
+ sg.setOutlineColour(ColorUtils.parseColourString(value));
}
+ else if (key.equalsIgnoreCase("displayBoxes"))
+ {
+ sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());
+ }
+ else if (key.equalsIgnoreCase("showUnconserved"))
+ {
+ sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());
+ }
+ else if (key.equalsIgnoreCase("displayText"))
+ {
+ sg.setDisplayText(Boolean.valueOf(value).booleanValue());
+ }
+ else if (key.equalsIgnoreCase("colourText"))
+ {
+ sg.setColourText(Boolean.valueOf(value).booleanValue());
+ }
+ else if (key.equalsIgnoreCase("textCol1"))
+ {
+ sg.textColour = ColorUtils.parseColourString(value);
+ }
+ else if (key.equalsIgnoreCase("textCol2"))
+ {
+ sg.textColour2 = ColorUtils.parseColourString(value);
+ }
+ else if (key.equalsIgnoreCase("textColThreshold"))
+ {
+ sg.thresholdTextColour = Integer.parseInt(value);
+ }
+ else if (key.equalsIgnoreCase("idColour"))
+ {
+ Color idColour = ColorUtils.parseColourString(value);
+ sg.setIdColour(idColour == null ? Color.black : idColour);
+ }
+ else if (key.equalsIgnoreCase("hide"))
+ {
+ // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
+ sg.setHidereps(true);
+ }
+ else if (key.equalsIgnoreCase("hidecols"))
+ {
+ // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
+ sg.setHideCols(true);
+ }
+ sg.recalcConservation();
+ }
+
+ if (sg.getColourScheme() == null)
+ {
+ sg.setColourScheme(def);
}
}
*/
package jalview.io;
+import java.util.Locale;
+
import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Alignment;
String data = dataObject.toString();
DataSourceType protocol = DataSourceType.PASTE;
- String ft = data.toLowerCase().trim();
+ String ft = data.toLowerCase(Locale.ROOT).trim();
if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
|| ft.indexOf("file:") == 0)
{
import java.util.TreeMap;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
{
String tempfilename = file.getName();
File tempdir = file.getParentFile();
- Cache.trace(
+ Console.trace(
"BACKUPFILES [file!=null] attempting to create temp file for "
+ tempfilename + " in dir " + tempdir);
temp = File.createTempFile(tempfilename,
TEMP_FILE_EXT + newTempFileSuffix, tempdir);
- Cache.debug(
+ Console.debug(
"BACKUPFILES using temp file " + temp.getAbsolutePath());
}
else
{
- Cache.trace(
+ Console.trace(
"BACKUPFILES [file==null] attempting to create default temp file "
+ DEFAULT_TEMP_FILE + " with extension "
+ TEMP_FILE_EXT);
}
} catch (IOException e)
{
- Cache.error("Could not create temp file to save to (IOException)");
- Cache.error(e.getMessage());
- Cache.debug(Cache.getStackTraceString(e));
+ Console.error("Could not create temp file to save to (IOException)");
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
} catch (Exception e)
{
- Cache.error("Exception creating temp file for saving");
- Cache.debug(Cache.getStackTraceString(e));
+ Console.error("Exception creating temp file for saving");
+ Console.debug(Cache.getStackTraceString(e));
}
this.setTempFile(temp);
}
public static void classInit()
{
- Cache.initLogger();
- Cache.trace("BACKUPFILES classInit");
+ Console.initLogger();
+ Console.trace("BACKUPFILES classInit");
boolean e = Cache.getDefault(ENABLED, !Platform.isJS());
setEnabled(e);
- Cache.trace("BACKUPFILES " + (e ? "enabled" : "disabled"));
+ Console.trace("BACKUPFILES " + (e ? "enabled" : "disabled"));
BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
.getSavedBackupEntry();
- Cache.trace("BACKUPFILES preset scheme " + bfpe.toString());
+ Console.trace("BACKUPFILES preset scheme " + bfpe.toString());
setConfirmDelete(bfpe.confirmDelete);
- Cache.trace("BACKUPFILES confirm delete " + bfpe.confirmDelete);
+ Console.trace("BACKUPFILES confirm delete " + bfpe.confirmDelete);
}
public static void setEnabled(boolean flag)
path = this.getTempFile().getCanonicalPath();
} catch (IOException e)
{
- Cache.error("IOException when getting Canonical Path of temp file '"
+ Console.error("IOException when getting Canonical Path of temp file '"
+ this.getTempFile().getName() + "'");
- Cache.debug(Cache.getStackTraceString(e));
+ Console.debug(Cache.getStackTraceString(e));
}
return path;
}
|| suffix.length() == 0)
{
// nothing to do
- Cache.debug("BACKUPFILES rollBackupFiles nothing to do." + ", "
+ Console.debug("BACKUPFILES rollBackupFiles nothing to do." + ", "
+ "filename: " + (file != null ? file.getName() : "null")
+ ", " + "file exists: " + file.exists() + ", " + "enabled: "
+ enabled + ", " + "max: " + max + ", " + "suffix: '" + suffix
return true;
}
- Cache.trace("BACKUPFILES rollBackupFiles starting");
+ Console.trace("BACKUPFILES rollBackupFiles starting");
String dir = "";
File dirFile;
{
dirFile = file.getParentFile();
dir = dirFile.getCanonicalPath();
- Cache.trace("BACKUPFILES dir: " + dir);
+ Console.trace("BACKUPFILES dir: " + dir);
} catch (Exception e)
{
- Cache.error("Could not get canonical path for file '" + file + "'");
- Cache.error(e.getMessage());
- Cache.debug(Cache.getStackTraceString(e));
+ Console.error("Could not get canonical path for file '" + file + "'");
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
return false;
}
String filename = file.getName();
String basename = filename;
- Cache.trace("BACKUPFILES filename is " + filename);
+ Console.trace("BACKUPFILES filename is " + filename);
boolean ret = true;
// Create/move backups up one
File[] backupFiles = dirFile.listFiles(bff);
int nextIndexNum = 0;
- Cache.trace("BACKUPFILES backupFiles.length: " + backupFiles.length);
+ Console.trace("BACKUPFILES backupFiles.length: " + backupFiles.length);
if (backupFiles.length == 0)
{
// No other backup files. Just need to move existing file to backupfile_1
- Cache.trace(
+ Console.trace(
"BACKUPFILES no existing backup files, setting index to 1");
nextIndexNum = 1;
}
if (reverseOrder)
{
// backup style numbering
- Cache.trace("BACKUPFILES rolling files in reverse order");
+ Console.trace("BACKUPFILES rolling files in reverse order");
int tempMax = noMax ? -1 : max;
// noMax == true means no limits
// no "oldest" file to delete
previousFile = backupfile_n;
fileToBeDeleted = null;
- Cache.trace("BACKUPFILES No oldest file to delete");
+ Console.trace("BACKUPFILES No oldest file to delete");
continue;
}
File replacementFile = backupfile_n;
long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
long replacementFileLMT = replacementFile.lastModified();
- Cache.trace("BACKUPFILES fileToBeDeleted is "
+ Console.trace("BACKUPFILES fileToBeDeleted is "
+ fileToBeDeleted.getAbsolutePath());
- Cache.trace("BACKUPFILES replacementFile is "
+ Console.trace("BACKUPFILES replacementFile is "
+ backupfile_n.getAbsolutePath());
try
.format(fileToBeDeletedLMT);
String replacementFileLMTString = sdf
.format(replacementFileLMT);
- Cache.warn("WARNING! I am set to delete backupfile "
+ Console.warn("WARNING! I am set to delete backupfile "
+ fileToBeDeleted.getName()
+ " has modification time "
+ fileToBeDeletedLMTString
boolean delete = confirmNewerDeleteFile(fileToBeDeleted,
replacementFile, true);
- Cache.trace("BACKUPFILES " + (delete ? "confirmed" : "not")
+ Console.trace("BACKUPFILES " + (delete ? "confirmed" : "not")
+ " deleting file "
+ fileToBeDeleted.getAbsolutePath()
+ " which is newer than "
}
else
{
- Cache.debug("BACKUPFILES moving "
+ Console.debug("BACKUPFILES moving "
+ fileToBeDeleted.getAbsolutePath() + " to "
+ oldestTempFile.getAbsolutePath());
moveFileToFile(fileToBeDeleted, oldestTempFile);
}
else
{
- Cache.debug("BACKUPFILES going to move "
+ Console.debug("BACKUPFILES going to move "
+ fileToBeDeleted.getAbsolutePath() + " to "
+ oldestTempFile.getAbsolutePath());
moveFileToFile(fileToBeDeleted, oldestTempFile);
} catch (Exception e)
{
- Cache.error(
+ Console.error(
"Error occurred, probably making new temp file for '"
+ fileToBeDeleted.getName() + "'");
- Cache.error(Cache.getStackTraceString(e));
+ Console.error(Cache.getStackTraceString(e));
}
// reset
}
bfsb.append(backupFiles[i].getName());
}
- Cache.trace("BACKUPFILES backupFiles: " + bfsb.toString());
+ Console.trace("BACKUPFILES backupFiles: " + bfsb.toString());
// noMax == true means keep all backup files
if ((!noMax) && bfTreeMap.size() >= max)
{
- Cache.trace("BACKUPFILES noMax: " + noMax + ", " + "max: " + max
+ Console.trace("BACKUPFILES noMax: " + noMax + ", " + "max: " + max
+ ", " + "bfTreeMap.size(): " + bfTreeMap.size());
// need to delete some files to keep number of backups to designated
// max.
int numToDelete = suffix.indexOf(NUM_PLACEHOLDER) > -1
? bfTreeMap.size() - max + 1
: 0;
- Cache.trace("BACKUPFILES numToDelete: " + numToDelete);
+ Console.trace("BACKUPFILES numToDelete: " + numToDelete);
// the "replacement" file is the latest backup file being kept (it's
// not replacing though)
File replacementFile = numToDelete < backupFiles.length
File fileToBeDeleted = backupFiles[i];
boolean delete = true;
- Cache.trace("BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
+ Console.trace("BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
boolean newer = false;
if (replacementFile != null)
String replacementFileLMTString = sdf
.format(replacementFileLMT);
- Cache.warn("WARNING! I am set to delete backupfile '"
+ Console.warn("WARNING! I am set to delete backupfile '"
+ fileToBeDeleted.getName()
+ "' has modification time "
+ fileToBeDeletedLMTString
{
// User has confirmed delete -- no need to add it to the list
fileToBeDeleted.delete();
- Cache.debug("BACKUPFILES deleting fileToBeDeleted: "
+ Console.debug("BACKUPFILES deleting fileToBeDeleted: "
+ fileToBeDeleted);
delete = false;
}
else
{
// keeping file, nothing to do!
- Cache.debug("BACKUPFILES keeping fileToBeDeleted: "
+ Console.debug("BACKUPFILES keeping fileToBeDeleted: "
+ fileToBeDeleted);
}
}
if (delete)
{
addDeleteFile(fileToBeDeleted);
- Cache.debug("BACKUPFILES addDeleteFile(fileToBeDeleted): "
+ Console.debug("BACKUPFILES addDeleteFile(fileToBeDeleted): "
+ fileToBeDeleted);
}
String latestBackupFilename = dir + File.separatorChar
+ BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
suffix, digits);
- Cache.trace("BACKUPFILES Moving old file [" + file
+ Console.trace("BACKUPFILES Moving old file [" + file
+ "] to latestBackupFilename [" + latestBackupFilename + "]");
// using boolean '&' instead of '&&' as don't want moveFileToFile attempt to
// be conditional (short-circuit)
ret = ret & moveFileToFile(file, new File(latestBackupFilename));
- Cache.debug("BACKUPFILES moving " + file + " to " + latestBackupFilename
+ Console.debug("BACKUPFILES moving " + file + " to " + latestBackupFilename
+ " was " + (ret ? "" : "NOT ") + "successful");
if (tidyUp)
{
- Cache.debug("BACKUPFILES tidying up files");
+ Console.debug("BACKUPFILES tidying up files");
tidyUpFiles();
}
saveFile = nextTempFile(ftbd.getName(), ftbd.getParentFile());
} catch (Exception e)
{
- Cache.error(
+ Console.error(
"Error when confirming to keep backup file newer than other backup files.");
e.printStackTrace();
}
for (int i = 0; i < deleteFiles.size(); i++)
{
File fileToDelete = deleteFiles.get(i);
- Cache.trace("BACKUPFILES about to delete fileToDelete:"
+ Console.trace("BACKUPFILES about to delete fileToDelete:"
+ fileToDelete);
fileToDelete.delete();
- Cache.warn("deleted '" + fileToDelete.getName() + "'");
+ Console.warn("deleted '" + fileToDelete.getName() + "'");
}
}
dirFile = file.getParentFile();
} catch (Exception e)
{
- Cache.error("Could not get canonical path for file '" + file + "'");
+ Console.error("Could not get canonical path for file '" + file + "'");
return new TreeMap<>();
}
int pos = deleteFiles.indexOf(fileToBeDeleted);
if (pos > -1)
{
- Cache.debug("BACKUPFILES not adding file "
+ Console.debug("BACKUPFILES not adding file "
+ fileToBeDeleted.getAbsolutePath()
+ " to the delete list (already at index" + pos + ")");
return true;
}
else
{
- Cache.debug("BACKUPFILES adding file "
+ Console.debug("BACKUPFILES adding file "
+ fileToBeDeleted.getAbsolutePath() + " to the delete list");
deleteFiles.add(fileToBeDeleted);
}
public static boolean moveFileToFile(File oldFile, File newFile)
{
- Cache.initLogger();
+ Console.initLogger();
boolean ret = false;
Path oldPath = Paths.get(oldFile.getAbsolutePath());
Path newPath = Paths.get(newFile.getAbsolutePath());
try
{
// delete destination file - not usually necessary but Just In Case...
- Cache.trace("BACKUPFILES deleting " + newFile.getAbsolutePath());
+ Console.trace("BACKUPFILES deleting " + newFile.getAbsolutePath());
newFile.delete();
- Cache.trace("BACKUPFILES moving " + oldFile.getAbsolutePath() + " to "
+ Console.trace("BACKUPFILES moving " + oldFile.getAbsolutePath() + " to "
+ newFile.getAbsolutePath());
Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
ret = true;
- Cache.trace("BACKUPFILES move seems to have succeeded");
+ Console.trace("BACKUPFILES move seems to have succeeded");
} catch (IOException e)
{
- Cache.warn("Could not move file '" + oldPath.toString() + "' to '"
+ Console.warn("Could not move file '" + oldPath.toString() + "' to '"
+ newPath.toString() + "'");
- Cache.error(e.getMessage());
- Cache.debug(Cache.getStackTraceString(e));
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
ret = false;
} catch (Exception e)
{
- Cache.error(e.getMessage());
- Cache.debug(Cache.getStackTraceString(e));
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
ret = false;
}
return ret;
import java.util.StringTokenizer;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.util.MessageManager;
public class BackupFilesPresetEntry
confirmDelete = Boolean.valueOf(st.nextToken());
} catch (Exception e)
{
- Cache.log.error("Error parsing backupfiles scheme '" + line + "'");
+ Console.error("Error parsing backupfiles scheme '" + line + "'");
}
return new BackupFilesPresetEntry(suffix, digits, reverse, keepAll,
*/
package jalview.io;
+import jalview.bin.Cache;
import jalview.gui.AlignmentPanel;
import jalview.gui.OOMWarning;
import jalview.json.binding.biojs.BioJSReleasePojo;
public static final String DEFAULT_DIR = System.getProperty("user.home")
+ File.separatorChar + ".biojs_templates" + File.separatorChar;
- public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
+ public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = Cache
.getDefault("biojs_template_directory", DEFAULT_DIR);
- public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache
+ public static final String BJS_TEMPLATE_GIT_REPO = Cache
.getDefault("biojs_template_git_repo",
"https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
--- /dev/null
+package jalview.io;
+
+import java.io.IOException;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.TreeMap;
+
+import jalview.bin.Console;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.DBRefUtils;
+import jalview.util.DnaUtils;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
+
+/**
+ * A base class to support parsing of GenBank, EMBL or DDBJ flat file format
+ * data. Example files (rather than formal specifications) are provided at
+ *
+ * <pre>
+ * https://ena-docs.readthedocs.io/en/latest/submit/fileprep/flat-file-example.html
+ * https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
+ * </pre>
+ *
+ * or to compare the same entry, see
+ *
+ * <pre>
+ * https://www.ebi.ac.uk/ena/browser/api/embl/X81322.1
+ * https://www.ncbi.nlm.nih.gov/nuccore/X81322.1
+ * </pre>
+ *
+ * The feature table part of the file has a common definition, only the start of
+ * each line is formatted differently in GenBank and EMBL. See
+ * http://www.insdc.org/files/feature_table.html#7.1.
+ */
+public abstract class EMBLLikeFlatFile extends AlignFile
+{
+ protected static final String LOCATION = "location";
+
+ protected static final String QUOTE = "\"";
+
+ protected static final String DOUBLED_QUOTE = QUOTE + QUOTE;
+
+ protected static final String WHITESPACE = "\\s+";
+
+ /**
+ * Removes leading or trailing double quotes (") unless doubled, and changes
+ * any 'escaped' (doubled) double quotes to single characters. As per the
+ * Feature Table specification for Qualifiers, Free Text.
+ *
+ * @param value
+ * @return
+ */
+ protected static String removeQuotes(String value)
+ {
+ if (value == null)
+ {
+ return null;
+ }
+ if (value.startsWith(QUOTE) && !value.startsWith(DOUBLED_QUOTE))
+ {
+ value = value.substring(1);
+ }
+ if (value.endsWith(QUOTE) && !value.endsWith(DOUBLED_QUOTE))
+ {
+ value = value.substring(0, value.length() - 1);
+ }
+ value = value.replace(DOUBLED_QUOTE, QUOTE);
+ return value;
+ }
+
+ /**
+ * Truncates (if necessary) the exon intervals to match 3 times the length of
+ * the protein(including truncation for stop codon included in exon)
+ *
+ * @param proteinLength
+ * @param exon
+ * an array of [start, end, start, end...] intervals
+ * @return the same array (if unchanged) or a truncated copy
+ */
+ protected static int[] adjustForProteinLength(int proteinLength,
+ int[] exon)
+ {
+ if (proteinLength <= 0 || exon == null)
+ {
+ return exon;
+ }
+ int expectedCdsLength = proteinLength * 3;
+ int exonLength = MappingUtils.getLength(Arrays.asList(exon));
+
+ /*
+ * if exon length matches protein, or is shorter, then leave it unchanged
+ */
+ if (expectedCdsLength >= exonLength)
+ {
+ return exon;
+ }
+
+ int origxon[];
+ int sxpos = -1;
+ int endxon = 0;
+ origxon = new int[exon.length];
+ System.arraycopy(exon, 0, origxon, 0, exon.length);
+ int cdspos = 0;
+ for (int x = 0; x < exon.length; x += 2)
+ {
+ cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
+ if (expectedCdsLength <= cdspos)
+ {
+ // advanced beyond last codon.
+ sxpos = x;
+ if (expectedCdsLength != cdspos)
+ {
+ // System.err
+ // .println("Truncating final exon interval on region by "
+ // + (cdspos - cdslength));
+ }
+
+ /*
+ * shrink the final exon - reduce end position if forward
+ * strand, increase it if reverse
+ */
+ if (exon[x + 1] >= exon[x])
+ {
+ endxon = exon[x + 1] - cdspos + expectedCdsLength;
+ }
+ else
+ {
+ endxon = exon[x + 1] + cdspos - expectedCdsLength;
+ }
+ break;
+ }
+ }
+
+ if (sxpos != -1)
+ {
+ // and trim the exon interval set if necessary
+ int[] nxon = new int[sxpos + 2];
+ System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
+ nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
+ // set
+ exon = nxon;
+ }
+ return exon;
+ }
+
+ /*
+ * when true, interpret the mol_type 'source' feature attribute
+ * and generate an RNA sequence from the DNA record
+ */
+ protected boolean produceRna=true;
+
+
+ /*
+ * values parsed from the data file
+ */
+ protected String sourceDb;
+
+ protected String accession;
+
+ protected String version;
+
+ protected String description;
+
+ protected int length = 128;
+
+ protected List<DBRefEntry> dbrefs;
+
+ protected boolean sequenceStringIsRNA=false;
+
+ protected String sequenceString;
+
+ protected Map<String, CdsData> cds;
+
+ /**
+ * Constructor
+ *
+ * @param fp
+ * @param sourceId
+ * @throws IOException
+ */
+ public EMBLLikeFlatFile(FileParse fp, String sourceId) throws IOException
+ {
+ super(false, fp); // don't parse immediately
+ this.sourceDb = sourceId;
+ dbrefs = new ArrayList<>();
+
+ /*
+ * using TreeMap gives CDS sequences in alphabetical, so readable, order
+ */
+ cds = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
+
+ parse();
+ }
+
+ /**
+ * process attributes for 'source' until the next FT feature entry
+ * only interested in 'mol_type'
+ * @param tokens
+ * @return
+ * @throws IOException
+ */
+ private String parseSourceQualifiers(String[] tokens) throws IOException
+ {
+ if (!"source".equals(tokens[0]))
+ {
+ throw (new RuntimeException("Not given a 'source' qualifier line"));
+ }
+ // search for mol_type attribute
+
+ StringBuilder sb = new StringBuilder().append(tokens[1]); // extent of
+ // sequence
+
+ String line = parseFeatureQualifier(sb, false);
+ while (line != null)
+ {
+ if (!line.startsWith("FT ")) // four spaces, end of this feature table
+ // entry
+ {
+ return line;
+ }
+
+ // case sensitive ?
+ int p = line.indexOf("\\mol_type");
+ int qs = line.indexOf("\"", p);
+ int qe = line.indexOf("\"", qs + 1);
+ String qualifier=line.substring(qs,qe).toLowerCase(Locale.ROOT);
+ if (qualifier.indexOf("rna") > -1)
+ {
+ sequenceStringIsRNA = true;
+ }
+ if (qualifier.indexOf("dna") > -1)
+ {
+ sequenceStringIsRNA = false;
+ }
+ line=parseFeatureQualifier(sb, false);
+ }
+ return line;
+ }
+
+
+ /**
+ * Parses one (GenBank or EMBL format) CDS feature, saves the parsed data, and
+ * returns the next line
+ *
+ * @param location
+ * @return
+ * @throws IOException
+ */
+ protected String parseCDSFeature(String location) throws IOException
+ {
+ String line;
+
+ /*
+ * parse location, which can be over >1 line e.g. EAW51554
+ */
+ CdsData data = new CdsData();
+ StringBuilder sb = new StringBuilder().append(location);
+ line = parseFeatureQualifier(sb, false);
+ data.cdsLocation = sb.toString();
+
+ while (line != null)
+ {
+ if (!isFeatureContinuationLine(line))
+ {
+ // e.g. start of next feature "FT source..."
+ break;
+ }
+
+ /*
+ * extract qualifier, e.g. FT /protein_id="CAA37824.1"
+ * - the value may extend over more than one line
+ * - if the value has enclosing quotes, these are removed
+ * - escaped double quotes ("") are reduced to a single character
+ */
+ int slashPos = line.indexOf('/');
+ if (slashPos == -1)
+ {
+ Console.error("Unexpected EMBL line ignored: " + line);
+ line = nextLine();
+ continue;
+ }
+ int eqPos = line.indexOf('=', slashPos + 1);
+ if (eqPos == -1)
+ {
+ // can happen, e.g. /ribosomal_slippage
+ line = nextLine();
+ continue;
+ }
+ String qualifier = line.substring(slashPos + 1, eqPos);
+ String value = line.substring(eqPos + 1);
+ value = removeQuotes(value);
+ sb = new StringBuilder().append(value);
+ boolean asText = !"translation".equals(qualifier);
+ line = parseFeatureQualifier(sb, asText);
+ String featureValue = sb.toString();
+
+ if ("protein_id".equals(qualifier))
+ {
+ data.proteinId = featureValue;
+ }
+ else if ("codon_start".equals(qualifier))
+ {
+ try
+ {
+ data.codonStart = Integer.parseInt(featureValue.trim());
+ } catch (NumberFormatException e)
+ {
+ Console.error("Invalid codon_start in XML for " + this.accession
+ + ": " + e.getMessage());
+ }
+ }
+ else if ("db_xref".equals(qualifier))
+ {
+ String[] parts = featureValue.split(":");
+ if (parts.length == 2)
+ {
+ String db = parts[0].trim();
+ db = DBRefUtils.getCanonicalName(db);
+ DBRefEntry dbref = new DBRefEntry(db, "0", parts[1].trim());
+ data.xrefs.add(dbref);
+ }
+ }
+ else if ("product".equals(qualifier))
+ {
+ data.proteinName = featureValue;
+ }
+ else if ("translation".equals(qualifier))
+ {
+ data.translation = featureValue;
+ }
+ else if (!"".equals(featureValue))
+ {
+ // throw anything else into the additional properties hash
+ data.cdsProps.put(qualifier, featureValue);
+ }
+ }
+
+ if (data.proteinId != null)
+ {
+ this.cds.put(data.proteinId, data);
+ }
+ else
+ {
+ Console.error("Ignoring CDS feature with no protein_id for "
+ + sourceDb + ":" + accession);
+ }
+
+ return line;
+ }
+
+ protected abstract boolean isFeatureContinuationLine(String line);
+
+ /**
+ * Output (print) is not (yet) implemented for flat file format
+ */
+ @Override
+ public String print(SequenceI[] seqs, boolean jvsuffix)
+ {
+ return null;
+ }
+
+ /**
+ * Constructs and saves the sequence from parsed components
+ */
+ protected void buildSequence()
+ {
+ if (this.accession == null || this.sequenceString == null)
+ {
+ Console.error("Failed to parse data from EMBL");
+ return;
+ }
+
+ String name = this.accession;
+ if (this.sourceDb != null)
+ {
+ name = this.sourceDb + "|" + name;
+ }
+
+ if (produceRna && sequenceStringIsRNA)
+ {
+ sequenceString = sequenceString.replace('T', 'U').replace('t', 'u');
+ }
+
+ SequenceI seq = new Sequence(name, this.sequenceString);
+ seq.setDescription(this.description);
+
+ /*
+ * add a DBRef to itself
+ */
+ DBRefEntry selfRef = new DBRefEntry(sourceDb, version, accession);
+ int[] startEnd = new int[] { 1, seq.getLength() };
+ selfRef.setMap(new Mapping(null, startEnd, startEnd, 1, 1));
+ seq.addDBRef(selfRef);
+
+ for (DBRefEntry dbref : this.dbrefs)
+ {
+ seq.addDBRef(dbref);
+ }
+
+ processCDSFeatures(seq);
+
+ seq.deriveSequence();
+
+ addSequence(seq);
+ }
+
+ /**
+ * Process the CDS features, including generation of cross-references and
+ * mappings to the protein products (translation)
+ *
+ * @param seq
+ */
+ protected void processCDSFeatures(SequenceI seq)
+ {
+ /*
+ * record protein products found to avoid duplication i.e. >1 CDS with
+ * the same /protein_id [though not sure I can find an example of this]
+ */
+ Map<String, SequenceI> proteins = new HashMap<>();
+ for (CdsData data : cds.values())
+ {
+ processCDSFeature(seq, data, proteins);
+ }
+ }
+
+ /**
+ * Processes data for one parsed CDS feature to
+ * <ul>
+ * <li>create a protein product sequence for the translation</li>
+ * <li>create a cross-reference to protein with mapping from dna</li>
+ * <li>add a CDS feature to the sequence for each CDS start-end range</li>
+ * <li>add any CDS dbrefs to the sequence and to the protein product</li>
+ * </ul>
+ *
+ * @param SequenceI
+ * dna
+ * @param proteins
+ * map of protein products so far derived from CDS data
+ */
+ void processCDSFeature(SequenceI dna, CdsData data,
+ Map<String, SequenceI> proteins)
+ {
+ /*
+ * parse location into a list of [start, end, start, end] positions
+ */
+ int[] exons = getCdsRanges(this.accession, data.cdsLocation);
+
+ MapList maplist = buildMappingToProtein(dna, exons, data);
+
+ int exonNumber = 0;
+
+ for (int xint = 0; exons != null && xint < exons.length - 1; xint += 2)
+ {
+ int exonStart = exons[xint];
+ int exonEnd = exons[xint + 1];
+ int begin = Math.min(exonStart, exonEnd);
+ int end = Math.max(exonStart, exonEnd);
+ exonNumber++;
+ String desc = String.format("Exon %d for protein EMBLCDS:%s",
+ exonNumber, data.proteinId);
+
+ SequenceFeature sf = new SequenceFeature("CDS", desc, begin, end,
+ this.sourceDb);
+ for (Entry<String, String> val : data.cdsProps.entrySet())
+ {
+ sf.setValue(val.getKey(), val.getValue());
+ }
+
+ sf.setEnaLocation(data.cdsLocation);
+ boolean forwardStrand = exonStart <= exonEnd;
+ sf.setStrand(forwardStrand ? "+" : "-");
+ sf.setPhase(String.valueOf(data.codonStart - 1));
+ sf.setValue(FeatureProperties.EXONPOS, exonNumber);
+ sf.setValue(FeatureProperties.EXONPRODUCT, data.proteinName);
+
+ dna.addSequenceFeature(sf);
+ }
+
+ boolean hasUniprotDbref = false;
+ for (DBRefEntry xref : data.xrefs)
+ {
+ dna.addDBRef(xref);
+ if (xref.getSource().equals(DBRefSource.UNIPROT))
+ {
+ /*
+ * construct (or find) the sequence for (data.protein_id, data.translation)
+ */
+ SequenceI protein = buildProteinProduct(dna, xref, data, proteins);
+ Mapping map = new Mapping(protein, maplist);
+ map.setMappedFromId(data.proteinId);
+ xref.setMap(map);
+
+ /*
+ * add DBRefs with mappings from dna to protein and the inverse
+ */
+ DBRefEntry db1 = new DBRefEntry(sourceDb, version, accession);
+ db1.setMap(new Mapping(dna, maplist.getInverse()));
+ protein.addDBRef(db1);
+
+ hasUniprotDbref = true;
+ }
+ }
+
+ /*
+ * if we have a product (translation) but no explicit Uniprot dbref
+ * (example: EMBL M19487 protein_id AAB02592.1)
+ * then construct mappings to an assumed EMBLCDSPROTEIN accession
+ */
+ if (!hasUniprotDbref)
+ {
+ SequenceI protein = proteins.get(data.proteinId);
+ if (protein == null)
+ {
+ protein = new Sequence(data.proteinId, data.translation);
+ protein.setDescription(data.proteinName);
+ proteins.put(data.proteinId, protein);
+ }
+ // assuming CDSPROTEIN sequence version = dna version (?!)
+ DBRefEntry db1 = new DBRefEntry(DBRefSource.EMBLCDSProduct,
+ this.version, data.proteinId);
+ protein.addDBRef(db1);
+
+ DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
+ DBRefSource.EMBLCDSProduct, this.version, data.proteinId);
+ Mapping map = new Mapping(protein, maplist);
+ map.setMappedFromId(data.proteinId);
+ dnaToEmblProteinRef.setMap(map);
+ dna.addDBRef(dnaToEmblProteinRef);
+ }
+
+ /*
+ * comment brought forward from EmblXmlSource, lines 447-451:
+ * TODO: if retrieved from EMBLCDS, add a DBRef back to the parent EMBL
+ * sequence with the exon map; if given a dataset reference, search
+ * dataset for parent EMBL sequence if it exists and set its map;
+ * make a new feature annotating the coding contig
+ */
+ }
+
+ /**
+ * Computes a mapping from CDS positions in DNA sequence to protein product
+ * positions, with allowance for stop codon or incomplete start codon
+ *
+ * @param dna
+ * @param exons
+ * @param data
+ * @return
+ */
+ MapList buildMappingToProtein(final SequenceI dna, final int[] exons,
+ final CdsData data)
+ {
+ MapList dnaToProteinMapping = null;
+ int peptideLength = data.translation.length();
+
+ int[] proteinRange = new int[] { 1, peptideLength };
+ if (exons != null && exons.length > 0)
+ {
+ /*
+ * We were able to parse 'location'; do a final
+ * product length truncation check
+ */
+ int[] cdsRanges = adjustForProteinLength(peptideLength, exons);
+ dnaToProteinMapping = new MapList(cdsRanges, proteinRange, 3, 1);
+ }
+ else
+ {
+ /*
+ * workaround until we handle all 'location' formats fully
+ * e.g. X53828.1:60..1058 or <123..>289
+ */
+ Console.error(String.format(
+ "Implementation Notice: EMBLCDS location '%s'not properly supported yet"
+ + " - Making up the CDNA region of (%s:%s)... may be incorrect",
+ data.cdsLocation, sourceDb, this.accession));
+
+ int completeCodonsLength = 1 - data.codonStart + dna.getLength();
+ int mappedDnaEnd = dna.getEnd();
+ if (peptideLength * 3 == completeCodonsLength)
+ {
+ // this might occur for CDS sequences where no features are marked
+ Console.warn("Assuming no stop codon at end of cDNA fragment");
+ mappedDnaEnd = dna.getEnd();
+ }
+ else if ((peptideLength + 1) * 3 == completeCodonsLength)
+ {
+ Console.warn("Assuming stop codon at end of cDNA fragment");
+ mappedDnaEnd = dna.getEnd() - 3;
+ }
+
+ if (mappedDnaEnd != -1)
+ {
+ int[] cdsRanges = new int[] {
+ dna.getStart() + (data.codonStart - 1), mappedDnaEnd };
+ dnaToProteinMapping = new MapList(cdsRanges, proteinRange, 3, 1);
+ }
+ }
+
+ return dnaToProteinMapping;
+ }
+
+ /**
+ * Constructs a sequence for the protein product for the CDS data (if there is
+ * one), and dbrefs with mappings from CDS to protein and the reverse
+ *
+ * @param dna
+ * @param xref
+ * @param data
+ * @param proteins
+ * @return
+ */
+ SequenceI buildProteinProduct(SequenceI dna, DBRefEntry xref,
+ CdsData data, Map<String, SequenceI> proteins)
+ {
+ /*
+ * check we have some data to work with
+ */
+ if (data.proteinId == null || data.translation == null)
+ {
+ return null;
+ }
+
+ /*
+ * Construct the protein sequence (if not already seen)
+ */
+ String proteinSeqName = xref.getSource() + "|" + xref.getAccessionId();
+ SequenceI protein = proteins.get(proteinSeqName);
+ if (protein == null)
+ {
+ protein = new Sequence(proteinSeqName, data.translation, 1,
+ data.translation.length());
+ protein.setDescription(data.proteinName != null ? data.proteinName
+ : "Protein Product from " + sourceDb);
+ proteins.put(proteinSeqName, protein);
+ }
+
+ return protein;
+ }
+
+ /**
+ * Returns the CDS location as a single array of [start, end, start, end...]
+ * positions. If on the reverse strand, these will be in descending order.
+ *
+ * @param accession
+ * @param location
+ * @return
+ */
+ protected int[] getCdsRanges(String accession, String location)
+ {
+ if (location == null)
+ {
+ return new int[] {};
+ }
+
+ try
+ {
+ List<int[]> ranges = DnaUtils.parseLocation(location);
+ return MappingUtils.rangeListToArray(ranges);
+ } catch (ParseException e)
+ {
+ Console.warn(
+ String.format("Not parsing inexact CDS location %s in ENA %s",
+ location, accession));
+ return new int[] {};
+ }
+ }
+
+ /**
+ * Reads the value of a feature (FT) qualifier from one or more lines of the
+ * file, and returns the next line after that. Values are appended to the
+ * string buffer, which should be already primed with the value read from the
+ * first line for the qualifier (with any leading double quote removed).
+ * Enclosing double quotes are removed, and escaped (repeated) double quotes
+ * reduced to one only. For example for
+ *
+ * <pre>
+ * FT /note="gene_id=hCG28070.3
+ * FT ""foobar"" isoform=CRA_b"
+ * the returned value is
+ * gene_id=hCG28070.3 "foobar" isoform=CRA_b
+ * </pre>
+ *
+ * Note the side-effect of this method, to advance data reading to the next
+ * line after the feature qualifier (which could be another qualifier, a
+ * different feature, a non-feature line, or null at end of file).
+ *
+ * @param sb
+ * a string buffer primed with the first line of the value
+ * @param asText
+ * @return
+ * @throws IOException
+ */
+ String parseFeatureQualifier(StringBuilder sb, boolean asText)
+ throws IOException
+ {
+ String line;
+ while ((line = nextLine()) != null)
+ {
+ if (!isFeatureContinuationLine(line))
+ {
+ break; // reached next feature or other input line
+ }
+ String[] tokens = line.split(WHITESPACE);
+ if (tokens.length < 2)
+ {
+ Console.error("Ignoring bad EMBL line for " + this.accession
+ + ": " + line);
+ break;
+ }
+ if (tokens[1].startsWith("/"))
+ {
+ break; // next feature qualifier
+ }
+
+ /*
+ * if text (e.g. /product), add a word separator for a new line,
+ * else (e.g. /translation) don't
+ */
+ if (asText)
+ {
+ sb.append(" ");
+ }
+
+ /*
+ * remove trailing " and unescape doubled ""
+ */
+ String data = removeQuotes(tokens[1]);
+ sb.append(data);
+ }
+
+ return line;
+ }
+
+ /**
+ * Reads and saves the sequence, read from the lines following the ORIGIN
+ * (GenBank) or SQ (EMBL) line. Whitespace and position counters are
+ * discarded. Returns the next line following the sequence data (the next line
+ * that doesn't start with whitespace).
+ *
+ * @throws IOException
+ */
+ protected String parseSequence() throws IOException
+ {
+ StringBuilder sb = new StringBuilder(this.length);
+ String line = nextLine();
+ while (line != null && line.startsWith(" "))
+ {
+ line = line.trim();
+ String[] blocks = line.split(WHITESPACE);
+
+ /*
+ * the first or last block on each line might be a position count - omit
+ */
+ for (int i = 0; i < blocks.length; i++)
+ {
+ try
+ {
+ Long.parseLong(blocks[i]);
+ // position counter - ignore it
+ } catch (NumberFormatException e)
+ {
+ // sequence data - append it
+ sb.append(blocks[i]);
+ }
+ }
+ line = nextLine();
+ }
+ this.sequenceString = sb.toString();
+
+ return line;
+ }
+
+ /**
+ * Processes a feature line. If it declares a feature type of interest
+ * (currently, only CDS is processed), processes all of the associated lines
+ * (feature qualifiers), and returns the next line after that, otherwise
+ * simply returns the next line.
+ *
+ * @param line
+ * the first line for the feature (with initial FT omitted for EMBL
+ * format)
+ * @return
+ * @throws IOException
+ */
+ protected String parseFeature(String line) throws IOException
+ {
+ String[] tokens = line.trim().split(WHITESPACE);
+ if (tokens.length < 2 || (!"CDS".equals(tokens[0]) && (!"source".equals(tokens[0]))))
+ {
+ return nextLine();
+ }
+ if (tokens[0].equals("source"))
+ {
+ return parseSourceQualifiers(tokens);
+ }
+ return parseCDSFeature(tokens[1]);
+ }
+}
+
+/**
+ * A data bean class to hold values parsed from one CDS Feature
+ */
+class CdsData
+{
+ String translation; // from /translation qualifier
+
+ String cdsLocation; // the raw value e.g. join(1..1234,2012..2837)
+
+ int codonStart = 1; // from /codon_start qualifier
+
+ String proteinName; // from /product qualifier; used for protein description
+
+ String proteinId; // from /protein_id qualifier
+
+ List<DBRefEntry> xrefs = new ArrayList<>(); // from /db_xref qualifiers
+
+ Map<String, String> cdsProps = new Hashtable<>(); // other qualifiers
+}
--- /dev/null
+package jalview.io;
+
+import java.io.IOException;
+
+import jalview.bin.Console;
+import jalview.datamodel.DBRefEntry;
+import jalview.util.DBRefUtils;
+
+/**
+ * A class that provides selective parsing of the EMBL flatfile format.
+ * <p>
+ * The initial implementation is limited to extracting fields used by Jalview
+ * after fetching an EMBL or EMBLCDS entry:
+ *
+ * <pre>
+ * accession, version, sequence, xref
+ * and (for CDS feature) location, protein_id, product, codon_start, translation
+ * </pre>
+ *
+ * For a complete parser, it may be best to adopt that provided in
+ * https://github.com/enasequence/sequencetools/tree/master/src/main/java/uk/ac/ebi/embl/flatfile
+ * (but note this has a dependency on the Apache Commons library)
+ *
+ * @author gmcarstairs
+ * @see ftp://ftp.ebi.ac.uk/pub/databases/ena/sequence/release/doc/usrman.txt
+ * @see ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html
+ */
+public class EmblFlatFile extends EMBLLikeFlatFile
+{
+ /**
+ * Constructor given a data source and the id of the source database
+ *
+ * @param fp
+ * @param sourceId
+ * @throws IOException
+ */
+ public EmblFlatFile(FileParse fp, String sourceId) throws IOException
+ {
+ super(fp, sourceId);
+ }
+
+ /**
+ * Parses the flatfile, and if successful, saves as an annotated sequence
+ * which may be retrieved by calling {@code getSequence()}
+ *
+ * @throws IOException
+ */
+ @Override
+ public void parse() throws IOException
+ {
+ String line = nextLine();
+ while (line != null)
+ {
+ if (line.startsWith("ID"))
+ {
+ line = parseID(line);
+ }
+ else if (line.startsWith("DE"))
+ {
+ line = parseDE(line);
+ }
+ else if (line.startsWith("DR"))
+ {
+ line = parseDR(line);
+ }
+ else if (line.startsWith("SQ"))
+ {
+ line = parseSequence();
+ }
+ else if (line.startsWith("FT"))
+ {
+ line = parseFeature(line.substring(2));
+ }
+ else
+ {
+ line = nextLine();
+ }
+ }
+ buildSequence();
+ }
+
+ /**
+ * Extracts and saves the primary accession and version (SV value) from an ID
+ * line, or null if not found. Returns the next line after the one processed.
+ *
+ * @param line
+ * @throws IOException
+ */
+ String parseID(String line) throws IOException
+ {
+ String[] tokens = line.substring(2).split(";");
+
+ /*
+ * first is primary accession
+ */
+ String token = tokens[0].trim();
+ if (!token.isEmpty())
+ {
+ this.accession = token;
+ }
+
+ /*
+ * second token is 'SV versionNo'
+ */
+ if (tokens.length > 1)
+ {
+ token = tokens[1].trim();
+ if (token.startsWith("SV"))
+ {
+ String[] bits = token.trim().split(WHITESPACE);
+ this.version = bits[bits.length - 1];
+ }
+ }
+
+ /*
+ * seventh token is 'length BP'
+ */
+ if (tokens.length > 6)
+ {
+ token = tokens[6].trim();
+ String[] bits = token.trim().split(WHITESPACE);
+ try
+ {
+ this.length = Integer.valueOf(bits[0]);
+ } catch (NumberFormatException e)
+ {
+ Console.error("bad length read in flatfile, line: " + line);
+ }
+ }
+
+ return nextLine();
+ }
+
+ /**
+ * Reads sequence description from the first DE line found. Any trailing
+ * period is discarded. If there are multiple DE lines, only the first (short
+ * description) is read, the rest are ignored.
+ *
+ * @param line
+ * @return
+ * @throws IOException
+ */
+ String parseDE(String line) throws IOException
+ {
+ String desc = line.substring(2).trim();
+ if (desc.endsWith("."))
+ {
+ desc = desc.substring(0, desc.length() - 1);
+ }
+ this.description = desc;
+
+ /*
+ * pass over any additional DE lines
+ */
+ while ((line = nextLine()) != null)
+ {
+ if (!line.startsWith("DE"))
+ {
+ break;
+ }
+ }
+
+ return line;
+ }
+
+ /**
+ * Processes one DR line and saves as a DBRefEntry cross-reference. Returns
+ * the line following the line processed.
+ *
+ * @param line
+ * @throws IOException
+ */
+ String parseDR(String line) throws IOException
+ {
+ String[] tokens = line.substring(2).split(";");
+ if (tokens.length > 1)
+ {
+ /*
+ * ensure UniProtKB/Swiss-Prot converted to UNIPROT
+ */
+ String db = tokens[0].trim();
+ db = DBRefUtils.getCanonicalName(db);
+ String acc = tokens[1].trim();
+ if (acc.endsWith("."))
+ {
+ acc = acc.substring(0, acc.length() - 1);
+ }
+ String version = "0";
+ if (tokens.length > 2)
+ {
+ String secondaryId = tokens[2].trim();
+ if (!secondaryId.isEmpty())
+ {
+ // todo: is this right? secondary id is not a version number
+ // version = secondaryId;
+ }
+ }
+ this.dbrefs.add(new DBRefEntry(db, version, acc));
+ }
+
+ return nextLine();
+ }
+
+ @Override
+ protected boolean isFeatureContinuationLine(String line)
+ {
+ return line.startsWith("FT "); // 4 spaces
+ }
+}
*/
package jalview.io;
+import java.io.IOException;
+
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import java.io.IOException;
-
/**
* DOCUMENT ME!
*
public FastaFile(FileParse source) throws IOException
{
- super(source);
+ this(source, true);
+ }
+
+ public FastaFile(FileParse source, boolean closeData) throws IOException
+ {
+ super(true, source, closeData);
}
public FastaFile(SequenceI[] seqs)
*/
package jalview.io;
+import java.util.Locale;
+
import java.awt.Color;
import java.io.IOException;
import java.util.ArrayList;
// skip comments/process pragmas
if (line.length() == 0 || line.startsWith("#"))
{
- if (line.toLowerCase().startsWith("##"))
+ if (line.toLowerCase(Locale.ROOT).startsWith("##"))
{
processGffPragma(line, gffProps, align, newseqs);
}
String line;
while ((line = nextLine()) != null)
{
- if (line.toUpperCase().startsWith(ENDFILTERS))
+ if (line.toUpperCase(Locale.ROOT).startsWith(ENDFILTERS))
{
return;
}
} catch (IOException q)
{
}
- FastaFile parser = new FastaFile(this);
+ // Opening a FastaFile object with the remainder of this object's dataIn.
+ // Tell the constructor to NOT close the dataIn when finished.
+ FastaFile parser = new FastaFile(this, false);
List<SequenceI> includedseqs = parser.getSeqs();
SequenceIdMatcher smatcher = new SequenceIdMatcher(newseqs);
*/
package jalview.io;
+import java.io.IOException;
+
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
-import java.io.IOException;
-
public enum FileFormat implements FileFormatI
{
Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
return new PhylipFile();
}
},
+ GenBank("GenBank Flatfile", "gb, gbk", true, false)
+ {
+ @Override
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
+ {
+ return new GenBankFile(source, "GenBank");
+ }
+
+ @Override
+ public AlignmentFileWriterI getWriter(AlignmentI al)
+ {
+ return null;
+ }
+ },
+ Embl("ENA Flatfile", "txt", true, false)
+ {
+ @Override
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
+ {
+ // Always assume we import from EMBL for now
+ return new EmblFlatFile(source, DBRefSource.EMBL);
+ }
+
+ @Override
+ public AlignmentFileWriterI getWriter(AlignmentI al)
+ {
+ return null;
+ }
+ },
Jnet("JnetFile", "", false, false)
{
@Override
* @param shortName
* @param extensions
* comma-separated list of file extensions associated with the format
- * @param isReadable
- * @param isWritable
+ * @param isReadable - can be recognised by IdentifyFile and imported with the given reader
+ * @param isWritable - can be exported with the returned writer
*/
private FileFormat(String shortName, String extensions,
boolean isReadable, boolean isWritable)
*/
package jalview.io;
+import java.util.Locale;
+
import java.util.ArrayList;
import java.util.HashSet;
import java.util.LinkedHashMap;
protected void registerFileFormat(FileFormatI format,
boolean isIdentifiable)
{
- String name = format.getName().toUpperCase();
+ String name = format.getName().toUpperCase(Locale.ROOT);
if (formats.containsKey(name))
{
System.err.println("Overwriting file format: " + format.getName());
*/
public void deregisterFileFormat(String name)
{
- FileFormatI ff = formats.remove(name.toUpperCase());
+ FileFormatI ff = formats.remove(name.toUpperCase(Locale.ROOT));
identifiable.remove(ff);
}
*/
public FileFormatI forName(String format)
{
- return format == null ? null : formats.get(format.toUpperCase());
+ return format == null ? null : formats.get(format.toUpperCase(Locale.ROOT));
}
/**
.getFeatureColourScheme();
if (viewport != null)
{
- if (proxyColourScheme != null)
- {
- viewport.applyFeaturesStyle(proxyColourScheme);
- }
// append to existing alignment
viewport.addAlignment(al, title);
+ viewport.applyFeaturesStyle(proxyColourScheme);
}
else
{
try
{
- alignFrame.setMaximum(jalview.bin.Cache
+ alignFrame.setMaximum(Cache
.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsModelI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.util.MessageManager;
import jalview.util.Platform;
{
if (!input.markSupported())
{
- Cache.log.error(
+ Console.error(
"FileParse.izGzipStream: input stream must support mark/reset");
return false;
}
input.mark(4);
-
+
// get first 2 bytes or return false
byte[] bytes = new byte[2];
int read = input.read(bytes);
{
return false;
}
-
+
int header = (bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00);
return (GZIPInputStream.GZIP_MAGIC == header);
}
*/
package jalview.io;
+import java.util.Locale;
+
import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
private void init()
{
- if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+ if (Cache.getDefault("STRUCT_FROM_PDB", true))
{
- annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+ annotFromStructure = Cache.getDefault("ADD_TEMPFACT_ANN",
true);
- localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+ localSecondaryStruct = Cache.getDefault("ADD_SS_ANN",
true);
- serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+ serviceSecondaryStruct = Cache.getDefault("USE_RNAVIEW",
true);
}
else
public boolean getCacheSuffixDefault(FileFormatI format)
{
- return Cache.getDefault(format.getName().toUpperCase() + "_JVSUFFIX",
+ return Cache.getDefault(format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX",
true);
}
--- /dev/null
+package jalview.io;
+
+import java.io.IOException;
+
+/**
+ * A class that provides selective parsing of the GenBank flatfile format.
+ * <p>
+ * The initial implementation is limited to extracting fields used by Jalview
+ * after fetching an EMBL or EMBLCDS entry:
+ *
+ * <pre>
+ * accession, version, sequence, xref
+ * and (for CDS feature) location, protein_id, product, codon_start, translation
+ * </pre>
+ *
+ * @author gmcarstairs
+ * @see https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
+ */
+public class GenBankFile extends EMBLLikeFlatFile
+{
+ private static final String DEFINITION = "DEFINITION";
+
+ /**
+ * Constructor given a data source and the id of the source database
+ *
+ * @param fp
+ * @param sourceId
+ * @throws IOException
+ */
+ public GenBankFile(FileParse fp, String sourceId) throws IOException
+ {
+ super(fp, sourceId);
+ }
+
+ /**
+ * Parses the flatfile, and if successful, saves as an annotated sequence
+ * which may be retrieved by calling {@code getSequence()}
+ *
+ * @throws IOException
+ * @see https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
+ */
+ @Override
+ public void parse() throws IOException
+ {
+ String line = nextLine();
+ while (line != null)
+ {
+ if (line.startsWith("LOCUS"))
+ {
+ line = parseLocus(line);
+ }
+ else if (line.startsWith(DEFINITION))
+ {
+ line = parseDefinition(line);
+ }
+ else if (line.startsWith("ACCESSION"))
+ {
+ this.accession = line.split(WHITESPACE)[1];
+ line = nextLine();
+ }
+ else if (line.startsWith("VERSION"))
+ {
+ line = parseVersion(line);
+ }
+ else if (line.startsWith("ORIGIN"))
+ {
+ line = parseSequence();
+ }
+ else if (line.startsWith("FEATURES"))
+ {
+ line = nextLine();
+ while (line.startsWith(" "))
+ {
+ line = parseFeature(line);
+ }
+ }
+ else
+ {
+ line = nextLine();
+ }
+ }
+ buildSequence();
+ }
+
+ /**
+ * Extracts and saves the primary accession and version (SV value) from an ID
+ * line, or null if not found. Returns the next line after the one processed.
+ *
+ * @param line
+ * @throws IOException
+ */
+ String parseLocus(String line) throws IOException
+ {
+ String[] tokens = line.split(WHITESPACE);
+
+ /*
+ * first should be "LOCUS"
+ */
+ if (tokens.length < 2 || !"LOCUS".equals(tokens[0]))
+ {
+ return nextLine();
+ }
+ /*
+ * second is primary accession
+ */
+ String token = tokens[1].trim();
+ if (!token.isEmpty())
+ {
+ this.accession = token;
+ }
+
+ // not going to guess the rest just yet, but third is length with unit (bp)
+
+ return nextLine();
+ }
+
+ /**
+ * Reads sequence description from DEFINITION lines. Any trailing period is
+ * discarded. Returns the next line after the definition line(s).
+ *
+ * @param line
+ * @return
+ * @throws IOException
+ */
+ String parseDefinition(String line) throws IOException
+ {
+ String desc = line.substring(DEFINITION.length()).trim();
+ if (desc.endsWith("."))
+ {
+ desc = desc.substring(0, desc.length() - 1);
+ }
+
+ /*
+ * pass over any additional DE lines
+ */
+ while ((line = nextLine()) != null)
+ {
+ if (line.startsWith(" "))
+ {
+ // definition continuation line
+ desc += line.trim();
+ }
+ else
+ {
+ break;
+ }
+ }
+ this.description = desc;
+
+ return line;
+ }
+
+ /**
+ * Parses the VERSION line e.g.
+ *
+ * <pre>
+ * VERSION X81322.1
+ * </pre>
+ *
+ * and returns the next line
+ *
+ * @param line
+ * @throws IOException
+ */
+ String parseVersion(String line) throws IOException
+ {
+ /*
+ * extract version part of <accession>.<version>
+ * https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#VersionB
+ */
+ String[] tokens = line.split(WHITESPACE);
+ if (tokens.length > 1)
+ {
+ tokens = tokens[1].split("\\.");
+ if (tokens.length > 1)
+ {
+ this.version = tokens[1];
+ }
+ }
+
+ return nextLine();
+ }
+
+ @Override
+ protected boolean isFeatureContinuationLine(String line)
+ {
+ return line.startsWith(" "); // 6 spaces
+ }
+}
public boolean isEmbedData()
{
return Boolean.valueOf(
- jalview.bin.Cache.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
+ Cache.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
}
@Override
*/
package jalview.io;
+import java.util.Locale;
+
import java.io.File;
import java.io.IOException;
break;
}
}
- data = data.toUpperCase();
+ data = data.toUpperCase(Locale.ROOT);
if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
{
reply = FileFormat.ScoreMatrix;
break;
}
+ if (data.startsWith("LOCUS"))
+ {
+ reply = FileFormat.GenBank;
+ break;
+ }
+ if (data.startsWith("ID "))
+ {
+ if (data.substring(2).trim().split(";").length == 7)
+ {
+ reply = FileFormat.Embl;
+ break;
+ }
+ }
if (data.startsWith("H ") && !aaIndexHeaderRead)
{
aaIndexHeaderRead = true;
if ((lessThan > -1)) // possible Markup Language data i.e HTML,
// RNAML, XML
{
- String upper = data.toUpperCase();
+ String upper = data.toUpperCase(Locale.ROOT);
if (upper.substring(lessThan).startsWith("<HTML"))
{
reply = FileFormat.Html;
*/
package jalview.io;
+import java.util.Locale;
+
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
// check that no stray annotations have been added at the end.
{
SequenceI sq = seqs.elementAt(j - 1);
- if (sq.getName().toUpperCase().startsWith("JPRED"))
+ if (sq.getName().toUpperCase(Locale.ROOT).startsWith("JPRED"))
{
annotSeqs.addElement(sq);
seqs.removeElementAt(--j);
{
private static String version = new BuildDetails().getVersion();
- private String webstartUrl = "http://www.jalview.org/services/launchApp";
+ private String webstartUrl = "https://www.jalview.org/services/launchApp";
private String application = "Jalview";
*/
package jalview.io;
+import java.util.Locale;
+
import java.io.File;
import java.util.Hashtable;
import java.util.Iterator;
if ((i > 0) && (i < (filename.length() - 1)))
{
- return filename.substring(i + 1).toLowerCase();
+ return filename.substring(i + 1).toLowerCase(Locale.ROOT);
}
;
filters = new LinkedHashMap<>(5);
}
- filters.put(extension.toLowerCase(), this);
+ filters.put(extension.toLowerCase(Locale.ROOT), this);
fullDescription = null;
}
*/
package jalview.io;
+import java.util.Locale;
+
import jalview.util.MessageManager;
import java.io.File;
String exts = ff.getExtensions();
for (String ext : exts.split(","))
{
- ext = ext.trim().toLowerCase();
+ ext = ext.trim().toLowerCase(Locale.ROOT);
extensions.put(ext,
desc + ("jar".equals(ext) ? " (old)" : ""));
}
if ((i > 0) && (i < (s.length() - 1)))
{
- ext = s.substring(i + 1).toLowerCase();
+ ext = s.substring(i + 1).toLowerCase(Locale.ROOT);
}
return ext;
*/
package jalview.io;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
while (i < preds.length)
{
- String id = preds[i].getName().toUpperCase();
+ String id = preds[i].getName().toUpperCase(Locale.ROOT);
if (id.startsWith("LUPAS") || id.startsWith("JNET")
|| id.startsWith("JPRED"))
*/
package jalview.io;
+import java.util.Locale;
+
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
public int checkSum(String seq)
{
int check = 0;
- String sequence = seq.toUpperCase();
+ String sequence = seq.toUpperCase(Locale.ROOT);
for (int i = 0; i < sequence.length(); i++)
{
*/
package jalview.io;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
{
value = r.stringMatched(1);
}
- // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
+ // Cache.debug("from '" + field + "' matched '" + value +
// "'");
try
{
}
else
{
- // jalview.bin.Cache.log.debug(
+ // Cache.debug(
// "Ignoring non-Modeller description: invalid integer-like
// field '" + field + "'");
type = -1; /* invalid field! - throw the FieldSet away */
// TODO: Extended SequenceNodeI to hold parsed NHX strings
package jalview.io;
+import java.util.Locale;
+
import jalview.datamodel.SequenceNode;
import jalview.util.MessageManager;
try
{
// parse out code/value pairs
- if (code.toLowerCase().equals("b"))
+ if (code.toLowerCase(Locale.ROOT).equals("b"))
{
int v = -1;
Float iv = Float.valueOf(value);
private static final String FEATURE_RES_NUM = PDBChain.RESNUM_FEATURE;
@Override
- public boolean isFeatureDisplayed(String type)
+ public boolean isFeatureHidden(String type)
{
- return type.equalsIgnoreCase(FEATURE_INSERTION)
- || type.equalsIgnoreCase(FEATURE_RES_NUM);
+ return type.equalsIgnoreCase(FEATURE_RES_NUM);
}
@Override
*/
package jalview.io;
+import java.util.Locale;
+
import java.util.Collection;
import java.util.Comparator;
import java.util.LinkedHashMap;
* if this is a virtual features, convert begin/end to the
* coordinates of the sequence it is mapped to
*/
- int[] beginRange = null;
- int[] endRange = null;
+ int[] beginRange = null; // feature start in local coordinates
+ int[] endRange = null; // feature end in local coordinates
if (mf != null)
{
- beginRange = mf.getMappedPositions(begin, begin);
- endRange = mf.getMappedPositions(end, end);
+ if (feature.isContactFeature())
+ {
+ /*
+ * map start and end points individually
+ */
+ beginRange = mf.getMappedPositions(begin, begin);
+ endRange = begin == end ? beginRange
+ : mf.getMappedPositions(end, end);
+ }
+ else
+ {
+ /*
+ * map the feature extent
+ */
+ beginRange = mf.getMappedPositions(begin, end);
+ endRange = beginRange;
+ }
if (beginRange == null || endRange == null)
{
// something went wrong
* truncate overlong descriptions unless they contain an href
* before the truncation point (as truncation could leave corrupted html)
*/
- int linkindex = description.toLowerCase().indexOf("<a ");
+ int linkindex = description.toLowerCase(Locale.ROOT).indexOf("<a ");
boolean hasLink = linkindex > -1
&& linkindex < MAX_DESCRIPTION_LENGTH;
if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
+ "\" target=\""
+ urllink.get(0)
+ "\">"
- + (urllink.get(0).toLowerCase()
- .equals(urllink.get(1).toLowerCase()) ? urllink
+ + (urllink.get(0).toLowerCase(Locale.ROOT)
+ .equals(urllink.get(1).toLowerCase(Locale.ROOT)) ? urllink
.get(0) : (urllink.get(0) + ":" + urllink
.get(1)))
+ "</a><br/>");
import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
import jalview.util.Format;
import jalview.util.MessageManager;
-// import org.apache.log4j.*;
-
/**
* This class is supposed to parse a Stockholm format file into Jalview There
* are TODOs in this class: we do not know what the database source and version
{
private static final String ANNOTATION = "annotation";
-// private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
-//
-// private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
+ // private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+ //
+ // private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
public static final Regex DETECT_BRACKETS = new Regex(
"(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
- // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using NOT_RNASS first.
+ // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using
+ // NOT_RNASS first.
public static final String RNASS_BRACKETS = "<>[](){}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz";
// use the following regex to decide an annotations (whole) line is NOT an RNA
Regex openparen = new Regex("(<|\\[)", "(");
Regex closeparen = new Regex("(>|\\])", ")");
-// // Detect if file is RNA by looking for bracket types
-// Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
+ // // Detect if file is RNA by looking for bracket types
+ // Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
rend.optimize();
p.optimize();
if (dbr != null)
{
// we could get very clever here - but for now - just try to
- // guess accession type from type of sequence, source of alignment plus
+ // guess accession type from type of sequence, source of alignment
+ // plus
// structure
// of accession
guessDatabaseFor(seqO, dbr, dbsource);
treeName = an.stringMatched(2);
treeString = new StringBuffer();
}
- // TODO: JAL-3532 - this is where GF comments and database references are lost
- // suggest overriding this method for Stockholm files to catch and properly
+ // TODO: JAL-3532 - this is where GF comments and database
+ // references are lost
+ // suggest overriding this method for Stockholm files to catch and
+ // properly
// process CC, DR etc into multivalued properties
setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
}
}
if (dbsource == null)
{
- // make up an origin based on whether the sequence looks like it is nucleotide
+ // make up an origin based on whether the sequence looks like it is
+ // nucleotide
// or protein
dbsource = (seqO.isProtein()) ? "PFAM" : "RFAM";
}
return ref.getSource().toString() + " ; "
+ ref.getAccessionId().toString();
}
+
@Override
public String print(SequenceI[] s, boolean jvSuffix)
{
}
else
{
- key = type2id(aa.label.toLowerCase());
+ key = type2id(aa.label.toLowerCase(Locale.ROOT));
if (key == null)
{
label = aa.label;
pdbSequence.setName(getId() + "|" + pdbSequence.getName());
PDBEntry entry = new PDBEntry();
entry.setId(getId());
+ entry.setFakedPDBId(!isPPDBIdAvailable());
entry.setType(getStructureFileType());
if (chain.id != null)
{
*/
package jalview.io;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.GraphLine;
Vobject obj = getjv2vObj(seqsetidobj);
if (obj != null && !(obj instanceof Alignment))
{
- Cache.log.warn(
+ Console.warn(
"IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:"
+ seqsetidobj + " to object " + obj);
}
}
else
{
- Cache.log.warn("Unexpected mapping for Jalview String Object ID "
+ Console.warn("Unexpected mapping for Jalview String Object ID "
+ seqsetidobj + " to another jalview dataset object "
+ seqsetidobj);
}
}
}
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Returning null VorbaID binding for jalview object " + jvobj);
}
return null;
if (id == null)
{
id = cdoc.registerObject(vobj);
- Cache.log.debug(
+ Console.debug(
"Registering new object and returning null for getvObj2jv");
return null;
}
if (id == null || vobj.getVorbaId() == null
|| cdoc.getObject(id) != vobj)
{
- Cache.log.error("Failed to get id for "
+ Console.error("Failed to get id for "
+ (vobj.isRegisterable() ? "registerable"
: "unregisterable")
+ " object " + vobj);
if (vobj2jv.containsKey(vobj.getVorbaId())
&& !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
- Cache.log.debug(
+ Console.debug(
"Warning? Overwriting existing vamsas id binding for "
+ vobj.getVorbaId(),
new Exception(MessageManager.getString(
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
{
- Cache.log.debug(
+ Console.debug(
"Warning? Overwriting existing jalview object binding for "
+ jvobj,
new Exception("Overwriting jalview object binding."));
}
/*
- * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
+ * Cache.error("Attempt to make conflicting object binding! "+vobj+" id "
* +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+"
* already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to
* bindjvvobj")); }
*/
// we just update the hash's regardless!
- Cache.log.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
+ Console.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
vobj2jv.put(vobj.getVorbaId(), jvobj);
// JBPNote - better implementing a hybrid invertible hash.
jv2vobj.put(jvobj, vobj.getVorbaId());
DataSet dataset = null;
if (jds == null)
{
- Cache.log.warn("Creating new dataset for an alignment.");
+ Console.warn("Creating new dataset for an alignment.");
jal.setDataset(null);
jds = jal.getDataset();
}
if (dataset == null)
{
- Cache.log.warn("Creating new vamsas dataset for alignment view "
+ Console.warn("Creating new vamsas dataset for alignment view "
+ av.getSequenceSetId());
// we create a new dataset on the default vamsas root.
root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.
if (aa[i].groupRef != null)
{
// TODO: store any group associated annotation references
- Cache.log.warn(
+ Console.warn(
"Group associated sequence annotation is not stored in VAMSAS document.");
continue;
}
// LOCK METHODS)
{
// verify annotation - update (perhaps)
- Cache.log.info(
+ Console.info(
"update alignment sequence annotation. not yet implemented.");
}
else
{
// verify annotation - update (perhaps)
- Cache.log.info(
+ Console.info(
"updated alignment sequence annotation added.");
}
}
}
if (getjv2vObj(jvalsq.getDatasetSequence()) == null)
{
- Cache.log.warn(
+ Console.warn(
"Serious Implementation error - Unbound dataset sequence in alignment: "
+ jvalsq.getDatasetSequence());
}
alseq.setDescription(valseq.getDescription());
modal = true;
}
- if (modal && Cache.log.isDebugEnabled())
+ if (modal && Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Updating apparently edited sequence " + alseq.getName());
}
}
}
else
{
- Cache.log.error(
+ Console.error(
"Invalid dataset sequence id (null) for alignment sequence "
+ valseq.getVorbaId());
}
@Override
public JarInputStream getJarInputStream() throws IOException
{
- jalview.bin.Cache.log.debug(
+ Console.debug(
"Returning client input stream for Jalview from Vamsas Document.");
return new JarInputStream(cappdata.getClientInputStream());
}
@Override
public JarInputStream getJarInputStream() throws IOException
{
- jalview.bin.Cache.log.debug(
+ Console.debug(
"Returning user input stream for Jalview from Vamsas Document.");
return new JarInputStream(cappdata.getUserInputStream());
}
// TODO implement this : af.getNumberOfViews
String seqsetidobj = av.getSequenceSetId();
views = Desktop.getViewports(seqsetidobj);
- Cache.log
- .debug("Found " + (views == null ? " no " : "" + views.length)
+ Console.debug("Found " + (views == null ? " no " : "" + views.length)
+ " views for '" + av.getSequenceSetId() + "'");
if (views.length > 1)
{
} catch (Exception e)
{
// TODO raise GUI warning if user requests it.
- jalview.bin.Cache.log.error(
+ Console.error(
"Couldn't update jalview client application data. Giving up - local settings probably lost.",
e);
}
}
else
{
- jalview.bin.Cache.log.error(
+ Console.error(
"Couldn't access client application data for vamsas session. This is probably a vamsas client bug.");
}
}
int jremain = 0;
if (jdataset == null)
{
- Cache.log.debug("Initialising new jalview dataset fields");
+ Console.debug("Initialising new jalview dataset fields");
newds = true;
dsseqs = new Vector();
}
else
{
- Cache.log.debug("Update jalview dataset from vamsas.");
+ Console.debug("Update jalview dataset from vamsas.");
jremain = jdataset.getHeight();
dsseqs = jdataset.getSequences();
}
dsseqs.set(i, null);
}
jdataset = new jalview.datamodel.Alignment(seqs);
- Cache.log.debug("New vamsas dataset imported into jalview.");
+ Console.debug("New vamsas dataset imported into jalview.");
bindjvvobj(jdataset, dataset);
}
// ////////
// annotations
if (dsSeq == null)
{
- jalview.bin.Cache.log.warn(
+ Console.warn(
"Couldn't resolve jalview sequenceI for dataset object reference "
+ ((Vobject) dataset
.getDataSetAnnotations(dsa)
// JBPNote: we could just add them to all alignments but
// that may complicate cross references in the jalview
// datamodel
- Cache.log.warn(
+ Console.warn(
"Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");
}
}
}
else
{
- Cache.log.warn(
+ Console.warn(
"Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features.");
}
}
// OBJECT LOCK
// METHODS)
{
- Cache.log.info(
+ Console.info(
"UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
// TODO: should at least replace with new one - otherwise
// things will break
dsseqs.set(i, null);
}
jal = new jalview.datamodel.Alignment(seqs);
- Cache.log.debug("New vamsas alignment imported into jalview "
+ Console.debug("New vamsas alignment imported into jalview "
+ alignment.getVorbaId().getId());
jal.setDataset(jdataset);
}
// jan.update(getjAlignmentAnnotation(jal, an[a])); // update
// from another annotation object in place.
- Cache.log.debug(
+ Console.debug(
"update from vamsas alignment annotation to existing jalview alignment annotation.");
if (an[j].getModifiable() == null) // TODO: USE VAMSAS
// LIBRARY OBJECT LOCK
{
// TODO: user defined annotation is totally mutable... - so
// load it up or throw away if locally edited.
- Cache.log.info(
+ Console.info(
"NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
}
// TODO: compare annotation element rows
AlignFrame alignFrame;
if (av == null)
{
- Cache.log.debug("New alignframe for alignment "
+ Console.debug("New alignframe for alignment "
+ alignment.getVorbaId());
// ///////////////////////////////
// construct alignment view
}
// TODO: automatically create meaningful title for a vamsas
// alignment using its provenance.
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
title = title + "(" + alignment.getVorbaId() + ")";
vstree.UpdateSequenceTreeMap(tp);
} catch (RuntimeException e)
{
- Cache.log.warn("update of labels failed.", e);
+ Console.warn("update of labels failed.", e);
}
}
else
{
- Cache.log.warn("Cannot create tree for tree " + t
+ Console.warn("Cannot create tree for tree " + t
+ " in document ("
+ alignment.getTree(t).getVorbaId());
}
if (anot[row][pos] != null)
{
// only time this should happen is if the After flag is set.
- Cache.log.debug("Ignoring duplicate annotation site at " + pos);
+ Console.debug("Ignoring duplicate annotation site at " + pos);
continue;
}
if (anot[1 - row][pos] != null)
else if (glyphs[g].getDict().equals(
uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
{
- Cache.log.debug("ignoring hydrophobicity glyph marker.");
+ Console.debug("ignoring hydrophobicity glyph marker.");
AeContent[HASHPHOB] = true;
char c = (dc = glyphs[g].getContent()).charAt(0);
// dc may get overwritten - but we still set the colour.
}
else
{
- Cache.log.debug(
+ Console.debug(
"IMPLEMENTATION TODO: Ignoring unknown glyph type "
+ glyphs[g].getDict());
}
AeContent[HASVALS] = true;
if (ae[aa].getValueCount() > 1)
{
- Cache.log.warn(
+ Console.warn(
"ignoring additional " + (ae[aa].getValueCount() - 1)
+ " values in annotation element.");
}
}
else
{
- Cache.log.warn("Ignoring out of bound annotation element " + aa
+ Console.warn("Ignoring out of bound annotation element " + aa
+ " in " + annotation.getVorbaId().getId());
}
}
val = Float.valueOf(props[p].getContent());
} catch (Exception e)
{
- Cache.log.warn("Failed to parse threshold property");
+ Console.warn("Failed to parse threshold property");
}
if (val != null)
{
}
if (parsedRangeAnnotation == null)
{
- Cache.log.debug(
+ Console.debug(
"Inserting empty annotation row elements for a whole-alignment annotation.");
}
else
{
if (parsedRangeAnnotation[3] != null)
{
- Cache.log.warn("Ignoring 'After' annotation row in "
+ Console.warn("Ignoring 'After' annotation row in "
+ annotation.getVorbaId());
}
jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) parsedRangeAnnotation[2];
}
if (annotation.getLinkCount() > 0)
{
- Cache.log.warn("Ignoring " + annotation.getLinkCount()
+ Console.warn("Ignoring " + annotation.getLinkCount()
+ "links added to AlignmentAnnotation.");
}
if (annotation.getModifiable() == null
}
} catch (Exception e)
{
- Cache.log.info(
+ Console.info(
"UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
}
return jan;
DataSet dataset = null;
if (jal.getDataset() == null)
{
- Cache.log.warn("Creating new dataset for an alignment.");
+ Console.warn("Creating new dataset for an alignment.");
jal.setDataset(null);
}
dataset = (DataSet) ((Alignment) getjv2vObj(
if (dataset == null)
{
dataset = (DataSet) getjv2vObj(jal.getDataset());
- Cache.log.error(
+ Console.error(
"Can't find the correct dataset for the alignment in this view. Creating new one.");
}
}
else
{
- Cache.log.warn(
+ Console.warn(
"NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR "
+ dmps[smp].getDisplayId(true) + " to "
+ mps[smp].getTo().getName());
*/
package jalview.io.gff;
+import java.util.Locale;
+
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.MappingType;
// e.g. exonerate:protein2genome:local
if (model != null)
{
- String mdl = model.toLowerCase();
+ String mdl = model.toLowerCase(Locale.ROOT);
if (mdl.contains(PROTEIN2DNA) || mdl.contains(PROTEIN2GENOME)
|| mdl.contains(CODING2CODING) || mdl.contains(CODING2GENOME)
|| mdl.contains(CDNA2GENOME) || mdl.contains(GENOME2GENOME))
*/
package jalview.io.packed;
+import java.util.Locale;
+
import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
String type = args[i++];
final String file = args[i++];
final JvDataType jtype = DataProvider.JvDataType
- .valueOf(type.toUpperCase());
+ .valueOf(type.toUpperCase(Locale.ROOT));
if (jtype != null)
{
final FileParse fp;
else
{
System.out.println("Couldn't parse source type token '"
- + type.toUpperCase() + "'");
+ + type.toUpperCase(Locale.ROOT) + "'");
}
}
if (i < args.length)
*/
package jalview.io.vamsas;
-import jalview.bin.Cache;
-import jalview.io.VamsasAppDatastore;
-import jalview.util.MessageManager;
-
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Vector;
+import jalview.bin.Console;
+import jalview.io.VamsasAppDatastore;
+import jalview.log.JLoggerLog4j;
+import jalview.util.MessageManager;
import uk.ac.vamsas.client.IClientDocument;
import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.client.VorbaId;
/**
* shared log instance
*/
- protected static org.apache.log4j.Logger log = org.apache.log4j.Logger
+ protected static JLoggerLog4j log = JLoggerLog4j
.getLogger(DatastoreItem.class);
/**
{
return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
}
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Returning null VorbaID binding for jalview object " + jvobj);
}
return null;
if (id == null)
{
id = cdoc.registerObject(vobj);
- Cache.log.debug(
+ Console.debug(
"Registering new object and returning null for getvObj2jv");
return null;
}
if (id == null || vobj.getVorbaId() == null
|| cdoc.getObject(id) != vobj)
{
- Cache.log.error("Failed to get id for "
+ Console.error("Failed to get id for "
+ (vobj.isRegisterable() ? "registerable"
: "unregisterable")
+ " object " + vobj);
if (vobj2jv.containsKey(vobj.getVorbaId())
&& !(vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
- Cache.log.debug(
+ Console.debug(
"Warning? Overwriting existing vamsas id binding for "
+ vobj.getVorbaId(),
new Exception(MessageManager.getString(
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
{
- Cache.log.debug(
+ Console.debug(
"Warning? Overwriting existing jalview object binding for "
+ jvobj,
new Exception(MessageManager.getString(
"exception.overwriting_jalview_id_binding")));
}
/*
- * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
+ * Cache.error("Attempt to make conflicting object binding! "+vobj+" id "
* +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+"
* already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to
* bindjvvobj")); }
*/
// we just update the hash's regardless!
- Cache.log.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
+ Console.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
vobj2jv.put(vobj.getVorbaId(), jvobj);
// JBPNote - better implementing a hybrid invertible hash.
jv2vobj.put(jvobj, vobj.getVorbaId());
{
if (this.jvobj != null && this.vobj != null)
{
- Cache.log.debug("updating dsobj registry. ("
- + this.getClass().getName() + ")");
+ Console.debug("updating dsobj registry. (" + this.getClass().getName()
+ + ")");
}
this.jvobj = jvobj;
this.vobj = vobj;
import java.util.Iterator;
import java.util.Map;
+import jalview.log.JLoggerLog4j;
+
public class DatastoreRegistry implements AutoCloseable
{
- protected static org.apache.log4j.Logger log = org.apache.log4j.Logger
+ protected static JLoggerLog4j log = JLoggerLog4j
.getLogger(DatastoreRegistry.class);
/**
*/
package jalview.io.vamsas;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
import jalview.io.VamsasAppDatastore;
}
else
{
- jalview.bin.Cache.log.debug(
+ Console.debug(
"Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
}
// TODO: Jalview ignores all the other maps
if (vobj.getMapCount() > 1)
{
- jalview.bin.Cache.log
- .debug("Ignoring additional mappings on DbRef: "
+ Console.debug("Ignoring additional mappings on DbRef: "
+ jvobj.getSource() + ":" + jvobj.getAccessionId());
}
jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
{
DbRef vobj = (DbRef) this.vobj;
DBRefEntry jvobj = (DBRefEntry) this.jvobj;
- jalview.bin.Cache.log
- .debug("Conflict in dbentry update for " + vobj.getAccessionId()
+ Console.debug("Conflict in dbentry update for " + vobj.getAccessionId()
+ vobj.getSource() + " " + vobj.getVorbaId());
// TODO Auto-generated method stub
// TODO: Jalview ignores all the other maps
if (vobj.getMapCount() > 1)
{
- jalview.bin.Cache.log
- .debug("Ignoring additional mappings on DbRef: "
+ Console.debug("Ignoring additional mappings on DbRef: "
+ jvobj.getSource() + ":" + jvobj.getAccessionId());
}
jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
}
else
{
- jalview.bin.Cache.log.debug(
+ Console.debug(
"Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
}
}
*/
package jalview.io.vamsas;
+import jalview.bin.Console;
import jalview.io.VamsasAppDatastore;
import jalview.util.MessageManager;
{
if (!map.getLocal().hasUnit() || map.getMapped().hasUnit())
{
- jalview.bin.Cache.log
- .warn("using default mapping length of 1:1 for map "
+ Console.warn("using default mapping length of 1:1 for map "
+ (map.isRegistered() ? map.getVorbaId().toString()
: ("<no Id registered> " + map.toString())));
}
*/
package jalview.io.vamsas;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.VamsasAppDatastore;
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
if (dsa.getSeqRefCount() != 1)
{
- Cache.log.warn("Not binding " + dsa.getVorbaId()
+ Console.warn("Not binding " + dsa.getVorbaId()
+ " to Sequence Feature - has multiple dataset sequence references.");
return;
}
if (dsa.getSeqRefCount() != 1)
{
replaceJvObjMapping(feature, null);
- Cache.log.warn(
+ Console.warn(
"Binding of annotation to jalview feature has changed. Removing binding and recreating.");
doSync(); // re-verify bindings.
}
getDSAnnotationFromJalview(dsa, feature);
if (oldref != dsa.hashCode())
{
- Cache.log
- .debug("Updated dataset sequence annotation from feature.");
+ Console.debug("Updated dataset sequence annotation from feature.");
addProvenance(dsa.getProvenance(), "modified");
}
}
{
// conflicting update from document - we cannot map this feature anymore.
replaceJvObjMapping(feature, null);
- Cache.log.warn("annotation (" + dsa.getVorbaId()
+ Console.warn("annotation (" + dsa.getVorbaId()
+ " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
// - consider deleting the feature ?
dsSeq.deleteFeature(feature);
vSeg.setInclusive(true);
if (dsa.getSegCount() > 1)
{
- Cache.log.debug(
+ Console.debug(
"About to destroy complex annotation in vamsas document mapped to sequence feature ("
+ dsa.getVorbaId() + ")");
}
*/
package jalview.io.vamsas;
+import jalview.bin.Console;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
}
if (from != null && sequenceMapping.getLoc() != from)
{
- jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + from
+ Console.warn("Probable IMPLEMENTATION ERROR: " + from
+ " doesn't match the local mapping sequence.");
}
if (ds != null && sequenceMapping.is__stored_in_document()
&& sequenceMapping.getV_parent() != ds)
{
- jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + ds
+ Console.warn("Probable IMPLEMENTATION ERROR: " + ds
+ " doesn't match the parent of the bound sequence mapping object.");
}
}
SequenceType to = (SequenceType) getjv2vObj(jvto);
if (to == null)
{
- jalview.bin.Cache.log.warn(
+ Console.warn(
"FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
return;
}
if (!dnaToProt)
{
- jalview.bin.Cache.log.warn(
+ Console.warn(
"Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
return;
}
// mapping
bindjvvobj(mjvmapping.getMap(), sequenceMapping);
- jalview.bin.Cache.log.debug(
+ Console.debug(
"Successfully created mapping " + sequenceMapping.getVorbaId());
}
// private void update(jalview.util.MapList mjvmapping,
// SequenceMapping sequenceMapping)
{
- jalview.bin.Cache.log
- .error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
+ Console.error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
}
private void update(SequenceMapping sequenceMapping,
jalview.datamodel.Mapping mjvmapping)
{
- jalview.bin.Cache.log
- .error("Not implemented: Update DBRef Mapping from Jalview");
+ Console.error("Not implemented: Update DBRef Mapping from Jalview");
}
private void update(jalview.datamodel.Mapping mjvmapping,
SequenceMapping sequenceMapping)
{
- jalview.bin.Cache.log.error(
+ Console.error(
"Not implemented: Jalview Update Sequence DBRef Mapping");
}
}
if (sdloc == null || sdmap == null)
{
- jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
+ Console.info("Ignoring non sequence-sequence mapping");
return;
}
mobj = this.getvObj2jv(sdloc);
if (from == null || to == null)
{
- jalview.bin.Cache.log.error(
+ Console.error(
"Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
return;
}
{
if (from.getDBRefs() == null && to.getDBRefs() == null)
{
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Not matching conjugate refs for "
+ Console.debug("Not matching conjugate refs for "
+ from.getName() + " and " + to.getName());
}
return;
}
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Matching conjugate refs for "
+ Console.debug("Matching conjugate refs for "
+ from.getName() + " and " + to.getName());
}
List<DBRefEntry> fdb = from.getDBRefs();
boolean fmpnnl = (fmp != null);
// if (fmpnnl && fmp.getTo()!=null)
// {
- // jalview.bin.Cache.log.debug("Not overwriting existing To reference in
+ // Cache.debug("Not overwriting existing To reference in
// "+fe);
// continue;
// }
import jalview.analysis.TreeBuilder;
import jalview.analysis.TreeModel;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
}
} catch (Exception e)
{
- Cache.log.warn("Problems parsing treefile '"
+ Console.warn("Problems parsing treefile '"
+ tree.getNewick(0).getContent() + "'", e);
}
}
@Override
public void conflict()
{
- Cache.log.info(
+ Console.info(
"Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
}
* idata[0] != null) { inputData = (AlignmentView) idata[0]; } ntree =
* getNtree(); title = tree.getNewick(0).getTitle(); if (title == null ||
* title.length() == 0) { title = tree.getTitle(); // hack!!!! } } catch
- * (Exception e) { Cache.log.warn("Problems parsing treefile '" +
+ * (Exception e) { Cache.warn("Problems parsing treefile '" +
* tree.getNewick(0).getContent() + "'", e); }
*/
log.debug("Update the local tree in jalview from the document.");
*/
private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
{
- Cache.log.debug("Making Tree provenance for " + tp.getTitle());
+ Console.debug("Making Tree provenance for " + tp.getTitle());
Provenance prov = new Provenance();
prov.addEntry(new Entry());
prov.getEntry(0).setAction("imported " + tp.getTitle());
vInput.addSeg(visSeg);
}
}
- Cache.log.debug("Finished Tree provenance for " + tp.getTitle());
+ Console.debug("Finished Tree provenance for " + tp.getTitle());
return prov;
}
}
if (alsq.size() < sequences.length)
{
- Cache.log.warn(
+ Console.warn(
"Not recovered all alignment sequences for given set of input sequence CIGARS");
}
return alsq;
if (tp.getTree() == null)
{
- Cache.log.warn(
+ Console.warn(
"Not updating SequenceTreeMap for " + tree.getVorbaId());
return;
}
{
if (tp.getEntry(pe).getInputCount() > 1)
{
- Cache.log.warn(
+ Console.warn(
"Ignoring additional input spec in provenance entry "
+ tp.getEntry(pe).toString());
}
// bidirection alignments yet.
if (to < se[1])
{
- Cache.log.warn("Ignoring invalid segment in InputData spec.");
+ Console.warn("Ignoring invalid segment in InputData spec.");
}
else
{
return new Object[] { new AlignmentView(view), jal };
}
}
- Cache.log.debug(
+ Console.debug(
"Returning null for input data recovery from provenance.");
return null;
}
return true;
} catch (Exception e)
{
- Cache.log.debug("Failed to parse newick tree string", e);
+ Console.debug("Failed to parse newick tree string", e);
}
return false;
}
*/
package jalview.io.vcf;
-import jalview.analysis.Dna;
-import jalview.api.AlignViewControllerGuiI;
-import jalview.bin.Cache;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.GeneLociI;
-import jalview.datamodel.Mapping;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.FeatureAttributeType;
-import jalview.datamodel.features.FeatureSource;
-import jalview.datamodel.features.FeatureSources;
-import jalview.ext.ensembl.EnsemblMap;
-import jalview.ext.htsjdk.HtsContigDb;
-import jalview.ext.htsjdk.VCFReader;
-import jalview.io.gff.Gff3Helper;
-import jalview.io.gff.SequenceOntologyI;
-import jalview.util.MapList;
-import jalview.util.MappingUtils;
-import jalview.util.MessageManager;
-import jalview.util.StringUtils;
+import java.util.Locale;
import java.io.File;
import java.io.IOException;
import htsjdk.variant.vcf.VCFHeaderLineCount;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
+import jalview.analysis.Dna;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLociI;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureAttributeType;
+import jalview.datamodel.features.FeatureSource;
+import jalview.datamodel.features.FeatureSources;
+import jalview.ext.ensembl.EnsemblMap;
+import jalview.ext.htsjdk.HtsContigDb;
+import jalview.ext.htsjdk.VCFReader;
+import jalview.io.gff.Gff3Helper;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+import jalview.util.StringUtils;
/**
* A class to read VCF data (using the htsjdk) and add variants as sequence
VCFHeaderLine headerLine = header.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
if (headerLine == null)
{
- Cache.log.error("VCF reference header not found");
+ Console.error("VCF reference header not found");
return null;
}
String ref = headerLine.getValue();
}
else
{
- Cache.log.error("VCF reference not found: " + ref);
+ Console.error("VCF reference not found: " + ref);
}
return seq;
{
if (reference == null)
{
- Cache.log.error("No VCF ##reference found, defaulting to "
+ Console.error("No VCF ##reference found, defaulting to "
+ DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
}
- reference = reference.toLowerCase();
+ reference = reference.toLowerCase(Locale.ROOT);
/*
* for a non-human species, or other assembly identifier,
String[] tokens = token.split("=");
if (tokens.length == 2)
{
- if (reference.contains(tokens[0].trim().toLowerCase()))
+ if (reference.contains(tokens[0].trim().toLowerCase(Locale.ROOT)))
{
vcfAssembly = tokens[1].trim();
break;
String[] tokens = token.split("=");
if (tokens.length == 2)
{
- if (reference.contains(tokens[0].trim().toLowerCase()))
+ if (reference.contains(tokens[0].trim().toLowerCase(Locale.ROOT)))
{
vcfSpecies = tokens[1].trim();
break;
{
for (Pattern p : filters)
{
- if (p.matcher(id.toUpperCase()).matches())
+ if (p.matcher(id.toUpperCase(Locale.ROOT)).matches())
{
return true;
}
{
try
{
- patterns.add(Pattern.compile(token.toUpperCase()));
+ patterns.add(Pattern.compile(token.toUpperCase(Locale.ROOT)));
} catch (PatternSyntaxException e)
{
System.err.println("Invalid pattern ignored: " + token);
/**
* Transfers VCF features to sequences to which this sequence has a mapping.
- * If the mapping is 3:1, computes peptide variants from nucleotide variants.
*
* @param seq
*/
GeneLociI seqCoords = seq.getGeneLoci();
if (seqCoords == null)
{
- Cache.log.warn(String.format(
+ Console.warn(String.format(
"Can't query VCF for %s as chromosome coordinates not known",
seq.getName()));
return null;
// returned with the Ensembl sequence; todo: support aliases?
if (!vcfSpecies.equalsIgnoreCase(species))
{
- Cache.log.warn("No VCF loaded to " + seq.getName()
+ Console.warn("No VCF loaded to " + seq.getName()
+ " as species not matched");
return null;
}
vcfAssembly);
if (newRange == null)
{
- Cache.log.error(
+ Console.error(
String.format("Failed to map %s:%s:%s:%d:%d to %s", species,
chromosome, seqRef, range[0], range[1],
vcfAssembly));
int[] featureRange = map.map.locateInFrom(variant.getStart(),
variant.getEnd());
+ /*
+ * only take features whose range is fully mappable to sequence positions
+ */
if (featureRange != null)
{
int featureStart = Math.min(featureRange[0], featureRange[1]);
int featureEnd = Math.max(featureRange[0], featureRange[1]);
- count += addAlleleFeatures(seq, variant, featureStart,
- featureEnd, forwardStrand);
+ if (featureEnd - featureStart == variant.getEnd()
+ - variant.getStart())
+ {
+ count += addAlleleFeatures(seq, variant, featureStart,
+ featureEnd, forwardStrand);
+ }
}
}
variants.close();
*/
String msg = String.format("Error reading VCF for %s:%d-%d: %s ",
map.chromosome, vcfStart, vcfEnd,e.getLocalizedMessage());
- Cache.log.error(msg);
+ Console.error(msg);
}
}
*/
String consequence = getConsequenceForAlleleAndFeature(variant, CSQ_FIELD,
altAlleleIndex, csqAlleleFieldIndex,
- csqAlleleNumberFieldIndex, seq.getName().toLowerCase(),
+ csqAlleleNumberFieldIndex, seq.getName().toLowerCase(Locale.ROOT),
csqFeatureFieldIndex);
/*
{
String featureIdentifier = csqFields[featureFieldIndex];
if (featureIdentifier.length() > 4
- && seqName.indexOf(featureIdentifier.toLowerCase()) > -1)
+ && seqName.indexOf(featureIdentifier.toLowerCase(Locale.ROOT)) > -1)
{
/*
* feature (transcript) matched - now check for allele match
VCFInfoHeaderLine infoHeader = header.getInfoHeaderLine(infoId);
if (infoHeader == null)
{
- Cache.log.error("Field " + infoId + " has no INFO header");
+ Console.error("Field " + infoId + " has no INFO header");
return false;
}
VCFHeaderLineType infoType = infoHeader.getType();
if (!badData.contains(token))
{
badData.add(token);
- Cache.log.error(String.format("Invalid VCF data at %s:%d %s=%s",
+ Console.error(String.format("Invalid VCF data at %s:%d %s=%s",
variant.getContig(), variant.getStart(), infoId, value));
}
}
if (seq != last || i != index)
{
// this should really be a trace message.
- // Cache.log.debug("Mouse over " + v.getId() + " bound to "
+ // Cache.debug("Mouse over " + v.getId() + " bound to "
// + seq + " at " + index);
last = seq;
i = index;
+++ /dev/null
-package jalview.javascript.log4j;
-
-import jalview.javascript.log4j.spi.LoggingEvent;
-
-public abstract class Appender
-{
- public abstract void append(LoggingEvent loggingEvent);
-
-}
+++ /dev/null
-package jalview.javascript.log4j;
-
-import jalview.javascript.log4j.spi.LoggingEvent;
-
-public class ConsoleAppender
-{
-
- private String name;
-
- private Layout layout;
-
-
- public ConsoleAppender()
- {
- }
-
- public ConsoleAppender(Layout layout, String name)
- {
- this.layout = layout;
- this.name = name;
- }
-
- public void setLayout(Layout layout)
- {
- this.layout = layout;
- }
-
- public void setName(String name)
- {
- this.name = name;
- }
-
- public void append(LoggingEvent event)
- {
-
- System.out
- .println(event.getLevel() + ": " + event.getRenderedMessage());
-
- }
-
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.javascript.log4j;
-
-import jalview.javascript.log4j.spi.LoggingEvent;
-import jalview.javascript.log4j.spi.OptionHandler;
-
-import org.apache.log4j.PatternLayout;
-import org.apache.log4j.TTCCLayout;
-
-public abstract class Layout implements OptionHandler
-{
-
- // Note that the line.separator property can be looked up even by
- // applets.
- public final static String LINE_SEP = System
- .getProperty("line.separator");
-
- public final static int LINE_SEP_LEN = LINE_SEP.length();
-
- /**
- * Implement this method to create your own layout format.
- */
- abstract public String format(LoggingEvent event);
-
- /**
- * Returns the content type output by this layout. The base class returns
- * "text/plain".
- */
- public String getContentType()
- {
- return "text/plain";
- }
-
- /**
- * Returns the header for the layout format. The base class returns
- * <code>null</code>.
- */
- public String getHeader()
- {
- return null;
- }
-
- /**
- * Returns the footer for the layout format. The base class returns
- * <code>null</code>.
- */
- public String getFooter()
- {
- return null;
- }
-
- /**
- * If the layout handles the throwable object contained within
- * {@link LoggingEvent}, then the layout should return <code>false</code>.
- * Otherwise, if the layout ignores throwable object, then the layout should
- * return <code>true</code>. If ignoresThrowable is true, the appender is
- * responsible for rendering the throwable.
- * <p>
- * The {@link SimpleLayout}, {@link TTCCLayout}, {@link PatternLayout} all
- * return <code>true</code>. The {@link org.apache.log4j.xml.XMLLayout}
- * returns <code>false</code>.
- *
- * @since 0.8.4
- */
- abstract public boolean ignoresThrowable();
-
-}
+++ /dev/null
-package jalview.javascript.log4j;
-
-import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
-import java.io.ObjectStreamException;
-import java.io.Serializable;
-
-/**
- * Defines the minimum set of levels recognized by the system, that is
- * <code>OFF</code>, <code>FATAL</code>, <code>ERROR</code>, <code>WARN</code>,
- * <code>INFO</code>, <code>DEBUG</code> and <code>ALL</code>.
- *
- * <p>
- * The <code>Level</code> class may be subclassed to define a larger level set.
- * </p>
- *
- * @author Ceki Gülcü
- */
-public class Level extends Priority implements Serializable
-{
-
- private static final String ALL_NAME = "ALL";
-
- private static final String TRACE_NAME = "TRACE";
-
- private static final String DEBUG_NAME = "DEBUG";
-
- private static final String INFO_NAME = "INFO";
-
- private static final String WARN_NAME = "WARN";
-
- private static final String ERROR_NAME = "ERROR";
-
- private static final String FATAL_NAME = "FATAL";
-
- private static final String OFF_NAME = "OFF";
-
- /**
- * TRACE level integer value.
- *
- * @since 1.2.12
- */
- public static final int TRACE_INT = 5000;
-
- /**
- * The <code>OFF</code> has the highest possible rank and is intended to turn
- * off logging.
- */
- final static public Level OFF = new Level(OFF_INT, OFF_NAME, 0);
-
- /**
- * The <code>FATAL</code> level designates very severe error events that will
- * presumably lead the application to abort.
- */
- final static public Level FATAL = new Level(FATAL_INT, FATAL_NAME, 0);
-
- /**
- * The <code>ERROR</code> level designates error events that might still allow
- * the application to continue running.
- */
- final static public Level ERROR = new Level(ERROR_INT, ERROR_NAME, 3);
-
- /**
- * The <code>WARN</code> level designates potentially harmful situations.
- */
- final static public Level WARN = new Level(WARN_INT, WARN_NAME, 4);
-
- /**
- * The <code>INFO</code> level designates informational messages that
- * highlight the progress of the application at coarse-grained level.
- */
- final static public Level INFO = new Level(INFO_INT, INFO_NAME, 6);
-
- /**
- * The <code>DEBUG</code> Level designates fine-grained informational events
- * that are most useful to debug an application.
- */
- final static public Level DEBUG = new Level(DEBUG_INT, DEBUG_NAME, 7);
-
- /**
- * The <code>TRACE</code> Level designates finer-grained informational events
- * than the <code>DEBUG</code level.
- *
- * @since 1.2.12
- */
- public static final Level TRACE = new Level(TRACE_INT, TRACE_NAME, 7);
-
- /**
- * The <code>ALL</code> has the lowest possible rank and is intended to turn
- * on all logging.
- */
- final static public Level ALL = new Level(ALL_INT, ALL_NAME, 7);
-
- /**
- * Serialization version id.
- */
- static final long serialVersionUID = 3491141966387921974L;
-
- /**
- * Instantiate a Level object.
- */
- protected Level(int level, String levelStr, int syslogEquivalent)
- {
- super(level, levelStr, syslogEquivalent);
- }
-
- /**
- * Convert the string passed as argument to a level. If the conversion fails,
- * then this method returns {@link #DEBUG}.
- */
- public static Level toLevel(String sArg)
- {
- return toLevel(sArg, Level.DEBUG);
- }
-
- /**
- * Convert an integer passed as argument to a level. If the conversion fails,
- * then this method returns {@link #DEBUG}.
- */
- public static Level toLevel(int val)
- {
- return toLevel(val, Level.DEBUG);
- }
-
- /**
- * Convert an integer passed as argument to a level. If the conversion fails,
- * then this method returns the specified default.
- */
- public static Level toLevel(int val, Level defaultLevel)
- {
- switch (val)
- {
- case ALL_INT:
- return ALL;
- case DEBUG_INT:
- return Level.DEBUG;
- case INFO_INT:
- return Level.INFO;
- case WARN_INT:
- return Level.WARN;
- case ERROR_INT:
- return Level.ERROR;
- case FATAL_INT:
- return Level.FATAL;
- case OFF_INT:
- return OFF;
- case TRACE_INT:
- return Level.TRACE;
- default:
- return defaultLevel;
- }
- }
-
- /**
- * Convert the string passed as argument to a level. If the conversion fails,
- * then this method returns the value of <code>defaultLevel</code>.
- */
- public static Level toLevel(String sArg, Level defaultLevel)
- {
- if (sArg == null)
- {
- return defaultLevel;
- }
- String s = sArg.toUpperCase();
-
- if (s.equals(ALL_NAME))
- {
- return Level.ALL;
- }
- if (s.equals(DEBUG_NAME))
- {
- return Level.DEBUG;
- }
- if (s.equals(INFO_NAME))
- {
- return Level.INFO;
- }
- if (s.equals(WARN_NAME))
- {
- return Level.WARN;
- }
- if (s.equals(ERROR_NAME))
- {
- return Level.ERROR;
- }
- if (s.equals(FATAL_NAME))
- {
- return Level.FATAL;
- }
- if (s.equals(OFF_NAME))
- {
- return Level.OFF;
- }
- if (s.equals(TRACE_NAME))
- {
- return Level.TRACE;
- }
- //
- // For Turkish i problem, see bug 40937
- //
- if (s.equals("\u0130NFO"))
- {
- return Level.INFO;
- }
- return defaultLevel;
- }
-
- /**
- * Custom deserialization of Level.
- *
- * @param s
- * serialization stream.
- * @throws IOException
- * if IO exception.
- * @throws ClassNotFoundException
- * if class not found.
- */
- private void readObject(final ObjectInputStream s)
- throws IOException, ClassNotFoundException
- {
- s.defaultReadObject();
- level = s.readInt();
- syslogEquivalent = s.readInt();
- levelStr = s.readUTF();
- if (levelStr == null)
- {
- levelStr = "";
- }
- }
-
- /**
- * Serialize level.
- *
- * @param s
- * serialization stream.
- * @throws IOException
- * if exception during serialization.
- */
- private void writeObject(final ObjectOutputStream s) throws IOException
- {
- s.defaultWriteObject();
- s.writeInt(level);
- s.writeInt(syslogEquivalent);
- s.writeUTF(levelStr);
- }
-
- /**
- * Resolved deserialized level to one of the stock instances. May be overriden
- * in classes derived from Level.
- *
- * @return resolved object.
- * @throws ObjectStreamException
- * if exception during resolution.
- */
- private Object readResolve() throws ObjectStreamException
- {
- //
- // if the deserizalized object is exactly an instance of Level
- //
- if (getClass() == Level.class)
- {
- return toLevel(level);
- }
- //
- // extension of Level can't substitute stock item
- //
- return this;
- }
-
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.javascript.log4j;
-
-import jalview.javascript.log4j.spi.LoggingEvent;
-
-import java.util.Hashtable;
-import java.util.Map;
-
-public class Logger
-{
-
- private static Map<String, Logger> registry;
-
- private String name;
-
- private Level level;
-
- private boolean enabled = true;
-
- private boolean isEnabled;
-
- private Appender appender;
-
- private Logger(String name)
- {
- this.name = name;
- }
-
- public static Logger getLogger(String name)
- {
- if (registry == null)
- {
- registry = new Hashtable<>();
- getLogger("root");
- }
- Logger logger = registry.get(name);
- if (logger == null)
- {
- registry.put(name, logger = new Logger(name));
- logger.setLevel(Level.INFO);
- }
- return logger;
- }
-
- public static Logger getRootLogger()
- {
- return getLogger("root");
- }
-
- public void setLevel(Level l)
- {
- this.level = l;
- }
-
- public void addAppender(Appender appender)
- {
- this.appender = appender;
- }
-
- public boolean isDebugEnabled()
- {
- return isEnabled;
- }
-
- public void debug(Object o)
- {
- debug(o, null);
- }
-
- public void debug(Object o, Throwable e)
- {
- switch (level.level)
- {
- case Priority.FATAL_INT:
- case Priority.ERROR_INT:
- case Priority.WARN_INT:
- case Priority.INFO_INT:
- case Priority.DEBUG_INT:
- log(o, e);
- break;
- }
- }
-
- public void info(Object o)
- {
- info(o, null);
- }
-
- public void info(Object o, Throwable e)
- {
- switch (level.level)
- {
- case Priority.FATAL_INT:
- case Priority.ERROR_INT:
- case Priority.WARN_INT:
- case Priority.INFO_INT:
- log(o, e);
- break;
- }
-
- }
-
- public void warn(Object o)
- {
- warn(o, null);
- }
-
- public void warn(Object o, Throwable e)
- {
- switch (level.level)
- {
- case Priority.FATAL_INT:
- case Priority.ERROR_INT:
- case Priority.WARN_INT:
- log(o, e);
- break;
- }
-
- }
-
- public void error(Object o)
- {
- error(o, null);
- }
-
- public void error(Object o, Throwable e)
- {
- switch (level.level)
- {
- case Priority.FATAL_INT:
- case Priority.ERROR_INT:
- log(o, e);
- break;
- }
-
- }
-
- private void log(Object s, Throwable e)
- {
- switch (level.level)
- {
- case Priority.ERROR_INT:
- if (appender == null)
- {
- System.err.println(s);
- return;
- }
- break;
- case Priority.WARN_INT:
- if (appender == null)
- {
- System.err.println(s);
- return;
- }
- break;
- case Priority.INFO_INT:
- if (appender == null)
- {
- System.out.println(s);
- return;
- }
- break;
- case Priority.DEBUG_INT:
- if (appender == null)
- {
- System.out.println(s);
- return;
- }
- break;
- }
- e.printStackTrace();
- appender.append(new LoggingEvent(this, s.toString(), level));
- }
-
-}
+++ /dev/null
-/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements. See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the "License"); you may not use this file except in compliance with
- * the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-// Contributors: Kitching Simon <Simon.Kitching@orange.ch>
-
-package jalview.javascript.log4j;
-
-/**
- <font color="#AA4444">Refrain from using this class directly, use
- the {@link Level} class instead</font>.
-
- @author Ceki Gülcü */
-public class Priority {
-
- transient int level;
- transient String levelStr;
- transient int syslogEquivalent;
-
- public final static int OFF_INT = Integer.MAX_VALUE;
- public final static int FATAL_INT = 50000;
- public final static int ERROR_INT = 40000;
- public final static int WARN_INT = 30000;
- public final static int INFO_INT = 20000;
- public final static int DEBUG_INT = 10000;
- //public final static int FINE_INT = DEBUG_INT;
- public final static int ALL_INT = Integer.MIN_VALUE;
-
- // too twisted for J2S -- Level class initializer initializes Priority, which
- // creates a
- // new Level before Priority is indicated to be a superclass of Level.
- /**
- * @deprecated Use {@link Level#FATAL} instead.
- */
- @Deprecated
- final static public Priority FATAL = null;// new Level(FATAL_INT, "FATAL", 0);
-
- /**
- * @deprecated Use {@link Level#ERROR} instead.
- */
- @Deprecated
- final static public Priority ERROR = null;// new Level(ERROR_INT, "ERROR", 3);
-
- /**
- * @deprecated Use {@link Level#WARN} instead.
- */
- @Deprecated
- final static public Priority WARN = null;// new Level(WARN_INT, "WARN", 4);
-
- /**
- * @deprecated Use {@link Level#INFO} instead.
- */
- @Deprecated
- final static public Priority INFO = null;// new Level(INFO_INT, "INFO", 6);
-
- /**
- * @deprecated Use {@link Level#DEBUG} instead.
- */
- @Deprecated
- final static public Priority DEBUG = null;// new Level(DEBUG_INT, "DEBUG", 7);
-
- /**
- * Default constructor for deserialization.
- */
- protected Priority() {
- level = DEBUG_INT;
- levelStr = "DEBUG";
- syslogEquivalent = 7;
- }
-
- /**
- Instantiate a level object.
- */
- protected
- Priority(int level, String levelStr, int syslogEquivalent) {
- this.level = level;
- this.levelStr = levelStr;
- this.syslogEquivalent = syslogEquivalent;
- }
-
- /**
- Two priorities are equal if their level fields are equal.
- @since 1.2
- */
- @Override
- public
- boolean equals(Object o) {
- if(o instanceof Priority) {
- Priority r = (Priority) o;
- return (this.level == r.level);
- } else {
- return false;
- }
- }
-
- /**
- Return the syslog equivalent of this priority as an integer.
- */
- public
- final
- int getSyslogEquivalent() {
- return syslogEquivalent;
- }
-
-
-
- /**
- Returns <code>true</code> if this level has a higher or equal
- level than the level passed as argument, <code>false</code>
- otherwise.
-
- <p>You should think twice before overriding the default
- implementation of <code>isGreaterOrEqual</code> method.
-
- */
- public
- boolean isGreaterOrEqual(Priority r) {
- return level >= r.level;
- }
-
- // /**
- // Return all possible priorities as an array of Level objects in
- // descending order.
- //
- // @deprecated This method will be removed with no replacement.
- // */
- // public
- // static
- // Priority[] getAllPossiblePriorities() {
- // return new Priority[] {Priority.FATAL, Priority.ERROR, Level.WARN,
- // Priority.INFO, Priority.DEBUG};
- // }
-
-
- /**
- Returns the string representation of this priority.
- */
- @Override
- final
- public
- String toString() {
- return levelStr;
- }
-
- /**
- Returns the integer representation of this level.
- */
- public
- final
- int toInt() {
- return level;
- }
-
- // /**
- // * @deprecated Please use the {@link Level#toLevel(String)} method instead.
- // */
- // public
- // static
- // Priority toPriority(String sArg) {
- // return Level.toLevel(sArg);
- // }
-
- // /**
- // * @deprecated Please use the {@link Level#toLevel(int)} method instead.
- // */
- // public
- // static
- // Priority toPriority(int val) {
- // return toPriority(val, Priority.DEBUG);
- // }
-
- // /**
- // * @deprecated Please use the {@link Level#toLevel(int, Level)} method
- // instead.
- // */
- // public
- // static
- // Priority toPriority(int val, Priority defaultPriority) {
- // return Level.toLevel(val, (Level) defaultPriority);
- // }
- //
- // /**
- // * @deprecated Please use the {@link Level#toLevel(String, Level)} method
- // instead.
- // */
- // public
- // static
- // Priority toPriority(String sArg, Priority defaultPriority) {
- // return Level.toLevel(sArg, (Level) defaultPriority);
- // }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.javascript.log4j;
-
-import jalview.javascript.log4j.spi.LoggingEvent;
-
-public class SimpleLayout extends Layout
-{
-
- StringBuffer sbuf = new StringBuffer(128);
-
- @Override
- public void activateOptions()
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public String format(LoggingEvent event)
- {
-
- sbuf.setLength(0);
- sbuf.append(event.getLevel().toString());
- sbuf.append(" - ");
- sbuf.append(event.getRenderedMessage());
- sbuf.append(LINE_SEP);
- return sbuf.toString();
- }
- @Override
- public boolean ignoresThrowable()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
-}
+++ /dev/null
-/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements. See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the "License"); you may not use this file except in compliance with
- * the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package jalview.javascript.log4j;
-
-public abstract class WriterAppender extends Appender
-{
-
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.javascript.log4j.spi;
-
-import jalview.javascript.log4j.Logger;
-
-public class LoggingEvent
-{
-
- private Object level;
-
- private String msg;
-
- private Logger logger;
-
- public LoggingEvent(Logger logger, String level, Object message)
- {
- this.logger = logger;
- this.level = level;
- this.msg = message.toString();
-
- }
-
- public Object getLevel()
- {
- return level;
- }
-
- public String getRenderedMessage()
- {
- return msg;
- }
-}
+++ /dev/null
-package jalview.javascript.log4j.spi;
-
-public interface OptionHandler
-{
-
- void activateOptions();
-
-}
--- /dev/null
+package jalview.jbgui;
+
+import jalview.gui.structurechooser.StructureChooserQuerySource;
+import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
+
+/**
+ * This inner class provides the data model for the structure filter combo-box
+ *
+ * @author tcnofoegbu
+ *
+ */
+public class FilterOption
+{
+ private String name;
+
+ private String value;
+
+ private String view;
+
+ private boolean addSeparatorAfter;
+
+ private StructureChooserQuerySource querySource;
+
+ /**
+ * Model for structure filter option
+ *
+ * @param name
+ * - the name of the Option
+ * @param value
+ * - the value of the option
+ * @param view
+ * - the category of the filter option
+ * @param addSeparatorAfter
+ * - if true, a horizontal separator is rendered immediately after
+ * this filter option, otherwise
+ * @param structureChooserQuerySource
+ * - the query source that actions this filter
+ */
+ public FilterOption(String name, String value, String view,
+ boolean addSeparatorAfter,
+ StructureChooserQuerySource structureChooserQuerySource)
+ {
+ this.name = name;
+ this.value = value;
+ this.view = view;
+ this.querySource = structureChooserQuerySource;
+ this.addSeparatorAfter = addSeparatorAfter;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+
+ public String getValue()
+ {
+ return value;
+ }
+
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
+
+ public String getView()
+ {
+ return view;
+ }
+
+ public void setView(String view)
+ {
+ this.view = view;
+ }
+
+ @Override
+ public String toString()
+ {
+ return this.name;
+ }
+
+ public boolean isAddSeparatorAfter()
+ {
+ return addSeparatorAfter;
+ }
+
+ public void setAddSeparatorAfter(boolean addSeparatorAfter)
+ {
+ this.addSeparatorAfter = addSeparatorAfter;
+ }
+
+ public StructureChooserQuerySource getQuerySource()
+ {
+ return querySource;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj instanceof FilterOption) {
+ FilterOption o=(FilterOption) obj;
+ return o.name.equals(name) && o.querySource==querySource && o.value.equals(value) && o.view==view;
+ } else {
+ return super.equals(obj);
+ }
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return ("" + name + ":" + value).hashCode()
+ + (view != null ? view.hashCode() : 0)
+ + (querySource != null ? querySource.hashCode() : 0);
+ }
+}
\ No newline at end of file
});
seqLimits.setText(
MessageManager.getString("label.show_sequence_limits"));
- seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+ seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true));
seqLimits.addActionListener(new ActionListener()
{
@Override
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
padGapsMenuitem
- .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+ .setState(Cache.getDefault("PAD_GAPS", false));
padGapsMenuitem.addActionListener(new ActionListener()
{
@Override
autoCalculate.setText(
MessageManager.getString("label.autocalculate_consensus"));
autoCalculate.setState(
- jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ Cache.getDefault("AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
{
@Override
sortByTree.setToolTipText("<html>" + MessageManager.getString(
"label.enable_automatically_sort_alignment_when_open_new_tree"));
sortByTree
- .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
+ .setState(Cache.getDefault("SORT_BY_TREE", false));
sortByTree.addActionListener(new ActionListener()
{
@Override
import javax.swing.AbstractCellEditor;
import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.DefaultListCellRenderer;
import javax.swing.JButton;
import javax.swing.JPasswordField;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
+import javax.swing.JSlider;
import javax.swing.JSpinner;
import javax.swing.JTabbedPane;
import javax.swing.JTable;
import javax.swing.table.TableCellRenderer;
import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.bin.MemorySetting;
import jalview.fts.core.FTSDataColumnPreferences;
import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.io.IntKeyStringValueEntry;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.StringUtils;
/**
* Base class for the Preferences panel.
protected JCheckBox structFromPdb = new JCheckBox();
- protected JCheckBox useRnaView = new JCheckBox();
-
protected JCheckBox addSecondaryStructure = new JCheckBox();
protected JCheckBox addTempFactor = new JCheckBox();
private JLabel messageLabel = new JLabel("", JLabel.CENTER);
+ /*
+ * Startup tab components
+ */
+
+ protected JCheckBox customiseMemorySetting = new JCheckBox();
+
+ protected JLabel exampleMemoryLabel = new JLabel();
+
+ protected JTextArea exampleMemoryMessageTextArea = new JTextArea();
+
+ protected JLabel maxMemoryLabel = new JLabel();
+
+ protected JLabel jvmMemoryPercentLabel = new JLabel();
+
+ protected JSlider jvmMemoryPercentSlider = new JSlider();
+
+ protected JLabel jvmMemoryPercentDisplay = new JLabel();
+
+ protected JLabel jvmMemoryMaxLabel = new JLabel();
+
+ protected JTextField jvmMemoryMaxTextField = new JTextField(null, 8);
+
+ protected JComboBox<Object> lafCombo = new JComboBox<>();
+
/**
* Creates a new GPreferences object.
*/
tabbedPane.add(initEditingTab(),
MessageManager.getString("label.editing"));
+ tabbedPane.add(initStartupTab(),
+ MessageManager.getString("label.startup"));
+
/*
* See WsPreferences for the real work of configuring this tab.
*/
}
}
- public final static int CONNECTIONS_TAB = 5;
+ public static enum TabRef
+ {
+ CONNECTIONS_TAB, STRUCTURE_TAB
+ };
- public void selectTab(int selectTab)
+ public void selectTab(TabRef selectTab)
{
// select a given tab - currently only for Connections
switch (selectTab)
case CONNECTIONS_TAB:
tabbedPane.setSelectedComponent(connectTab);
break;
+ case STRUCTURE_TAB:
+ tabbedPane.setSelectedComponent(structureTab);
+ break;
default:
}
}
{
boolean selected = structFromPdb.isSelected();
// enable other options only when the first is checked
- useRnaView.setEnabled(selected);
addSecondaryStructure.setEnabled(selected);
addTempFactor.setEnabled(selected);
}
// indent checkboxes that are conditional on the first one
ypos += lineSpacing;
- useRnaView.setFont(LABEL_FONT);
- useRnaView.setText(MessageManager.getString("label.use_rnaview"));
- useRnaView.setBounds(new Rectangle(25, ypos, width, height));
- structureTab.add(useRnaView);
-
- ypos += lineSpacing;
addSecondaryStructure.setFont(LABEL_FONT);
addSecondaryStructure
.setText(MessageManager.getString("label.autoadd_secstr"));
}
/**
- * Show a dialog for the user to choose a file. Returns the chosen path, or
- * null on Cancel.
+ * Show a dialog for the user to choose a file. Returns the chosen path, or null
+ * on Cancel.
*
* @return
*/
updateBackupFilesExampleLabel();
}
+ /*
+ * Load the saved Memory settings
+ */
+ protected void loadLastSavedMemorySettings()
+ {
+ customiseMemorySetting.setSelected(
+ Cache.getDefault(MemorySetting.CUSTOMISED_SETTINGS, false));
+ jvmMemoryPercentSlider
+ .setValue(Cache.getDefault(MemorySetting.MEMORY_JVMMEMPC, 90));
+ jvmMemoryMaxTextField.setText(
+ Cache.getDefault(MemorySetting.MEMORY_JVMMEMMAX, "32g"));
+ }
+
private boolean warnAboutSuffixReverseChange()
{
BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
&& nowSuffixTemplate.equals(savedSuffixTemplate);
}
+ /* Initialises the Startup tabbed panel.
+ *
+ * @return
+ * */
+
+ private JPanel initStartupTab()
+ {
+ JPanel startupTab = new JPanel();
+ startupTab.setBorder(
+ new TitledBorder(MessageManager.getString("label.memory")));
+ startupTab.setLayout(new GridBagLayout());
+
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.weightx = 0.0;
+ gbc.weighty = 0.0;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+ gbc.fill = GridBagConstraints.NONE;
+
+ initMemoryPanel();
+
+ gbc.gridheight = 1;
+ gbc.gridwidth = 3;
+
+ gbc.gridy = 0; // row 1
+ gbc.gridx = 0;
+ JLabel memoryText = new JLabel();
+ memoryText.setFont(LABEL_FONT_ITALIC);
+ memoryText
+ .setText(MessageManager.getString("label.memory_setting_text"));
+ startupTab.add(memoryText, gbc);
+
+ gbc.gridy++; // row 2
+ gbc.gridx = 0;
+ JPanel exampleMemoryPanel = new JPanel();
+ exampleMemoryPanel
+ .setLayout(new BoxLayout(exampleMemoryPanel, BoxLayout.Y_AXIS));
+ exampleMemoryPanel.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.memory_example_tooltip")));
+ JLabel exampleTextLabel = new JLabel();
+ exampleTextLabel
+ .setText(MessageManager.getString("label.memory_example_text"));
+ exampleTextLabel.setForeground(Color.GRAY);
+ exampleTextLabel.setFont(LABEL_FONT);
+ exampleMemoryPanel.add(exampleTextLabel);
+ exampleMemoryPanel.add(exampleMemoryLabel);
+ exampleMemoryPanel.setBackground(Color.WHITE);
+ exampleMemoryPanel.setBorder(BorderFactory.createEtchedBorder());
+ startupTab.add(exampleMemoryPanel, gbc);
+
+ gbc.gridy++; // row 3
+ gbc.gridx = 0;
+ startupTab.add(customiseMemorySetting, gbc);
+
+ gbc.gridy += 2; // row 4 with a gap
+ gbc.gridx = 0;
+ startupTab.add(maxMemoryLabel, gbc);
+
+ gbc.gridy += 2; // row 5
+ gbc.gridx = 0;
+ gbc.gridwidth = 1;
+ startupTab.add(jvmMemoryPercentLabel, gbc);
+ gbc.gridx++;
+ startupTab.add(jvmMemoryPercentSlider, gbc);
+ gbc.gridx++;
+ // gbc.weightx = 0.1;
+ startupTab.add(jvmMemoryPercentDisplay, gbc);
+ // gbc.weightx = 1.0;
+ gbc.gridwidth = 3;
+
+ gbc.gridy++; // row 6
+ gbc.gridx = 0;
+ startupTab.add(jvmMemoryMaxLabel, gbc);
+ gbc.gridx++;
+ startupTab.add(jvmMemoryMaxTextField, gbc);
+
+ gbc.gridy++; // row 7
+ gbc.gridx = 0;
+ gbc.gridwidth = 4;
+ exampleMemoryMessageTextArea.setBackground(startupTab.getBackground());
+ JScrollPane sp = new JScrollPane(exampleMemoryMessageTextArea);
+ sp.setBorder(BorderFactory.createEmptyBorder());
+ sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
+ startupTab.add(sp, gbc);
+
+ // fill empty space to push widget to top left
+ gbc.gridy++;
+ gbc.weighty = 1.0;
+ gbc.gridx = 100;
+ gbc.gridwidth = 1;
+ gbc.weightx = 1.0;
+ startupTab.add(new JPanel(), gbc);
+
+ setMemoryPercentDisplay();
+ memoryOptionsSetEnabled();
+ return startupTab;
+ }
+
+ private void initMemoryPanel()
+ {
+ // Enable memory settings checkbox
+ customiseMemorySetting.setFont(LABEL_FONT_BOLD);
+ customiseMemorySetting.setText(
+ MessageManager.getString("label.customise_memory_settings"));
+ customiseMemorySetting.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ memoryOptionsSetEnabled();
+ }
+ });
+
+ loadLastSavedMemorySettings();
+
+ exampleMemoryLabel.setFont(LABEL_FONT_BOLD);
+ exampleMemoryLabel.setBackground(Color.WHITE);
+
+ maxMemoryLabel = new JLabel(
+ MessageManager.getString("label.maximum_memory_used"));
+ maxMemoryLabel.setFont(LABEL_FONT_BOLD);
+
+ // Maximum memory percentage slider
+ jvmMemoryPercentLabel.setFont(LABEL_FONT);
+ jvmMemoryPercentLabel.setText(
+ MessageManager.getString("label.percent_of_physical_memory"));
+ jvmMemoryPercentSlider.setPaintLabels(true);
+ jvmMemoryPercentSlider.setPaintTicks(true);
+ jvmMemoryPercentSlider.setPaintTrack(true);
+ jvmMemoryPercentSlider.setMajorTickSpacing(50);
+ jvmMemoryPercentSlider.setMinorTickSpacing(10);
+ jvmMemoryPercentSlider.addChangeListener(new ChangeListener()
+ {
+ @Override
+ public void stateChanged(ChangeEvent e)
+ {
+ setMemoryPercentDisplay();
+ }
+ });
+ jvmMemoryPercentDisplay.setFont(LABEL_FONT);
+ setMemoryPercentDisplay();
+
+ // Maximum memory cap textbox
+ jvmMemoryMaxLabel.setFont(LABEL_FONT);
+ jvmMemoryMaxLabel
+ .setText(MessageManager.getString("label.maximum_memory"));
+ initMemoryMaxTextField();
+
+ exampleMemoryMessageTextArea.setFont(LABEL_FONT_ITALIC);
+ exampleMemoryMessageTextArea.setForeground(Color.GRAY);
+ exampleMemoryMessageTextArea.setEditable(false);
+ exampleMemoryMessageTextArea.setLineWrap(true);
+ exampleMemoryMessageTextArea.setWrapStyleWord(true);
+ exampleMemoryMessageTextArea.setText(" ");
+ exampleMemoryMessageTextArea.setRows(2);
+ exampleMemoryMessageTextArea.setColumns(40);
+
+ setExampleMemoryLabel();
+ }
+
+ private void initMemoryMaxTextField()
+ {
+ jvmMemoryMaxTextField.setToolTipText(
+ MessageManager.getString("label.maximum_memory_tooltip"));
+ jvmMemoryMaxTextField.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ validateMemoryMaxTextField();
+ setExampleMemoryLabel();
+ }
+ });
+
+ jvmMemoryMaxTextField.addKeyListener(new KeyListener()
+ {
+ @Override
+ public void keyReleased(KeyEvent e)
+ {
+ validateMemoryMaxTextField();
+ setExampleMemoryLabel();
+ }
+
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ }
+
+ // try and stop invalid typing
+ @Override
+ public void keyTyped(KeyEvent e)
+ {
+ char c = Character.toLowerCase(e.getKeyChar());
+ String text = jvmMemoryMaxTextField.getText();
+ String suffixes = "tgmkb";
+ int pos = jvmMemoryMaxTextField.getCaretPosition();
+ int suffixPos = StringUtils.firstCharPosIgnoreCase(text, suffixes);
+ if (!((('0' <= c && c <= '9')
+ && (suffixPos == -1 || pos <= suffixPos)) // digits only allowed
+ // before suffix
+ || (suffixes.indexOf(Character.toLowerCase(c)) >= 0 // valid
+ // suffix
+ && pos == text.length() // at end of text and
+ && suffixPos == -1) // there isn't already one
+ ))
+ {
+ // don't process
+ e.consume();
+ }
+ }
+ });
+ }
+
+ private boolean isMemoryMaxTextFieldValid()
+ {
+ return MemorySetting
+ .isValidMemoryString(jvmMemoryMaxTextField.getText());
+ }
+
+ private void validateMemoryMaxTextField()
+ {
+ if (isMemoryMaxTextFieldValid())
+ {
+ jvmMemoryMaxTextField.setBackground(Color.WHITE);
+ }
+ else
+ {
+ jvmMemoryMaxTextField.setBackground(Color.PINK);
+ }
+ }
+
+ private void setMemoryPercentDisplay()
+ {
+ jvmMemoryPercentDisplay
+ .setText(jvmMemoryPercentSlider.getValue() + "%");
+ setExampleMemoryLabel();
+ }
+
+ private void setExampleMemoryLabel()
+ {
+ boolean selected = customiseMemorySetting.isSelected();
+ int jvmmempc = jvmMemoryPercentSlider.getValue();
+ String jvmmemmax = jvmMemoryMaxTextField.getText();
+
+ long mem;
+ if (selected && (0 <= jvmmempc && jvmmempc <= 100)
+ && MemorySetting.isValidMemoryString(jvmmemmax))
+ {
+ mem = MemorySetting.getMemorySetting(jvmmemmax,
+ String.valueOf(jvmmempc), false, true);
+ }
+ else
+ {
+ mem = MemorySetting.getMemorySetting(null, null, false, true);
+ }
+ exampleMemoryLabel.setText(MemorySetting.memoryLongToString(mem));
+ String message = MemorySetting.getAdjustmentMessage();
+ exampleMemoryMessageTextArea.setText(
+ MessageManager.getString("label.adjustments_for_this_computer")
+ + ": "
+ + (message == null
+ ? MessageManager.getString("label.none")
+ : message));
+ }
+
+ private void memoryOptionsSetEnabled()
+ {
+ boolean enabled = customiseMemorySetting.isSelected();
+ // leave exampleMemoryLabel enabled always
+ maxMemoryLabel.setEnabled(enabled);
+ jvmMemoryPercentLabel.setEnabled(enabled);
+ jvmMemoryPercentSlider.setEnabled(enabled);
+ jvmMemoryPercentDisplay.setEnabled(enabled);
+ jvmMemoryMaxLabel.setEnabled(enabled);
+ jvmMemoryMaxTextField.setEnabled(enabled);
+ exampleMemoryMessageTextArea.setEnabled(enabled);
+ setExampleMemoryLabel();
+ }
+
/**
* Initialises the Backups tabbed panel.
*
}
else
{
- Cache.log.error(
+ Console.error(
"Preset '" + value + "' [key:" + key + "] not implemented");
}
.getSelectedItem();
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Problem casting Combo entry to IntKeyStringValueEntry.");
e = null;
}
e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
continue;
}
i = ((Integer) s.getValue()).intValue();
} catch (Exception e)
{
- Cache.log.error(
+ Console.error(
"Exception casting the initial value of s.getValue()");
}
}
i = (Integer) s.getValue();
} catch (Exception e)
{
- Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
+ Console.error("Failed casting (Integer) JSpinner s.getValue()");
}
return i;
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void ok_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void cancel_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void annotations_actionPerformed(ActionEvent e)
{
import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.GridLayout;
+import java.awt.Point;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import javax.swing.JTextField;
import javax.swing.ListCellRenderer;
import javax.swing.Timer;
+import javax.swing.UIManager;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.event.DocumentEvent;
{
private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
- protected static final String VIEWS_FILTER = "VIEWS_FILTER";
+ public static final String VIEWS_FILTER = "VIEWS_FILTER";
protected static final String VIEWS_FROM_FILE = "VIEWS_FROM_FILE";
protected JButton btn_newView;
protected JButton btn_pdbFromFile = new JButton();
+
+ protected JButton btn_queryTDB = new JButton();
protected JCheckBox chk_superpose = new JCheckBox(
MessageManager.getString("label.superpose_structures"));
protected ImageIcon warningImage = new ImageIcon(
getClass().getResource("/images/warning.gif"));
+ protected ImageIcon tdbImage = new ImageIcon(
+ getClass().getResource("/images/3d-beacons-logo-transparent.png"));
+
protected JLabel lbl_loading = new JLabel(loadingImage);
protected JLabel lbl_pdbManualFetchStatus = new JLabel(errorImage);
protected JTabbedPane pnl_filter = new JTabbedPane();
- protected FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences(
- PreferenceSource.STRUCTURE_CHOOSER,
- PDBFTSRestClient.getInstance());
+ protected abstract FTSDataColumnPreferences getFTSDocFieldPrefs();
+ protected abstract void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs);
+
protected FTSDataColumnI[] previousWantedFields;
+ "...\"")
: JvSwingUtils.wrapTooltip(true, toolTipText)));
return toolTipText;
- }
+ }
};
public GStructureChooser()
{
+ }
+ protected void initDialog()
+ {
+
try
{
jbInit();
e.printStackTrace();
}
}
-
+
// BH SwingJS optimization
// (a) 100-ms interruptable timer for text entry -- BH 1/10/2019
// (b) two-character minimum, at least for JavaScript.
tbl_summary.addMouseListener(new MouseAdapter()
{
@Override
+ public void mousePressed(MouseEvent e)
+ {
+ if (!popupAction(e))
+ {
+ super.mousePressed(e);
+ }
+ }
+ @Override
public void mouseClicked(MouseEvent e)
{
- validateSelections();
+ if (!popupAction(e))
+ {
+ validateSelections();
+ }
}
@Override
public void mouseReleased(MouseEvent e)
{
+ if (!popupAction(e))
+ {
validateSelections();
+ }
+ }
+ boolean popupAction(MouseEvent e)
+ {
+ if (e.isPopupTrigger())
+ {
+ Point pt = e.getPoint();
+ int selectedRow = tbl_summary.rowAtPoint(pt);
+ if (showPopupFor(selectedRow,pt.x,pt.y))
+ {
+ return true;
+ }
+ }
+ return false;
}
});
tbl_summary.addKeyListener(new KeyAdapter()
}
});
- btn_newView = new JButton(MessageManager.getString("action.new_view"));
+ btn_newView = new JButton(
+ MessageManager.formatMessage("action.new_structure_view_with",
+ StructureViewer.getViewerType().toString()));
btn_newView.setFont(VERDANA_12);
btn_newView.addActionListener(new java.awt.event.ActionListener()
{
}
}
});
+
+ // TODO: JAL-3898 - get list of available external programs to view structures with
btn_add = new JButton(MessageManager.getString("action.add"));
btn_add.setFont(VERDANA_12);
});
chk_invertFilter.addItemListener(this);
+ btn_queryTDB.setFont(VERDANA_12);
+ //btn_queryTDB.setPreferredSize(new Dimension(200,22));
+ btn_queryTDB.setText(MessageManager.getString("label.search_3dbeacons"));
+ btn_queryTDB.setToolTipText(MessageManager.getString("label.find_models_from_3dbeacons"));
+ btn_queryTDB.setIcon(tdbImage);
+ btn_queryTDB.setVisible(false);
targetView.setVisible(false);
actionsPanel.add(btn_newView);
actionsPanel.add(btn_cancel, "right");
- JPanel pnl_main = new JPanel();
- pnl_main.add(cmb_filterOption);
- pnl_main.add(lbl_loading);
- pnl_main.add(chk_invertFilter);
+ JPanel pnl_main = new JPanel(new BorderLayout());
+ JPanel pnl_controls = new JPanel();
+ pnl_main.add(btn_queryTDB,BorderLayout.NORTH);
+ pnl_controls.add(cmb_filterOption);
+ pnl_controls.add(lbl_loading);
+ pnl_controls.add(chk_invertFilter);
+ pnl_main.add(pnl_controls,BorderLayout.CENTER);
lbl_loading.setVisible(false);
JPanel pnl_fileChooser = new JPanel(new FlowLayout());
btn_add.setVisible(false);
btn_newView.setEnabled(false);
btn_cancel.setVisible(false);
- previousWantedFields = pdbDocFieldPrefs
+ previousWantedFields = getFTSDocFieldPrefs()
.getStructureSummaryFields()
.toArray(new FTSDataColumnI[0]);
}
pnl_filter.addChangeListener(changeListener);
pnl_filter.setPreferredSize(new Dimension(width, height));
pnl_filter.add(foundStructureSummary, scrl_foundStructures);
- pnl_filter.add(configureCols, pdbDocFieldPrefs);
+ pnl_filter.add(configureCols, getFTSDocFieldPrefs());
JPanel pnl_locPDB = new JPanel(new BorderLayout());
pnl_locPDB.add(scrl_localPDB);
}
+protected abstract boolean showPopupFor(int selectedRow, int x, int y);
protected void closeAction(int preferredHeight)
{
// System.out.println(">>>>>>>>>> closing internal frame!!!");
return true;
}
- FTSDataColumnI[] currentWantedFields = pdbDocFieldPrefs
+ FTSDataColumnI[] currentWantedFields = getFTSDocFieldPrefs()
.getStructureSummaryFields().toArray(new FTSDataColumnI[0]);
return Arrays.equals(currentWantedFields, previousWantedFields) ? false
: true;
}
/**
- * This inner class provides the data model for the structure filter combo-box
- *
- * @author tcnofoegbu
- *
- */
- public class FilterOption
- {
- private String name;
-
- private String value;
-
- private String view;
-
- private boolean addSeparatorAfter;
-
- /**
- * Model for structure filter option
- *
- * @param name
- * - the name of the Option
- * @param value
- * - the value of the option
- * @param view
- * - the category of the filter option
- * @param addSeparatorAfter
- * - if true, a horizontal separator is rendered immediately after
- * this filter option, otherwise
- */
- public FilterOption(String name, String value, String view,
- boolean addSeparatorAfter)
- {
- this.name = name;
- this.value = value;
- this.view = view;
- this.addSeparatorAfter = addSeparatorAfter;
- }
-
- public String getName()
- {
- return name;
- }
-
- public void setName(String name)
- {
- this.name = name;
- }
-
- public String getValue()
- {
- return value;
- }
-
- public void setValue(String value)
- {
- this.value = value;
- }
-
- public String getView()
- {
- return view;
- }
-
- public void setView(String view)
- {
- this.view = view;
- }
-
- @Override
- public String toString()
- {
- return this.name;
- }
-
- public boolean isAddSeparatorAfter()
- {
- return addSeparatorAfter;
- }
-
- public void setAddSeparatorAfter(boolean addSeparatorAfter)
- {
- this.addSeparatorAfter = addSeparatorAfter;
- }
- }
-
- /**
* This inner class provides the provides the data model for associate
* sequence combo-box - cmb_assSeq
*
*/
package jalview.jbgui;
+import jalview.bin.Cache;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
wsMenuRefreshButs.add(resetWs, null);
wsMenuRefreshButs.add(progressBar, null);
myBorderlayout.setHgap(3);
- if (jalview.bin.Cache.getDefault("ENABLE_RSBS_EDITOR", false))
+ if (Cache.getDefault("ENABLE_RSBS_EDITOR", false))
{
JTabbedPane listPanels = new JTabbedPane();
listPanels.addTab("JABAWS Servers", wsListPanel);
*/
package jalview.json.binding.biojson.v1;
+import java.util.Locale;
+
import jalview.datamodel.AnnotatedCollectionI;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
public static ColourSchemeI getJalviewColourScheme(
String colourSchemeName, AnnotatedCollectionI annotCol)
{
- switch (colourSchemeName.toUpperCase())
+ switch (colourSchemeName.toUpperCase(Locale.ROOT))
{
case "ZAPPO":
return csZappo;
--- /dev/null
+package jalview.log;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import jalview.bin.Console;
+import jalview.util.Platform;
+
+public abstract class JLogger implements JLoggerI
+{
+ protected String name;
+
+ protected LogLevel level;
+
+ private Object logger = null;
+
+ private static Map<String, JLogger> registry = new HashMap<>();
+
+ // implement these abstract methods
+ protected abstract void loggerSetup();
+
+ public abstract boolean loggerExists();
+
+ protected abstract void loggerSetLevel(LogLevel level);
+
+ protected abstract void loggerLogMessage(LogLevel level, String message,
+ Throwable t);
+
+ public static LogLevel toLevel(String levelString)
+ {
+ try
+ {
+ return LogLevel.valueOf(levelString);
+ } catch (IllegalArgumentException e)
+ {
+ Console.error("Could not parse LogLevel '" + levelString + "'", e);
+ return LogLevel.INFO;
+ }
+ }
+
+ public static JLogger getLogger(Class c)
+ {
+ return getLogger(c);
+ }
+
+ public static JLogger getLogger(Class c, LogLevel loglevel)
+ {
+ return getLogger(c.getCanonicalName(), loglevel);
+ }
+
+ public static JLogger getLogger(String name)
+ {
+ return getLogger(name, LogLevel.INFO);
+ }
+
+ public static JLogger getLogger(String name, LogLevel loglevel)
+ {
+ return registry.containsKey(name) ? (JLogger) registry.get(name) : null;
+ }
+
+ protected JLogger()
+ {
+ }
+
+ protected JLogger(String name, LogLevel level)
+ {
+ this.name = name;
+ this.level = level;
+ this.loggerSetup();
+ this.registryStore();
+ }
+
+ protected void registryStore()
+ {
+ registry.put(this.name, this);
+ }
+
+ protected static boolean registryContainsKey(String name)
+ {
+ return registry.containsKey(name);
+ }
+
+ protected static JLogger registryGet(String name)
+ {
+ return registry.get(name);
+ }
+
+ public LogLevel getLevel()
+ {
+ return this.level;
+ }
+
+ public void setLevel(LogLevel level)
+ {
+ this.level = level;
+ if (loggerExists())
+ loggerSetLevel(level);
+ }
+
+ private boolean println(LogLevel loglevel, String message, Throwable t)
+ {
+ if (loglevel.compareTo(this.level) < 0)
+ {
+ return false;
+ }
+ if (!loggerExists() || Platform.isJS())
+ {
+ String logLine = String.format("%s: %s", loglevel.toString(),
+ message);
+ System.out.println(logLine);
+ if (t != null)
+ {
+ if (loglevel.compareTo(LogLevel.DEBUG) <= 0)
+ t.printStackTrace(System.err);
+ else
+ System.err.println(t.getMessage());
+ }
+ return false;
+ }
+ else
+ {
+ loggerLogMessage(loglevel, message, t);
+ return true;
+ }
+ }
+
+ public void trace(String message)
+ {
+ trace(message, null);
+ }
+
+ public void trace(String message, Throwable t)
+ {
+ println(LogLevel.TRACE, message, t);
+ }
+
+ public void debug(String message)
+ {
+ debug(message, null);
+ }
+
+ public void debug(String message, Throwable t)
+ {
+ println(LogLevel.DEBUG, message, t);
+ }
+
+ public void info(String message)
+ {
+ info(message, null);
+ }
+
+ public void info(String message, Throwable t)
+ {
+ println(LogLevel.INFO, message, t);
+ }
+
+ public void warn(String message)
+ {
+ warn(message, null);
+ }
+
+ public void warn(String message, Throwable t)
+ {
+ println(LogLevel.WARN, message, t);
+ }
+
+ public void error(String message)
+ {
+ error(message, null);
+ }
+
+ public void error(String message, Throwable t)
+ {
+ println(LogLevel.ERROR, message, t);
+ }
+
+ public void fatal(String message)
+ {
+ fatal(message, null);
+ }
+
+ public void fatal(String message, Throwable t)
+ {
+ println(LogLevel.FATAL, message, t);
+ }
+
+ public boolean isDebugEnabled()
+ {
+ return level.compareTo(LogLevel.DEBUG) <= 0;
+ }
+
+ public boolean isTraceEnabled()
+ {
+ return level.compareTo(LogLevel.TRACE) <= 0;
+ }
+}
--- /dev/null
+package jalview.log;
+
+public interface JLoggerI
+{
+ public enum LogLevel
+ {
+ ALL, TRACE, DEBUG, INFO, WARN, ERROR, FATAL
+ }
+
+ public LogLevel getLevel();
+
+ public void setLevel(LogLevel level);
+
+ public void trace(String message);
+
+ public void trace(String message, Throwable t);
+
+ public void debug(String message);
+
+ public void debug(String message, Throwable t);
+
+ public void info(String message);
+
+ public void info(String message, Throwable t);
+
+ public void warn(String message);
+
+ public void warn(String message, Throwable t);
+
+ public void error(String message);
+
+ public void error(String message, Throwable t);
+
+ public void fatal(String message);
+
+ public void fatal(String message, Throwable t);
+
+ public boolean isDebugEnabled();
+
+ public boolean isTraceEnabled();
+}
--- /dev/null
+package jalview.log;
+
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.core.Appender;
+
+import jalview.util.Log4j;
+import jalview.util.Platform;
+
+public class JLoggerLog4j extends JLogger implements JLoggerI
+{
+ private Logger logger = null;
+
+ public static JLoggerLog4j getLogger(Class c)
+ {
+ return getLogger(c);
+ }
+
+ public static JLoggerLog4j getLogger(Class c, LogLevel loglevel)
+ {
+ return getLogger(c.getCanonicalName(), loglevel);
+ }
+
+ public static JLoggerLog4j getLogger(String name)
+ {
+ return getLogger(name, LogLevel.INFO);
+ }
+
+ public static JLoggerLog4j getLogger(String name, LogLevel loglevel)
+ {
+ return registryContainsKey(name) ? (JLoggerLog4j) registryGet(name)
+ : new JLoggerLog4j(name, loglevel);
+ }
+
+ private JLoggerLog4j(String name, LogLevel level)
+ {
+ this.name = name;
+ this.level = level;
+ this.loggerSetup();
+ this.registryStore();
+ }
+
+ @Override
+ protected void loggerSetup()
+ {
+ if (!Platform.isJS())
+ this.logger = Log4j.isInit() ? Log4j.getLogger(this.name, this.level)
+ : null;
+ }
+
+ @Override
+ public boolean loggerExists()
+ {
+ return logger != null;
+ }
+
+ @Override
+ protected void loggerSetLevel(JLoggerI.LogLevel level)
+ {
+ if (loggerExists())
+ {
+ Log4j.setLevel(logger, level);
+ }
+ }
+
+ @Override
+ protected void loggerLogMessage(LogLevel level, String message,
+ Throwable t)
+ {
+ if (!loggerExists())
+ return;
+ if (t != null)
+ {
+ switch (level)
+ {
+ case FATAL:
+ logger.fatal(message, t);
+ break;
+ case ERROR:
+ logger.error(message, t);
+ break;
+ case WARN:
+ logger.warn(message, t);
+ break;
+ case INFO:
+ logger.info(message, t);
+ break;
+ case DEBUG:
+ logger.debug(message, t);
+ break;
+ case TRACE:
+ logger.trace(message, t);
+ break;
+ case ALL:
+ logger.trace(message, t);
+ break;
+ }
+ }
+ else
+ {
+ switch (level)
+ {
+ case FATAL:
+ logger.fatal(message);
+ break;
+ case ERROR:
+ logger.error(message);
+ break;
+ case WARN:
+ logger.warn(message);
+ break;
+ case INFO:
+ logger.info(message);
+ break;
+ case DEBUG:
+ logger.debug(message);
+ break;
+ case TRACE:
+ logger.trace(message);
+ break;
+ case ALL:
+ logger.trace(message);
+ break;
+ }
+ }
+ }
+
+ private Logger getLoggerObject()
+ {
+ return this.logger;
+ }
+
+ public synchronized static void addAppender(JLoggerLog4j level,
+ Appender appender)
+ {
+ if (!Platform.isJS())
+ Log4j.addAppender(level.getLoggerObject(), appender);
+ }
+
+ public synchronized static void addAppender(JLoggerLog4j l1,
+ JLoggerLog4j l2, String name)
+ {
+ if (!Platform.isJS())
+ Log4j.addAppender(l1.getLoggerObject(), l2.getLoggerObject(), name);
+ }
+
+}
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.gui;
+package jalview.log;
+
+import java.io.Serializable;
+import java.nio.charset.StandardCharsets;
import javax.swing.JTextArea;
import javax.swing.SwingUtilities;
-import org.apache.log4j.WriterAppender;
-import org.apache.log4j.spi.LoggingEvent;
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.core.Filter;
+import org.apache.logging.log4j.core.Layout;
+import org.apache.logging.log4j.core.LogEvent;
+import org.apache.logging.log4j.core.appender.AbstractAppender;
+import org.apache.logging.log4j.core.config.Property;
+
+import jalview.log.JLoggerI.LogLevel;
+import jalview.util.Log4j;
/**
* From http://textareaappender.zcage.com/ the means to capture the logs, too.
* Simple example of creating a Log4j appender that will write to a JTextArea.
*/
-public class JalviewAppender extends WriterAppender
+public class JalviewAppender extends AbstractAppender
{
+ public final static String NAME = "JalviewAppender";
+
+ public JalviewAppender()
+ {
+ this(LogLevel.INFO);
+ }
+
+ public JalviewAppender(LogLevel loglevel)
+ {
+ super(NAME,
+ Log4j.getThresholdFilter(loglevel == null ? Level.INFO
+ : Log4j.log4jLevel(loglevel)),
+ Log4j.getSimpleLayout(), false, new Property[0]);
+ }
+
+ protected JalviewAppender(String name, Filter filter,
+ Layout<? extends Serializable> layout, boolean ignoreExceptions,
+ Property[] properties)
+ {
+ super(name, filter, layout, ignoreExceptions, properties);
+ // TODO Auto-generated constructor stub
+ }
static private JTextArea jTextArea = null;
/**
* Format and then append the loggingEvent to the stored JTextArea.
*/
- public void append(LoggingEvent loggingEvent)
+ public void append(LogEvent logEvent)
{
- final String message = this.layout.format(loggingEvent);
+ final String message = new String(
+ this.getLayout().toByteArray(logEvent), StandardCharsets.UTF_8);
// Append formatted message to textarea using the Swing Thread.
SwingUtilities.invokeLater(new Runnable()
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import jalview.api.analysis.SimilarityParamsI;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
} catch (Exception e)
{
- Cache.log.error("Couln't write Jalview state to " + statefile, e);
+ Console.error("Couln't write Jalview state to " + statefile, e);
// TODO: inform user of the problem - they need to know if their data was
// not saved !
if (errorMessage == null)
System.err.println("error writing date: " + e.toString());
}
object.setVersion(
- jalview.bin.Cache.getDefault("VERSION", "Development Build"));
+ Cache.getDefault("VERSION", "Development Build"));
/**
* rjal is full height alignment, jal is actual alignment with full metadata
}
else
{
- Cache.log.error(
+ Console.error(
"Failed to save viewer state for " + viewerType);
}
}
.getHiddenColumns();
if (hidden == null)
{
- warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
+ Console.warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
}
else
{
object.getPcaViewer().add(viewer);
} catch (Throwable t)
{
- Cache.log.error("Error saving PCA: " + t.getMessage());
+ Console.error("Error saving PCA: " + t.getMessage());
}
}
{
final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
final String pdbId = pdbentry.getId();
- if (!pdbId.equals(entry.getId())
- && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
- .startsWith(pdbId.toLowerCase())))
+ if (!pdbId.equals(entry.getId()) && !(entry.getId().length() > 4
+ && entry.getId().toLowerCase(Locale.ROOT)
+ .startsWith(pdbId.toLowerCase(Locale.ROOT))))
{
/*
* not interested in a binding to a different PDB entry here
}
else if (!matchedFile.equals(pdbentry.getFile()))
{
- Cache.log.warn(
+ Console.warn(
"Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+ pdbentry.getFile());
}
calcIdParam.getParameters().replace("|\\n|", "\n"));
} catch (IOException x)
{
- warn("Couldn't parse parameter data for "
+ Console.warn("Couldn't parse parameter data for "
+ calcIdParam.getCalcId(), x);
return false;
}
}
else
{
- warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
+ Console.warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
return false;
}
}
return id.toString();
}
// give up and warn that something has gone wrong
- warn("Cannot find ID for object in external mapping : " + jvobj);
+ Console.warn("Cannot find ID for object in external mapping : " + jvobj);
}
return altCode;
}
dbref.setSource(ref.getSource());
dbref.setVersion(ref.getVersion());
dbref.setAccessionId(ref.getAccessionId());
+ dbref.setCanonical(ref.isCanonical());
if (ref instanceof GeneLocus)
{
dbref.setLocus(true);
mp.setDseqFor(jmpid);
if (!seqRefIds.containsKey(jmpid))
{
- jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+ Console.debug("creatign new DseqFor ID");
seqRefIds.put(jmpid, ps);
}
else
{
- jalview.bin.Cache.log.debug("reusing DseqFor ID");
+ Console.debug("reusing DseqFor ID");
}
// mp.setMappingChoice(mpc);
for (int i = 0; i < colours.length; i++)
{
Colour col = new Colour();
- col.setName(ResidueProperties.aa[i].toLowerCase());
+ col.setName(ResidueProperties.aa[i].toLowerCase(Locale.ROOT));
col.setRGB(jalview.util.Format.getHexString(colours[i]));
// jbucs.addColour(col);
jbucs.getColour().add(col);
entryCount++;
}
} while (jarentry != null);
+ jin.close();
resolveFrefedSequences();
} catch (IOException ex)
{
}
else
{
- warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
+ Console.warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
}
} catch (Exception ex)
{
tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
if (tp == null)
{
- warn("There was a problem recovering stored Newick tree: \n"
+ Console.warn("There was a problem recovering stored Newick tree: \n"
+ tree.getNewick());
continue;
}
else
{
errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
- warn(errorMessage);
+ Console.warn(errorMessage);
}
}
}
} catch (IllegalArgumentException | NullPointerException e)
{
// TODO JAL-3619 show error dialog / offer an alternative viewer
- Cache.log.error("Invalid structure viewer type: " + type);
+ Console.error("Invalid structure viewer type: " + type);
}
}
}
else
{
- warn("Couldn't recover parameters for "
+ Console.warn("Couldn't recover parameters for "
+ calcIdParam.getCalcId());
}
}
String id = object.getViewport().get(0).getSequenceSetId();
if (skipList.containsKey(id))
{
- if (Cache.log != null && Cache.log.isDebugEnabled())
- {
- Cache.log.debug("Skipping seuqence set id " + id);
- }
+ Console.debug("Skipping seuqence set id " + id);
return true;
}
return false;
{
if (ds != null && ds != seqSetDS)
{
- warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
+ Console.warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
+ " - CDS/Protein crossreference data may be lost");
if (xtant_ds != null)
{
// This can only happen if the unique sequence set ID was bound to a
// dataset that did not contain any of the sequences in the view
// currently being restored.
- warn("JAL-3171 SERIOUS! TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed.");
+ Console.warn("JAL-3171 SERIOUS! TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed.");
}
}
ds = seqSetDS;
SequenceI[] dsseqs = new SequenceI[dseqs.size()];
dseqs.copyInto(dsseqs);
ds = new jalview.datamodel.Alignment(dsseqs);
- debug("Created new dataset " + vamsasSet.getDatasetId()
+ Console.debug("Created new dataset " + vamsasSet.getDatasetId()
+ " for alignment " + System.identityHashCode(al));
addDatasetRef(vamsasSet.getDatasetId(), ds);
}
AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
if (prevDS != null && prevDS != ds)
{
- warn("Dataset sequence appears in many datasets: "
+ Console.warn("Dataset sequence appears in many datasets: "
+ restoredSeq.getDsseqid());
// TODO: try to merge!
}
{
if (dataset.getDataset() != null)
{
- warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
+ Console.warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
}
String datasetId = makeHashCode(dataset, null);
if (datasetId == null)
{
entry.setMap(addMapping(dr.getMapping()));
}
+ entry.setCanonical(dr.isCanonical());
datasetSequence.addDBRef(entry);
}
}
seqRefIds.put(sqid, djs);
}
- jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
+ Console.debug("about to recurse on addDBRefs.");
addDBRefs(djs, ms);
}
private Hashtable jvids2vobj;
- private void warn(String msg)
- {
- warn(msg, null);
- }
-
- private void warn(String msg, Exception e)
- {
- if (Cache.log != null)
- {
- if (e != null)
- {
- Cache.log.warn(msg, e);
- }
- else
- {
- Cache.log.warn(msg);
- }
- }
- else
- {
- System.err.println("Warning: " + msg);
- if (e != null)
- {
- e.printStackTrace();
- }
- }
- }
-
- private void debug(String string)
- {
- debug(string, null);
- }
-
- private void debug(String msg, Exception e)
- {
- if (Cache.log != null)
- {
- if (e != null)
- {
- Cache.log.debug(msg, e);
- }
- else
- {
- Cache.log.debug(msg);
- }
- }
- else
- {
- System.err.println("Warning: " + msg);
- if (e != null)
- {
- e.printStackTrace();
- }
- }
- }
-
/**
* set the object to ID mapping tables used to write/recover objects and XML
* ID strings for the jalview project. If external tables are provided then
if (!jvann.annotationId.equals(anid))
{
// TODO verify that this is the correct behaviour
- this.warn("Overriding Annotation ID for " + anid
+ Console.warn("Overriding Annotation ID for " + anid
+ " from different id : " + jvann.annotationId);
jvann.annotationId = anid;
}
}
else
{
- Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+ Console.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
}
}
}
}
else
{
- warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
+ Console.warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
}
} catch (Exception ex)
{
}
} catch (Exception ex)
{
- Cache.log.error("Error loading PCA: " + ex.toString());
+ Console.error("Error loading PCA: " + ex.toString());
}
}
});
} catch (InvocationTargetException | InterruptedException ex)
{
- warn("Unexpected error when opening " + viewerType
+ Console.warn("Unexpected error when opening " + viewerType
+ " structure viewer", ex);
}
}
}
} catch (IOException e)
{
- Cache.log.error("Error restoring Jmol session: " + e.toString());
+ Console.error("Error restoring Jmol session: " + e.toString());
}
return null;
}
maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
} catch (Exception e)
{
- Cache.log.warn("Couldn't parse out graduated feature color.", e);
+ Console.warn("Couldn't parse out graduated feature color.", e);
}
NoValueColour noCol = colourModel.getNoValueColour();
.deriveFont(AffineTransform.getScaleInstance(sx, sy));
g.setFont(font);
g.drawChars(dc, 0, dc.length, x * charWidth, hght);
+ g.setFont(ofont);
+
ht += newHeight;
}
}
*/
package jalview.schemes;
+import java.awt.Color;
+import java.util.List;
+import java.util.Map;
+
import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
-import java.awt.Color;
-import java.util.List;
-import java.util.Map;
-
public class ClustalxColourScheme extends ResidueColourScheme
{
private static final int EIGHTY_FIVE = 85;
}
@Override
- public void alignmentChanged(AnnotatedCollectionI alignment,
+ public synchronized void alignmentChanged(AnnotatedCollectionI alignment,
Map<SequenceI, SequenceCollectionI> hiddenReps)
{
int maxWidth = alignment.getWidth();
}
@Override
- protected Color findColour(char c, int j, SequenceI seq)
+ protected synchronized Color findColour(char c, int j, SequenceI seq)
{
// TODO why the test for includeGaps here?
if (cons2.length <= j || Comparison.isGap(c)
*/
package jalview.schemes;
+import java.util.Locale;
+
import jalview.xml.binding.jalview.JalviewUserColours;
import java.awt.Color;
Color color = new Color(
Integer.parseInt(jucs.getColour().get(i).getRGB(), 16));
- if (name.toLowerCase().equals(name))
+ if (name.toLowerCase(Locale.ROOT).equals(name))
{
caseSensitive = true;
lowerCase[index] = color;
*/
package jalview.schemes;
+import java.util.Locale;
+
import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
* name is lower-case for non-case-sensitive lookup
* (name in the colour keeps its true case)
*/
- String lower = name.toLowerCase();
+ String lower = name.toLowerCase(Locale.ROOT);
if (schemes.containsKey(lower))
{
System.err
{
if (name != null)
{
- schemes.remove(name.toLowerCase());
+ schemes.remove(name.toLowerCase(Locale.ROOT));
}
}
{
return null;
}
- ColourSchemeI cs = schemes.get(name.toLowerCase());
+ ColourSchemeI cs = schemes.get(name.toLowerCase(Locale.ROOT));
return cs == null ? null
: cs.getInstance(viewport, forData);
}
{
return false;
}
- return schemes.containsKey(name.toLowerCase());
+ return schemes.containsKey(name.toLowerCase(Locale.ROOT));
}
}
*/
package jalview.schemes;
+import java.util.Locale;
+
import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.features.FeatureMatcher;
"Expected either 'label' or a colour specification in the line: "
+ descriptor);
}
- if (nextToken.toLowerCase().startsWith(LABEL))
+ if (nextToken.toLowerCase(Locale.ROOT).startsWith(LABEL))
{
byLabel = true;
// get the token after the next delimiter:
mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
}
- else if (nextToken.toLowerCase().startsWith(SCORE))
+ else if (nextToken.toLowerCase(Locale.ROOT).startsWith(SCORE))
{
mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
}
- else if (nextToken.toLowerCase().startsWith(ATTRIBUTE))
+ else if (nextToken.toLowerCase(Locale.ROOT).startsWith(ATTRIBUTE))
{
byAttribute = true;
attName = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
}
gcol.nextToken(); // skip next '|'
- if (tok.toLowerCase().startsWith(ABSOLUTE))
+ if (tok.toLowerCase(Locale.ROOT).startsWith(ABSOLUTE))
{
minval = gcol.nextToken();
gcol.nextToken(); // skip next '|'
{
// threshold type and possibly a threshold value
ttype = gcol.nextToken();
- if (ttype.toLowerCase().startsWith(BELOW))
+ if (ttype.toLowerCase(Locale.ROOT).startsWith(BELOW))
{
featureColour.setBelowThreshold(true);
}
- else if (ttype.toLowerCase().startsWith(ABOVE))
+ else if (ttype.toLowerCase(Locale.ROOT).startsWith(ABOVE))
{
featureColour.setAboveThreshold(true);
}
else
{
- if (!ttype.toLowerCase().startsWith("no"))
+ if (!ttype.toLowerCase(Locale.ROOT).startsWith("no"))
{
System.err.println(
"Ignoring unrecognised threshold type : " + ttype);
}
@Override
+ public boolean isFeatureHidden(String type)
+ {
+ return false;
+ }
+
+ @Override
public boolean isGroupDisplayed(String group)
{
return true;
*/
package jalview.schemes;
+import java.util.Locale;
+
import jalview.analysis.GeneticCodes;
import java.awt.Color;
{
continue;
}
- nuc = nuc.toUpperCase();
+ nuc = nuc.toUpperCase(Locale.ROOT);
if (!result.contains(nuc))
{
result.add(nuc);
{
continue;
}
- res = res.toUpperCase();
+ res = res.toUpperCase(Locale.ROOT);
if (!result.contains(res))
{
result.add(res);
return '0';
}
Integer index = ResidueProperties.aa3Hash
- .get(threeLetterCode.toUpperCase());
+ .get(threeLetterCode.toUpperCase(Locale.ROOT));
return index == null ? '0' : aa[index].charAt(0);
}
}
*/
package jalview.schemes;
+import java.util.Locale;
+
import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.util.ColorUtils;
continue;
}
- if (residue.equals(residue.toLowerCase()))
+ if (residue.equals(residue.toLowerCase(Locale.ROOT)))
{
if (lowerCaseColours == null)
{
c = lowerCaseColours[index];
if (c != null && !c.equals(Color.white))
{
- residue = residue.toLowerCase();
+ residue = residue.toLowerCase(Locale.ROOT);
if (colours.get(c) == null)
{
colours.put(c, new ArrayList<String>());
protected StructureCommandI getColourCommand(AtomSpecModel atomSpecModel,
Color colour)
{
- String atomSpec = getAtomSpec(atomSpecModel, false);
+ String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
return colourResidues(atomSpec, colour);
}
*
* @param refAtoms
* @param atomSpec
+ * @param backbone - superpose based on which kind of atomType
* @return
*/
List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec);
+ AtomSpecModel atomSpec, AtomSpecType backbone);
/**
* Returns a command to open a file of commands at the given path
*/
StructureCommandI saveSession(String filepath);
+ enum AtomSpecType { RESIDUE_ONLY, ALPHA, PHOSPHATE };
/**
* Returns a representation of the atom set represented by the model, in
* viewer syntax format. If {@code alphaOnly} is true, this is restricted to
* Alpha Carbon (peptide) or Phosphorous (rna) only
*
* @param model
- * @param alphaOnly
+ * @param specType
* @return
*/
- String getAtomSpec(AtomSpecModel model, boolean alphaOnly);
+ String getAtomSpec(AtomSpecModel model, AtomSpecType specType);
/**
* Returns the lowest model number used by the structure viewer (likely 0 or
*/
package jalview.structure;
+import java.util.Locale;
+
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
String defaultStructureFileFormat)
{
StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
- .valueOf(defaultStructureFileFormat.toUpperCase());
+ .valueOf(defaultStructureFileFormat.toUpperCase(Locale.ROOT));
}
public static String getDefaultPDBFileParser()
public static void setDefaultPDBFileParser(String defaultPDBFileParser)
{
StructureImportSettings.defaultPDBFileParser = StructureParser
- .valueOf(defaultPDBFileParser.toUpperCase());
+ .valueOf(defaultPDBFileParser.toUpperCase(Locale.ROOT));
}
}
import java.util.HashMap;
import java.util.IdentityHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
import jalview.analysis.AlignSeq;
import jalview.api.StructureSelectionManagerProvider;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.OrderCommand;
registerPDBFile(pdb.getId().trim(), pdbFile);
}
// if PDBId is unavailable then skip SIFTS mapping execution path
- isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable() && !pdb.getId().startsWith("AF-");
+ // TODO: JAL-3868 need to know if structure is actually from
+ // PDB (has valid PDB ID and has provenance suggesting it
+ // actually came from PDB)
+ boolean isProtein = false;
+ for (SequenceI s:sequenceArray) {
+ if (s.isProtein()) {
+ isProtein = true;
+ break;
+ }
+ }
+ isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable() && !pdb.getId().startsWith("AF-") && isProtein;
} catch (Exception ex)
{
} catch (SiftsException e)
{
isMapUsingSIFTs = false;
- Cache.log.error("SIFTS mapping failed", e);
- Cache.log.error("Falling back on Needleman & Wunsch alignment");
+ Console.error("SIFTS mapping failed", e);
+ Console.error("Falling back on Needleman & Wunsch alignment");
siftsClient = null;
}
pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
seqToStrucMapping.add(siftsMapping);
maxChain.makeExactMapping(siftsMapping, seq);
- maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");
+ maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT));
maxChain.transferResidueAnnotation(siftsMapping, null);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
} catch (SiftsException e)
{
// fall back to NW alignment
- Cache.log.error(e.getMessage());
+ Console.error(e.getMessage());
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
targetChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, "IEA:Jalview"); // FIXME: is
+ maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
// this
// "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
siftsClient);
foundSiftsMappings.add(siftsMapping);
chain.makeExactMapping(siftsMapping, seq);
- chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
+ chain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT));// FIXME: is this
// "IEA:SIFTS" ?
chain.transferResidueAnnotation(siftsMapping, null);
} catch (SiftsException e)
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
maxChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
- maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+ maxChain.transferRESNUMFeatures(seq, null,pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is this
// "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
maxChain.makeExactMapping(maxAlignseq, seq);
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
- maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferRESNUMFeatures(seq, null, pdb.getId().toLowerCase(Locale.ROOT));
HashMap<Integer, int[]> mapping = new HashMap<>();
int resNum = -10000;
*/
package jalview.structures.models;
+import java.util.Locale;
+
import java.awt.Color;
import java.io.File;
import java.io.IOException;
import jalview.api.SequenceRenderer;
import jalview.api.StructureSelectionManagerProvider;
import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.MappedFeatures;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
/**
*
- * A base class to hold common function for protein structure model binding.
+ * A base class to hold common function for 3D structure model binding.
* Initial version created by refactoring JMol and Chimera binding models, but
* other structure viewers could in principle be accommodated in future.
*
public String chain = "";
+ /**
+ * is the mapped sequence not protein ?
+ */
public boolean isRna;
/*
protected boolean colourBySequence = true;
+ /**
+ * true if all sequences appear to be nucleotide
+ */
private boolean nucleotide;
private boolean finishedInit = false;
}
}
}
+
@Override
public abstract void highlightAtoms(List<AtomSpec> atoms);
structures[pdbfnum].chain = chain;
}
structures[pdbfnum].pdbId = mapping.getPdbId();
- structures[pdbfnum].isRna = theSequence.getRNA() != null;
+ structures[pdbfnum].isRna = !theSequence.isProtein();
/*
* move on to next pdb file (ignore sequences for other chains
*/
// todo better way to ensure synchronous than setting getReply true!!
executeCommands(commandGenerator.showBackbone(), true, null);
-
+
+ AtomSpecType backbone = structures[refStructure].isRna ? AtomSpecType.PHOSPHATE : AtomSpecType.ALPHA;
/*
* superpose each (other) structure to the reference in turn
*/
{
AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
List<StructureCommandI> commands = commandGenerator
- .superposeStructures(refAtoms, atomSpec);
+ .superposeStructures(refAtoms, atomSpec, backbone);
List<String> replies = executeCommands(commands, true, null);
for (String reply : replies)
{
// return this error (Chimera only) to the user
- if (reply.toLowerCase().contains("unequal numbers of atoms"))
+ if (reply.toLowerCase(Locale.ROOT).contains("unequal numbers of atoms"))
{
error += "; " + reply;
}
* executed.
* <p>
* If a reply is wanted, the execution is done synchronously (waits),
- * otherwise it is done in a separate thread (doesn't wait).
+ * otherwise it is done in a separate thread (doesn't wait). WARNING: if you
+ * are sending commands that need to execute before later calls to
+ * executeCommand (e.g. mouseovers, which clean up after previous ones) then
+ * set getReply true to ensure that commands are not executed out of order.
*
* @param getReply
* @param msg
}
/**
- * Returns the FeatureRenderer for the given alignment view, or null if
- * feature display is turned off in the view.
+ * Returns the FeatureRenderer for the given alignment view
*
* @param avp
* @return
{
return null;
}
- return ap.getAlignViewport().isShowSequenceFeatures()
- ? ap.getFeatureRenderer()
- : null;
+ return ap.getFeatureRenderer();
}
protected void setStructureCommands(StructureCommandsI cmd)
saveSession(f);
} catch (IOException e)
{
- Cache.log.error(String.format("Error saving %s session: %s", prefix,
+ Console.error(String.format("Error saving %s session: %s", prefix,
e.toString()));
}
package jalview.urls;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.urls.api.UrlProviderI;
import jalview.util.UrlLink;
dataProvider.setUrlData(data);
} catch (IllegalArgumentException ex)
{
- Cache.log.error(ex.getMessage());
+ Console.error(ex.getMessage());
}
}
});
*/
package jalview.util;
+import jalview.bin.Cache;
+
import java.io.File;
import java.io.IOException;
import java.lang.reflect.Constructor;
case OTHER:
default:
- browser = jalview.bin.Cache.getDefault("DEFAULT_BROWSER", "firefox");
+ browser = Cache.getDefault("DEFAULT_BROWSER", "firefox");
break;
}
* want to preserve case, but do not want to duplicate upper and lower case
* variants
*/
+import java.util.Locale;
+
public final class CaseInsensitiveString
{
String value;
public int hashCode()
{
return value == null ? super.hashCode()
- : value.toUpperCase().hashCode();
+ : value.toUpperCase(Locale.ROOT).hashCode();
}
}
package jalview.util;
import java.awt.Image;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import javax.swing.ImageIcon;
-import jalview.bin.Cache;
-
public class ChannelProperties
{
- private static final String CHANNEL_PROPERTIES_FILENAME = "/channel.props";
+ public static final String CHANNEL_PROPERTIES_FILENAME = "channel.props";
- private static final Properties channelProps;
+ private static Properties channelProps;
private static final Properties defaultProps;
// load channel_properties
Properties tryChannelProps = new Properties();
URL channelPropsURL = ChannelProperties.class
- .getResource(CHANNEL_PROPERTIES_FILENAME);
+ .getResource("/" + CHANNEL_PROPERTIES_FILENAME);
if (channelPropsURL == null)
{
// complete failure of channel_properties, set all properties to defaults
- System.err.println("Failed to find '" + CHANNEL_PROPERTIES_FILENAME
+ System.err.println("Failed to find '/" + CHANNEL_PROPERTIES_FILENAME
+ "' file at '"
+ (channelPropsURL == null ? "null"
: channelPropsURL.toString())
channelPropsIS.close();
} catch (IOException e)
{
- Cache.log.warn(e.getMessage());
+ System.err.println(e.getMessage());
// return false;
}
}
Image logo = null;
String path = defaultProps.getProperty("logo." + size);
URL imageURL = ChannelProperties.class.getResource(path);
- logo = new ImageIcon(imageURL).getImage();
+ ImageIcon imgIcon = imageURL == null ? null
+ : new ImageIcon(imageURL);
+ logo = imgIcon == null ? null : imgIcon.getImage();
if (logo != null)
{
iconList.add(logo);
}
}
+ protected static void loadProps(File dir)
+ {
+ File channelPropsFile = new File(dir, CHANNEL_PROPERTIES_FILENAME);
+ if (channelPropsFile.exists())
+ {
+ try
+ {
+ InputStream is = new FileInputStream(channelPropsFile);
+ channelProps.load(is);
+ } catch (FileNotFoundException e)
+ {
+ System.err.println(e.getMessage());
+ } catch (IOException e)
+ {
+ System.err.println(e.getMessage());
+ }
+ }
+ }
+
private static Properties channelProps()
{
return channelProps;
}
URL imageURL = ChannelProperties.class.getResource(path);
- img = new ImageIcon(imageURL).getImage();
+ ImageIcon imgIcon = imageURL == null ? null : new ImageIcon(imageURL);
+ img = imgIcon == null ? null : imgIcon.getImage();
if (img == null)
{
System.err.println(
package jalview.util;
+import java.util.Locale;
+
import java.awt.Color;
import java.util.HashMap;
import java.util.Map;
return null;
}
Color col = null;
- name = name.toLowerCase();
+ name = name.toLowerCase(Locale.ROOT);
// or make a static map; or use reflection on the field name
switch (name)
/**
* Overloaded method signature to test whether a single sequence is nucleotide
- * (that is, more than 85% CGTA)
+ * (that is, more than 85% CGTAUNX)
*
* @param seq
* @return
}
long ntCount = 0;
long aaCount = 0;
+ long nCount = 0;
int len = seq.getLength();
for (int i = 0; i < len; i++)
{
char c = seq.getCharAt(i);
- if (isNucleotide(c))
+ if (isNucleotide(c) || isX(c))
{
ntCount++;
}
else if (!isGap(c))
{
aaCount++;
+ if (isN(c))
+ {
+ nCount++;
+ }
}
}
/*
* Check for nucleotide count > 85% of total count (in a form that evades
* int / float conversion or divide by zero).
*/
- if (ntCount * 100 > EIGHTY_FIVE * (ntCount + aaCount))
+ if ((ntCount+nCount) * 100 > EIGHTY_FIVE * (ntCount + aaCount))
{
- return true;
+ return ntCount>0; // all N is considered protein. Could use a threshold here too
}
else
{
return false;
}
// true if we have seen a nucleotide sequence
- boolean na=false;
+ boolean na = false;
for (SequenceI seq : seqs)
{
if (seq == null)
{
continue;
}
- na=true;
+ na = true;
// TODO could possibly make an informed guess just from the first sequence
// to save a lengthy calculation
- if (seq.isProtein()) {
+ if (seq.isProtein())
+ {
// if even one looks like protein, the alignment is protein
return false;
}
{
c -= TO_UPPER_CASE;
}
-
switch (c)
{
case 'A':
return false;
}
+ public static boolean isN(char c)
+ {
+ switch (c)
+ {
+ case 'N':
+ case 'n':
+ return true;
+ }
+ return false;
+ }
+
+ public static boolean isX(char c)
+ {
+ switch (c)
+ {
+ case 'X':
+ case 'x':
+ return true;
+ }
+ return false;
+ }
+
/**
* Answers true if every character in the string is one of aAcCgGtTuU, or
* (optionally) a gap character (dot, dash, space), else false
*/
package jalview.util;
+import java.util.Locale;
+
import java.util.ArrayList;
import java.util.BitSet;
import java.util.HashMap;
// guarantee we always have lowercase entries for canonical string lookups
for (String k : canonicalSourceNameLookup.keySet())
{
- canonicalSourceNameLookup.put(k.toLowerCase(),
+ canonicalSourceNameLookup.put(k.toLowerCase(Locale.ROOT),
canonicalSourceNameLookup.get(k));
}
}
HashSet<String> srcs = new HashSet<String>();
for (String src : sources)
{
- srcs.add(src.toUpperCase());
+ srcs.add(src.toUpperCase(Locale.ROOT));
}
int nrefs = dbrefs.size();
{
DBRefEntry dbr = dbrefs.get(ib);
String source = getCanonicalName(dbr.getSource());
- if (srcs.contains(source.toUpperCase()))
+ if (srcs.contains(source.toUpperCase(Locale.ROOT)))
{
res.add(dbr);
}
{
return null;
}
- String canonical = canonicalSourceNameLookup.get(source.toLowerCase());
+ String canonical = canonicalSourceNameLookup.get(source.toLowerCase(Locale.ROOT));
return canonical == null ? source : canonical;
}
public static List<int[]> parseLocation(String location)
throws ParseException
{
+ location = location.trim(); // failsafe for untidy input data
if (location.startsWith("join("))
{
return parseJoin(location);
--- /dev/null
+package jalview.util;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.Properties;
+
+public class LaunchUtils
+{
+
+ public static void loadChannelProps(File dir)
+ {
+ ChannelProperties.loadProps(dir);
+ }
+
+ private static Properties userPreferences = null;
+
+ public static String getUserPreference(String key)
+ {
+ if (userPreferences == null)
+ {
+ String channelPrefsFilename = ChannelProperties
+ .getProperty("preferences.filename");
+ if (channelPrefsFilename == null)
+ {
+ return null;
+ }
+ File propertiesFile = new File(System.getProperty("user.home"),
+ channelPrefsFilename);
+ if (!propertiesFile.exists())
+ {
+ return null;
+ }
+ try
+ {
+ userPreferences = new Properties();
+ userPreferences.load(new FileInputStream(propertiesFile));
+ } catch (FileNotFoundException e)
+ {
+ // didn't find user preferences file
+ return null;
+ } catch (IOException e)
+ {
+ System.err.println(e.getMessage());
+ return null;
+ }
+ }
+ return userPreferences.getProperty(key);
+ }
+
+ public static boolean getBooleanUserPreference(String key)
+ {
+ return Boolean.parseBoolean(getUserPreference(key));
+ }
+}
--- /dev/null
+package jalview.util;
+
+import java.util.Map;
+
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.core.Appender;
+import org.apache.logging.log4j.core.Filter;
+import org.apache.logging.log4j.core.Layout;
+import org.apache.logging.log4j.core.LoggerContext;
+import org.apache.logging.log4j.core.appender.ConsoleAppender;
+import org.apache.logging.log4j.core.config.Configuration;
+import org.apache.logging.log4j.core.config.ConfigurationFactory;
+import org.apache.logging.log4j.core.config.Configurator;
+import org.apache.logging.log4j.core.config.LoggerConfig;
+import org.apache.logging.log4j.core.config.builder.api.AppenderComponentBuilder;
+import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilder;
+import org.apache.logging.log4j.core.config.builder.api.FilterComponentBuilder;
+import org.apache.logging.log4j.core.config.builder.api.LayoutComponentBuilder;
+import org.apache.logging.log4j.core.config.builder.impl.BuiltConfiguration;
+import org.apache.logging.log4j.core.filter.ThresholdFilter;
+import org.apache.logging.log4j.core.layout.PatternLayout;
+
+import jalview.log.JLogger;
+import jalview.log.JalviewAppender;
+
+public class Log4j
+{
+
+ public final static String SIMPLE_PATTERN = "%level - %m%n";
+
+ private static boolean init = false;
+
+ public static boolean isInit()
+ {
+ return init;
+ }
+
+ public static Level log4jLevel(JLogger.LogLevel loglevel)
+ {
+ return Level.toLevel(loglevel.toString());
+ }
+
+ public static void init(JLogger.LogLevel myLevel)
+ {
+ init(log4jLevel(myLevel));
+ }
+
+ public static void init(Level myLevel)
+ {
+ if (init)
+ return;
+ try
+ {
+ // configure the root logger to stderr
+ ConfigurationBuilder<BuiltConfiguration> configBuilder = Log4j
+ .getConfigurationBuilder();
+
+ configBuilder.setStatusLevel(Level.WARN);
+
+ String consoleLoggerName = "STDERR";
+ AppenderComponentBuilder appenderBuilder = configBuilder
+ .newAppender(consoleLoggerName, "Console");
+ appenderBuilder.addAttribute("target",
+ ConsoleAppender.Target.SYSTEM_ERR);
+ appenderBuilder.add(Log4j.getSimpleLayoutBuilder());
+ appenderBuilder.add(Log4j.getThresholdFilterBuilder());
+ configBuilder.add(appenderBuilder);
+
+ configBuilder.add(configBuilder.newRootLogger(myLevel)
+ .add(configBuilder.newAppenderRef(consoleLoggerName)));
+
+ Configurator.initialize(configBuilder.build());
+
+ init = true;
+ } catch (Exception e)
+ {
+ System.err.println("Problems initializing the log4j system\n");
+ e.printStackTrace(System.err);
+ }
+ }
+
+ public static Logger getLogger(String name)
+ {
+ return getLogger(name, Level.INFO);
+ }
+
+ public static Logger getLogger(String name, JLogger.LogLevel loglevel)
+ {
+ return getLogger(name, log4jLevel(loglevel));
+ }
+
+ public static Logger getLogger(String name, Level level)
+ {
+ Logger logger = LogManager.getLogger(name);
+ Log4j.setLevel(logger, level);
+ return logger;
+ }
+
+ public static ConfigurationBuilder<BuiltConfiguration> getConfigurationBuilder()
+ {
+ return ConfigurationFactory.newConfigurationBuilder();
+ }
+
+ public static Layout getSimpleLayout()
+ {
+ return PatternLayout.newBuilder().withPattern(SIMPLE_PATTERN).build();
+ }
+
+ public static LayoutComponentBuilder getSimpleLayoutBuilder()
+ {
+ return getConfigurationBuilder().newLayout("PatternLayout")
+ .addAttribute("pattern", Log4j.SIMPLE_PATTERN);
+ }
+
+ public static Filter getThresholdFilter(Level level)
+ {
+ return ThresholdFilter.createFilter(level, Filter.Result.ACCEPT,
+ Filter.Result.NEUTRAL);
+ }
+
+ public static FilterComponentBuilder getThresholdFilterBuilder()
+ {
+ return getConfigurationBuilder().newFilter("ThresholdFilter",
+ Filter.Result.ACCEPT, Filter.Result.NEUTRAL);
+ }
+
+ public static void setLevel(Logger logger, JLogger.LogLevel loglevel)
+ {
+ setLevel(logger, log4jLevel(loglevel));
+ }
+
+ public static void setLevel(Logger logger, Level level)
+ {
+ if (!Platform.isJS())
+ {
+ LoggerContext context = (LoggerContext) LogManager.getContext(false);
+ Configuration config = context.getConfiguration();
+ LoggerConfig loggerConfig = config.getLoggerConfig(logger.getName());
+ loggerConfig.setLevel(level);
+
+ Map<String, Appender> appenders = config.getAppenders();
+
+ Appender jappender = config.getAppender(JalviewAppender.NAME);
+
+ context.updateLoggers();
+ }
+ }
+
+ public static void setRootLevel(JLogger.LogLevel loglevel)
+ {
+ setRootLevel(log4jLevel(loglevel));
+ }
+
+ public static void setRootLevel(Level level)
+ {
+ setLevel(LogManager.getRootLogger(), level);
+ }
+
+ public static Appender getAppender(String name)
+ {
+ LoggerContext context = (LoggerContext) LogManager.getContext(false);
+ Configuration config = context.getConfiguration();
+ Map<String, Appender> appenders = config.getAppenders();
+ return appenders.get(name);
+ }
+
+ public static void addAppender(Logger logger, Logger logger2,
+ String name2)
+ {
+ LoggerContext context = (LoggerContext) LogManager.getContext(false);
+ Configuration config = context.getConfiguration();
+ LoggerConfig logger2Config = config.getLoggerConfig(logger2.getName());
+ Map<String, Appender> logger2AppendersMap = logger2Config
+ .getAppenders();
+ Appender appender = logger2AppendersMap.get(name2);
+ addAppender(logger, appender);
+ context.updateLoggers();
+ }
+
+ public static void addAppender(Logger logger, Appender appender)
+ {
+ if (appender == null)
+ return;
+ LoggerContext context = (LoggerContext) LogManager.getContext(false);
+ Configuration config = context.getConfiguration();
+ LoggerConfig loggerConfig = config.getLoggerConfig(logger.getName());
+ if (loggerConfig == null)
+ return;
+
+ Level level = loggerConfig.getLevel();
+
+ config.addAppender(appender);
+ loggerConfig.addAppender(appender, null, null);
+
+ context.updateLoggers();
+ }
+
+ public static void addAppenderToRootLogger(Appender appender)
+ {
+ Log4j.addAppender(LogManager.getRootLogger(), appender);
+ }
+}
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.BitSet;
import java.util.List;
+import jalview.bin.Console;
+
/**
* A simple way of bijectively mapping a non-contiguous linear range to another
* non-contiguous linear range.
*
* Use at your own risk!
*
- * TODO: efficient implementation of private posMap method
- *
* TODO: test/ensure that sense of from and to ratio start position is conserved
* (codon start position recovery)
*/
/**
* Constructor given from and to ranges as [start1, end1, start2, end2,...].
- * If any end is equal to the next start, the ranges will be merged. There is
- * no validation check that the ranges do not overlap each other.
+ * There is no validation check that the ranges do not overlap each other.
*
* @param from
* contiguous regions as [start1, end1, start2, end2, ...]
this.toRatio = toRatio;
fromLowest = Integer.MAX_VALUE;
fromHighest = Integer.MIN_VALUE;
- int added = 0;
for (int i = 0; i < from.length; i += 2)
{
*/
fromLowest = Math.min(fromLowest, Math.min(from[i], from[i + 1]));
fromHighest = Math.max(fromHighest, Math.max(from[i], from[i + 1]));
- if (added > 0 && from[i] == fromShifts.get(added - 1)[1])
- {
- /*
- * this range starts where the last ended - just extend it
- */
- fromShifts.get(added - 1)[1] = from[i + 1];
- }
- else
- {
- fromShifts.add(new int[] { from[i], from[i + 1] });
- added++;
- }
+ fromShifts.add(new int[] { from[i], from[i + 1] });
}
toLowest = Integer.MAX_VALUE;
toHighest = Integer.MIN_VALUE;
- added = 0;
for (int i = 0; i < to.length; i += 2)
{
toLowest = Math.min(toLowest, Math.min(to[i], to[i + 1]));
toHighest = Math.max(toHighest, Math.max(to[i], to[i + 1]));
- if (added > 0 && to[i] == toShifts.get(added - 1)[1])
- {
- toShifts.get(added - 1)[1] = to[i + 1];
- }
- else
- {
- toShifts.add(new int[] { to[i], to[i + 1] });
- added++;
- }
+ toShifts.add(new int[] { to[i], to[i + 1] });
}
}
if (range.length != 2)
{
// throw new IllegalArgumentException(range);
- System.err.println(
- "Invalid format for fromRange " + Arrays.toString(range)
- + " may cause errors");
+ Console.error("Invalid format for fromRange "
+ + Arrays.toString(range) + " may cause errors");
}
fromLowest = Math.min(fromLowest, Math.min(range[0], range[1]));
fromHighest = Math.max(fromHighest, Math.max(range[0], range[1]));
if (range.length != 2)
{
// throw new IllegalArgumentException(range);
- System.err.println("Invalid format for toRange "
- + Arrays.toString(range)
- + " may cause errors");
+ Console.error("Invalid format for toRange "
+ + Arrays.toString(range) + " may cause errors");
}
toLowest = Math.min(toLowest, Math.min(range[0], range[1]));
toHighest = Math.max(toHighest, Math.max(range[0], range[1]));
/**
* Consolidates a list of ranges so that any contiguous ranges are merged.
* This assumes the ranges are already in start order (does not sort them).
+ * <p>
+ * The main use case for this method is when mapping cDNA sequence to its
+ * protein product, based on CDS feature ranges which derive from spliced
+ * exons, but are contiguous on the cDNA sequence. For example
+ *
+ * <pre>
+ * CDS 1-20 // from exon1
+ * CDS 21-35 // from exon2
+ * CDS 36-71 // from exon3
+ * 'coalesce' to range 1-71
+ * </pre>
*
* @param ranges
* @return the same list (if unchanged), else a new merged list, leaving the
first = false;
continue;
}
- if (range[0] == lastRange[0] && range[1] == lastRange[1])
- {
- // drop duplicate range
- changed = true;
- continue;
- }
-
- /*
- * drop this range if it lies within the last range
- */
- if ((lastDirection == 1 && range[0] >= lastRange[0]
- && range[0] <= lastRange[1] && range[1] >= lastRange[0]
- && range[1] <= lastRange[1])
- || (lastDirection == -1 && range[0] <= lastRange[0]
- && range[0] >= lastRange[1]
- && range[1] <= lastRange[0]
- && range[1] >= lastRange[1]))
- {
- changed = true;
- continue;
- }
int direction = range[1] >= range[0] ? 1 : -1;
boolean sameDirection = range[1] == range[0]
|| direction == lastDirection;
boolean extending = range[0] == lastRange[1] + lastDirection;
- boolean overlapping = (lastDirection == 1 && range[0] >= lastRange[0]
- && range[0] <= lastRange[1])
- || (lastDirection == -1 && range[0] <= lastRange[0]
- && range[0] >= lastRange[1]);
- if (sameDirection && (overlapping || extending))
+ if (sameDirection && extending)
{
lastRange[1] = range[1];
changed = true;
*/
protected int[][] makeFromMap()
{
- // TODO not used - remove??
+ // TODO only used for test - remove??
return posMap(fromShifts, fromRatio, toShifts, toRatio);
}
*/
protected int[][] makeToMap()
{
- // TODO not used - remove??
+ // TODO only used for test - remove??
return posMap(toShifts, toRatio, fromShifts, fromRatio);
}
* @return int[] { from, to pos in range }, int[range.to-range.from+1]
* returning mapped position
*/
- private int[][] posMap(List<int[]> shiftTo, int ratio,
- List<int[]> shiftFrom, int toRatio)
+ private int[][] posMap(List<int[]> shiftTo, int sourceRatio,
+ List<int[]> shiftFrom, int targetRatio)
{
- // TODO not used - remove??
+ // TODO only used for test - remove??
int iv = 0, ivSize = shiftTo.size();
if (iv >= ivSize)
{
int mp[][] = new int[to - from + 2][];
for (int i = 0; i < mp.length; i++)
{
- int[] m = shift(i + from, shiftTo, ratio, shiftFrom, toRatio);
+ int[] m = shift(i + from, shiftTo, sourceRatio, shiftFrom,
+ targetRatio);
if (m != null)
{
if (i == 0)
List<int[]> shiftFrom, int toRatio)
{
// TODO: javadoc; tests
- int[] fromCount = countPos(shiftTo, pos);
+ int[] fromCount = countPositions(shiftTo, pos);
if (fromCount == null)
{
return null;
}
int fromRemainder = (fromCount[0] - 1) % fromRatio;
int toCount = 1 + (((fromCount[0] - 1) / fromRatio) * toRatio);
- int[] toPos = countToPos(shiftFrom, toCount);
+ int[] toPos = traverseToPosition(shiftFrom, toCount);
if (toPos == null)
{
- return null; // throw new Error("Bad Mapping!");
+ return null;
}
- // System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
return new int[] { toPos[0], fromRemainder, toPos[1] };
}
/**
- * count how many positions pos is along the series of intervals.
+ * Counts how many positions pos is along the series of intervals. Returns an
+ * array of two values:
+ * <ul>
+ * <li>the number of positions traversed (inclusive) to reach {@code pos}</li>
+ * <li>+1 if the last interval traversed is forward, -1 if in a negative
+ * direction</li>
+ * </ul>
+ * Returns null if {@code pos} does not lie in any of the given intervals.
*
- * @param shiftTo
+ * @param intervals
+ * a list of start-end intervals
* @param pos
- * @return number of positions or null if pos is not within intervals
+ * a position that may lie in one (or more) of the intervals
+ * @return
*/
- protected static int[] countPos(List<int[]> shiftTo, int pos)
+ protected static int[] countPositions(List<int[]> intervals, int pos)
{
- int count = 0, intv[], iv = 0, ivSize = shiftTo.size();
+ int count = 0;
+ int iv = 0;
+ int ivSize = intervals.size();
+
while (iv < ivSize)
{
- intv = shiftTo.get(iv++);
+ int[] intv = intervals.get(iv++);
if (intv[0] <= intv[1])
{
+ /*
+ * forwards interval
+ */
if (pos >= intv[0] && pos <= intv[1])
{
return new int[] { count + pos - intv[0] + 1, +1 };
}
else
{
+ /*
+ * reverse interval
+ */
if (pos >= intv[1] && pos <= intv[0])
{
return new int[] { count + intv[0] - pos + 1, -1 };
}
/**
- * count out pos positions into a series of intervals and return the position
+ * Reads through the given intervals until {@code count} positions have been
+ * traversed, and returns an array consisting of two values:
+ * <ul>
+ * <li>the value at the {@code count'th} position</li>
+ * <li>+1 if the last interval read is forwards, -1 if reverse direction</li>
+ * </ul>
+ * Returns null if the ranges include less than {@code count} positions, or if
+ * {@code count < 1}.
*
- * @param shiftFrom
- * @param pos
- * @return position pos in interval set
+ * @param intervals
+ * a list of [start, end] ranges
+ * @param count
+ * the number of positions to traverse
+ * @return
*/
- protected static int[] countToPos(List<int[]> shiftFrom, int pos)
+ protected static int[] traverseToPosition(List<int[]> intervals,
+ final int count)
{
- int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size();
- int[] intv = { 0, 0 };
+ int traversed = 0;
+ int ivSize = intervals.size();
+ int iv = 0;
+
+ if (count < 1)
+ {
+ return null;
+ }
+
while (iv < ivSize)
{
- intv = shiftFrom.get(iv++);
- diff = intv[1] - intv[0];
+ int[] intv = intervals.get(iv++);
+ int diff = intv[1] - intv[0];
if (diff >= 0)
{
- if (pos <= count + 1 + diff)
+ if (count <= traversed + 1 + diff)
{
- return new int[] { pos - count - 1 + intv[0], +1 };
+ return new int[] { intv[0] + (count - traversed - 1), +1 };
}
else
{
- count += 1 + diff;
+ traversed += 1 + diff;
}
}
else
{
- if (pos <= count + 1 - diff)
+ if (count <= traversed + 1 - diff)
{
- return new int[] { intv[0] - (pos - count - 1), -1 };
+ return new int[] { intv[0] - (count - traversed - 1), -1 };
}
else
{
- count += 1 - diff;
+ traversed += 1 - diff;
}
}
}
- return null;// (diff<0) ? (intv[1]-1) : (intv[0]+1);
- }
-
- /**
- * find series of intervals mapping from start-end in the From map.
- *
- * @param start
- * position mapped 'to'
- * @param end
- * position mapped 'to'
- * @return series of [start, end] ranges in sequence mapped 'from'
- */
- public int[] locateInFrom(int start, int end)
- {
- // inefficient implementation
- int fromStart[] = shiftTo(start);
- // needs to be inclusive of end of symbol position
- int fromEnd[] = shiftTo(end);
-
- return getIntervals(fromShifts, fromStart, fromEnd, fromRatio);
- }
-
- /**
- * find series of intervals mapping from start-end in the to map.
- *
- * @param start
- * position mapped 'from'
- * @param end
- * position mapped 'from'
- * @return series of [start, end] ranges in sequence mapped 'to'
- */
- public int[] locateInTo(int start, int end)
- {
- int toStart[] = shiftFrom(start);
- int toEnd[] = shiftFrom(end);
- return getIntervals(toShifts, toStart, toEnd, toRatio);
+ return null;
}
/**
*/
public int getToPosition(int mpos)
{
- // TODO not used - remove??
int[] mp = shiftTo(mpos);
if (mp != null)
{
}
/**
- * get range of positions in To frame for the mpos word in From
- *
- * @param mpos
- * position in From
- * @return null or int[] first position in To for mpos, last position in to
- * for Mpos
- */
- public int[] getToWord(int mpos)
- {
- int[] mp = shiftTo(mpos);
- if (mp != null)
- {
- return new int[] { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) };
- }
- return null;
- }
-
- /**
- * get From position in the associated reference frame for position pos in the
- * associated sequence.
- *
- * @param pos
- * @return
- */
- public int getMappedPosition(int pos)
- {
- // TODO not used - remove??
- int[] mp = shiftFrom(pos);
- if (mp != null)
- {
- return mp[0];
- }
- return pos;
- }
-
- public int[] getMappedWord(int pos)
- {
- // TODO not used - remove??
- int[] mp = shiftFrom(pos);
- if (mp != null)
- {
- return new int[] { mp[0], mp[0] + mp[2] * (getToRatio() - 1) };
- }
- return null;
- }
-
- /**
*
* @return a MapList whose From range is this maplist's To Range, and vice
* versa
}
/**
- * test for containment rather than equivalence to another mapping
- *
- * @param map
- * to be tested for containment
- * @return true if local or mapped range map contains or is contained by this
- * mapping
- */
- public boolean containsEither(boolean local, MapList map)
- {
- // TODO not used - remove?
- if (local)
- {
- return ((getFromLowest() >= map.getFromLowest()
- && getFromHighest() <= map.getFromHighest())
- || (getFromLowest() <= map.getFromLowest()
- && getFromHighest() >= map.getFromHighest()));
- }
- else
- {
- return ((getToLowest() >= map.getToLowest()
- && getToHighest() <= map.getToHighest())
- || (getToLowest() <= map.getToLowest()
- && getToHighest() >= map.getToHighest()));
- }
- }
-
- /**
* String representation - for debugging, not guaranteed not to change
*/
@Override
}
/**
- * A helper method that returns true unless at least one range has start > end.
- * Behaviour is undefined for a mixture of forward and reverse ranges.
+ * A helper method that returns true unless at least one range has start >
+ * end. Behaviour is undefined for a mixture of forward and reverse ranges.
*
* @param ranges
* @return
List<int[]> toRanges = new ArrayList<>();
for (int[] range : getToRanges())
{
+ int fromLength = Math.abs(range[1] - range[0]) + 1;
int[] transferred = map.locateInTo(range[0], range[1]);
if (transferred == null || transferred.length % 2 != 0)
{
* convert [start1, end1, start2, end2, ...]
* to [[start1, end1], [start2, end2], ...]
*/
+ int toLength = 0;
for (int i = 0; i < transferred.length;)
{
toRanges.add(new int[] { transferred[i], transferred[i + 1] });
+ toLength += Math.abs(transferred[i + 1] - transferred[i]) + 1;
i += 2;
}
+
+ /*
+ * check we mapped the full range - if not, abort
+ */
+ if (fromLength * map.getToRatio() != toLength * map.getFromRatio())
+ {
+ return null;
+ }
}
return new MapList(getFromRanges(), toRanges, outFromRatio, outToRatio);
{
return fromShifts.size() == 1 && toShifts.size() == 1;
}
+
+ /**
+ * <<<<<<< HEAD Returns the [start1, end1, start2, end2, ...] positions in the
+ * 'from' range that map to positions between {@code start} and {@code end} in
+ * the 'to' range. Note that for a reverse strand mapping this will return
+ * ranges with end < start. Returns null if no mapped positions are found in
+ * start-end.
+ *
+ * @param start
+ * @param end
+ * @return
+ */
+ public int[] locateInFrom(int start, int end)
+ {
+ return mapPositions(start, end, toShifts, fromShifts, toRatio,
+ fromRatio);
+ }
+
+ /**
+ * Returns the [start1, end1, start2, end2, ...] positions in the 'to' range
+ * that map to positions between {@code start} and {@code end} in the 'from'
+ * range. Note that for a reverse strand mapping this will return ranges with
+ * end < start. Returns null if no mapped positions are found in start-end.
+ *
+ * @param start
+ * @param end
+ * @return
+ */
+ public int[] locateInTo(int start, int end)
+ {
+ return mapPositions(start, end, fromShifts, toShifts, fromRatio,
+ toRatio);
+ }
+
+ /**
+ * Helper method that returns the [start1, end1, start2, end2, ...] positions
+ * in {@code targetRange} that map to positions between {@code start} and
+ * {@code end} in {@code sourceRange}. Note that for a reverse strand mapping
+ * this will return ranges with end < start. Returns null if no mapped
+ * positions are found in start-end.
+ *
+ * @param start
+ * @param end
+ * @param sourceRange
+ * @param targetRange
+ * @param sourceWordLength
+ * @param targetWordLength
+ * @return
+ */
+ final static int[] mapPositions(int start, int end,
+ List<int[]> sourceRange, List<int[]> targetRange,
+ int sourceWordLength, int targetWordLength)
+ {
+ if (end < start)
+ {
+ int tmp = end;
+ end = start;
+ start = tmp;
+ }
+
+ /*
+ * traverse sourceRange and mark offsets in targetRange
+ * of any positions that lie in [start, end]
+ */
+ BitSet offsets = getMappedOffsetsForPositions(start, end, sourceRange,
+ sourceWordLength, targetWordLength);
+
+ /*
+ * traverse targetRange and collect positions at the marked offsets
+ */
+ List<int[]> mapped = getPositionsForOffsets(targetRange, offsets);
+
+ // TODO: or just return the List and adjust calling code to match
+ return mapped.isEmpty() ? null : MappingUtils.rangeListToArray(mapped);
+ }
+
+ /**
+ * Scans the list of {@code ranges} for any values (positions) that lie
+ * between start and end (inclusive), and records the <em>offsets</em> from
+ * the start of the list as a BitSet. The offset positions are converted to
+ * corresponding words in blocks of {@code wordLength2}.
+ *
+ * <pre>
+ * For example:
+ * 1:1 (e.g. gene to CDS):
+ * ranges { [10-20], [31-40] }, wordLengthFrom = wordLength 2 = 1
+ * for start = 1, end = 9, returns a BitSet with no bits set
+ * for start = 1, end = 11, returns a BitSet with bits 0-1 set
+ * for start = 15, end = 35, returns a BitSet with bits 5-15 set
+ * 1:3 (peptide to codon):
+ * ranges { [1-200] }, wordLengthFrom = 1, wordLength 2 = 3
+ * for start = 9, end = 9, returns a BitSet with bits 24-26 set
+ * 3:1 (codon to peptide):
+ * ranges { [101-150], [171-180] }, wordLengthFrom = 3, wordLength 2 = 1
+ * for start = 101, end = 102 (partial first codon), returns a BitSet with bit 0 set
+ * for start = 150, end = 171 (partial 17th codon), returns a BitSet with bit 16 set
+ * 3:1 (circular DNA to peptide):
+ * ranges { [101-150], [21-30] }, wordLengthFrom = 3, wordLength 2 = 1
+ * for start = 24, end = 40 (spans codons 18-20), returns a BitSet with bits 17-19 set
+ * </pre>
+ *
+ * @param start
+ * @param end
+ * @param sourceRange
+ * @param sourceWordLength
+ * @param targetWordLength
+ * @return
+ */
+ protected final static BitSet getMappedOffsetsForPositions(int start,
+ int end, List<int[]> sourceRange, int sourceWordLength,
+ int targetWordLength)
+ {
+ BitSet overlaps = new BitSet();
+ int offset = 0;
+ final int s1 = sourceRange.size();
+ for (int i = 0; i < s1; i++)
+ {
+ int[] range = sourceRange.get(i);
+ final int offset1 = offset;
+ int overlapStartOffset = -1;
+ int overlapEndOffset = -1;
+
+ if (range[1] >= range[0])
+ {
+ /*
+ * forward direction range
+ */
+ if (start <= range[1] && end >= range[0])
+ {
+ /*
+ * overlap
+ */
+ int overlapStart = Math.max(start, range[0]);
+ overlapStartOffset = offset1 + overlapStart - range[0];
+ int overlapEnd = Math.min(end, range[1]);
+ overlapEndOffset = offset1 + overlapEnd - range[0];
+ }
+ }
+ else
+ {
+ /*
+ * reverse direction range
+ */
+ if (start <= range[0] && end >= range[1])
+ {
+ /*
+ * overlap
+ */
+ int overlapStart = Math.max(start, range[1]);
+ int overlapEnd = Math.min(end, range[0]);
+ overlapStartOffset = offset1 + range[0] - overlapEnd;
+ overlapEndOffset = offset1 + range[0] - overlapStart;
+ }
+ }
+
+ if (overlapStartOffset > -1)
+ {
+ /*
+ * found an overlap
+ */
+ if (sourceWordLength != targetWordLength)
+ {
+ /*
+ * convert any overlap found to whole words in the target range
+ * (e.g. treat any partial codon overlap as if the whole codon)
+ */
+ overlapStartOffset -= overlapStartOffset % sourceWordLength;
+ overlapStartOffset = overlapStartOffset / sourceWordLength
+ * targetWordLength;
+
+ /*
+ * similar calculation for range end, adding
+ * (wordLength2 - 1) for end of mapped word
+ */
+ overlapEndOffset -= overlapEndOffset % sourceWordLength;
+ overlapEndOffset = overlapEndOffset / sourceWordLength
+ * targetWordLength;
+ overlapEndOffset += targetWordLength - 1;
+ }
+ overlaps.set(overlapStartOffset, overlapEndOffset + 1);
+ }
+ offset += 1 + Math.abs(range[1] - range[0]);
+ }
+ return overlaps;
+ }
+
+ /**
+ * Returns a (possibly empty) list of the [start-end] values (positions) at
+ * offsets in the {@code targetRange} list that are marked by 'on' bits in the
+ * {@code offsets} bitset.
+ *
+ * @param targetRange
+ * @param offsets
+ * @return
+ */
+ protected final static List<int[]> getPositionsForOffsets(
+ List<int[]> targetRange, BitSet offsets)
+ {
+ List<int[]> mapped = new ArrayList<>();
+ if (offsets.isEmpty())
+ {
+ return mapped;
+ }
+
+ /*
+ * count of positions preceding ranges[i]
+ */
+ int traversed = 0;
+
+ /*
+ * for each [from-to] range in ranges:
+ * - find subranges (if any) at marked offsets
+ * - add the start-end values at the marked positions
+ */
+ final int toAdd = offsets.cardinality();
+ int added = 0;
+ final int s2 = targetRange.size();
+ for (int i = 0; added < toAdd && i < s2; i++)
+ {
+ int[] range = targetRange.get(i);
+ added += addOffsetPositions(mapped, traversed, range, offsets);
+ traversed += Math.abs(range[1] - range[0]) + 1;
+ }
+ return mapped;
+ }
+
+ /**
+ * Helper method that adds any start-end subranges of {@code range} that are
+ * at offsets in {@code range} marked by set bits in overlaps.
+ * {@code mapOffset} is added to {@code range} offset positions. Returns the
+ * count of positions added.
+ *
+ * @param mapped
+ * @param mapOffset
+ * @param range
+ * @param overlaps
+ * @return
+ */
+ final static int addOffsetPositions(List<int[]> mapped,
+ final int mapOffset, final int[] range, final BitSet overlaps)
+ {
+ final int rangeLength = 1 + Math.abs(range[1] - range[0]);
+ final int step = range[1] < range[0] ? -1 : 1;
+ int offsetStart = 0; // offset into range
+ int added = 0;
+
+ while (offsetStart < rangeLength)
+ {
+ /*
+ * find the start of the next marked overlap offset;
+ * if there is none, or it is beyond range, then finished
+ */
+ int overlapStart = overlaps.nextSetBit(mapOffset + offsetStart);
+ if (overlapStart == -1 || overlapStart - mapOffset >= rangeLength)
+ {
+ /*
+ * no more overlaps, or no more within range[]
+ */
+ return added;
+ }
+ overlapStart -= mapOffset;
+
+ /*
+ * end of the overlap range is just before the next clear bit;
+ * restrict it to end of range if necessary;
+ * note we may add a reverse strand range here (end < start)
+ */
+ int overlapEnd = overlaps.nextClearBit(mapOffset + overlapStart + 1);
+ overlapEnd = (overlapEnd == -1) ? rangeLength - 1
+ : Math.min(rangeLength - 1, overlapEnd - mapOffset - 1);
+ int startPosition = range[0] + step * overlapStart;
+ int endPosition = range[0] + step * overlapEnd;
+ mapped.add(new int[] { startPosition, endPosition });
+ offsetStart = overlapEnd + 1;
+ added += Math.abs(endPosition - startPosition) + 1;
+ }
+
+ return added;
+ }
+
+ /*
+ * Returns the [start, end...] positions in the range mapped from, that are
+ * mapped to by part or all of the given begin-end of the range mapped to.
+ * Returns null if begin-end does not overlap any position mapped to.
+ *
+ * @param begin
+ * @param end
+ * @return
+ */
+ public int[] getOverlapsInFrom(final int begin, final int end)
+ {
+ int[] overlaps = MappingUtils.findOverlap(toShifts, begin, end);
+
+ return overlaps == null ? null : locateInFrom(overlaps[0], overlaps[1]);
+ }
+
+ /**
+ * Returns the [start, end...] positions in the range mapped to, that are
+ * mapped to by part or all of the given begin-end of the range mapped from.
+ * Returns null if begin-end does not overlap any position mapped from.
+ *
+ * @param begin
+ * @param end
+ * @return
+ */
+ public int[] getOverlapsInTo(final int begin, final int end)
+ {
+ int[] overlaps = MappingUtils.findOverlap(fromShifts, begin, end);
+
+ return overlaps == null ? null : locateInTo(overlaps[0], overlaps[1]);
+ }
}
*/
package jalview.util;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
import jalview.analysis.AlignmentSorter;
import jalview.api.AlignViewportI;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Mapping;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
/**
* Helper methods for manipulations involving sequence mappings.
*
action = action.getUndoAction();
}
// TODO write this
- System.err.println("MappingUtils.mapCutOrPaste not yet implemented");
+ Console.error("MappingUtils.mapCutOrPaste not yet implemented");
}
/**
*/
int startResiduePos = selected.findPosition(firstUngappedPos);
int endResiduePos = selected.findPosition(lastUngappedPos);
-
- for (AlignedCodonFrame acf : codonFrames)
+ for (SequenceI seq : mapTo.getAlignment().getSequences())
{
- SequenceI mappedSequence = targetIsNucleotide
- ? acf.getDnaForAaSeq(selected)
- : acf.getAaForDnaSeq(selected);
- if (mappedSequence != null)
+ int mappedStartResidue = 0;
+ int mappedEndResidue = 0;
+ for (AlignedCodonFrame acf : codonFrames)
{
- for (SequenceI seq : mapTo.getAlignment().getSequences())
+ // rather than use acf.getCoveringMapping() we iterate through all
+ // mappings to make sure all CDS are selected for a protein
+ for (SequenceToSequenceMapping map: acf.getMappings())
{
- int mappedStartResidue = 0;
- int mappedEndResidue = 0;
- if (seq.getDatasetSequence() == mappedSequence)
+ if (map.covers(selected) && map.covers(seq))
+ {
+ /*
+ * Found a sequence mapping. Locate the start/end mapped residues.
+ */
+ List<AlignedCodonFrame> mapping = Arrays
+ .asList(new AlignedCodonFrame[]
+ { acf });
+ // locate start
+ SearchResultsI sr = buildSearchResults(selected,
+ startResiduePos, mapping);
+ for (SearchResultMatchI m : sr.getResults())
{
- /*
- * Found a sequence mapping. Locate the start/end mapped residues.
- */
- List<AlignedCodonFrame> mapping = Arrays
- .asList(new AlignedCodonFrame[]
- { acf });
- SearchResultsI sr = buildSearchResults(selected,
- startResiduePos, mapping);
- for (SearchResultMatchI m : sr.getResults())
- {
- mappedStartResidue = m.getStart();
- mappedEndResidue = m.getEnd();
- }
- sr = buildSearchResults(selected, endResiduePos, mapping);
- for (SearchResultMatchI m : sr.getResults())
- {
- mappedStartResidue = Math.min(mappedStartResidue,
- m.getStart());
- mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
- }
-
- /*
- * Find the mapped aligned columns, save the range. Note findIndex
- * returns a base 1 position, SequenceGroup uses base 0
- */
- int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
- minStartCol = minStartCol == -1 ? mappedStartCol
- : Math.min(minStartCol, mappedStartCol);
- int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
- maxEndCol = maxEndCol == -1 ? mappedEndCol
- : Math.max(maxEndCol, mappedEndCol);
- mappedGroup.addSequence(seq, false);
- break;
+ mappedStartResidue = m.getStart();
+ mappedEndResidue = m.getEnd();
}
+ // locate end - allowing for adjustment of start range
+ sr = buildSearchResults(selected, endResiduePos, mapping);
+ for (SearchResultMatchI m : sr.getResults())
+ {
+ mappedStartResidue = Math.min(mappedStartResidue,
+ m.getStart());
+ mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
+ }
+
+ /*
+ * Find the mapped aligned columns, save the range. Note findIndex
+ * returns a base 1 position, SequenceGroup uses base 0
+ */
+ int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
+ minStartCol = minStartCol == -1 ? mappedStartCol
+ : Math.min(minStartCol, mappedStartCol);
+ int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
+ maxEndCol = maxEndCol == -1 ? mappedEndCol
+ : Math.max(maxEndCol, mappedEndCol);
+ mappedGroup.addSequence(seq, false);
+ break;
}
- }
+ }}
}
}
mappedGroup.setStartRes(minStartCol < 0 ? 0 : minStartCol);
{
for (AlignedCodonFrame acf : mappings)
{
- SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq)
- : acf.getAaForDnaSeq(seq);
- if (mappedSeq != null)
- {
for (SequenceI seq2 : mapTo.getSequences())
{
- if (seq2.getDatasetSequence() == mappedSeq)
+ /*
+ * the corresponding peptide / CDS is the one for which there is
+ * a complete ('covering') mapping to 'seq'
+ */
+ SequenceI peptide = mappingToNucleotide ? seq2 : seq;
+ SequenceI cds = mappingToNucleotide ? seq : seq2;
+ SequenceToSequenceMapping s2s = acf.getCoveringMapping(cds,
+ peptide);
+ if (s2s != null)
{
mappedOrder.add(seq2);
j++;
break;
}
}
- }
}
}
if (colsel == null)
{
- return; // mappedColumns;
+ return;
}
char fromGapChar = mapFrom.getAlignment().getGapCharacter();
while (regions.hasNext())
{
mapHiddenColumns(regions.next(), codonFrames, newHidden,
- fromSequences,
- toSequences, fromGapChar);
+ fromSequences, toSequences, fromGapChar);
}
- return; // mappedColumns;
+ return;
}
/**
*/
for (SequenceI toSeq : toSequences)
{
- if (toSeq.getDatasetSequence() == mappedSeq)
+ if (toSeq.getDatasetSequence() == mappedSeq
+ && mappedStartResidue >= toSeq.getStart()
+ && mappedEndResidue <= toSeq.getEnd())
{
int mappedStartCol = toSeq.findIndex(mappedStartResidue);
int mappedEndCol = toSeq.findIndex(mappedEndResidue);
{
if (range.length % 2 != 0)
{
- System.err.println(
+ Console.error(
"Error unbalance start/end ranges: " + ranges.toString());
return 0;
}
int min = Math.min(range[0], range[1]);
int max = Math.max(range[0], range[1]);
-
+
return (min <= queryRange[0] && max >= queryRange[0]
&& min <= queryRange[1] && max >= queryRange[1]);
}
* a list of (single) [start, end] ranges
* @return
*/
- public static void removeEndPositions(int positions,
- List<int[]> ranges)
+ public static void removeEndPositions(int positions, List<int[]> ranges)
{
int toRemove = positions;
Iterator<int[]> it = new ReverseListIterator<>(ranges);
/*
* not coded for [start1, end1, start2, end2, ...]
*/
- System.err
- .println("MappingUtils.removeEndPositions doesn't handle multiple ranges");
+ Console.error(
+ "MappingUtils.removeEndPositions doesn't handle multiple ranges");
return;
}
/*
* not coded for a reverse strand range (end < start)
*/
- System.err
- .println("MappingUtils.removeEndPositions doesn't handle reverse strand");
+ Console.error(
+ "MappingUtils.removeEndPositions doesn't handle reverse strand");
return;
}
if (length > toRemove)
}
}
}
+
+ /**
+ * Converts a list of {@code start-end} ranges to a single array of
+ * {@code start1, end1, start2, ... } ranges
+ *
+ * @param ranges
+ * @return
+ */
+ public static int[] rangeListToArray(List<int[]> ranges)
+ {
+ int rangeCount = ranges.size();
+ int[] result = new int[rangeCount * 2];
+ int j = 0;
+ for (int i = 0; i < rangeCount; i++)
+ {
+ int[] range = ranges.get(i);
+ result[j++] = range[0];
+ result[j++] = range[1];
+ }
+ return result;
+ }
+
+ /*
+ * Returns the maximal start-end positions in the given (ordered) list of
+ * ranges which is overlapped by the given begin-end range, or null if there
+ * is no overlap.
+ *
+ * <pre>
+ * Examples:
+ * if ranges is {[4, 8], [10, 12], [16, 19]}
+ * then
+ * findOverlap(ranges, 1, 20) == [4, 19]
+ * findOverlap(ranges, 6, 11) == [6, 11]
+ * findOverlap(ranges, 9, 15) == [10, 12]
+ * findOverlap(ranges, 13, 15) == null
+ * </pre>
+ *
+ * @param ranges
+ * @param begin
+ * @param end
+ * @return
+ */
+ protected static int[] findOverlap(List<int[]> ranges, final int begin,
+ final int end)
+ {
+ boolean foundStart = false;
+ int from = 0;
+ int to = 0;
+
+ /*
+ * traverse the ranges to find the first position (if any) >= begin,
+ * and the last position (if any) <= end
+ */
+ for (int[] range : ranges)
+ {
+ if (!foundStart)
+ {
+ if (range[0] >= begin)
+ {
+ /*
+ * first range that starts with, or follows, begin
+ */
+ foundStart = true;
+ from = Math.max(range[0], begin);
+ }
+ else if (range[1] >= begin)
+ {
+ /*
+ * first range that contains begin
+ */
+ foundStart = true;
+ from = begin;
+ }
+ }
+
+ if (range[0] <= end)
+ {
+ to = Math.min(end, range[1]);
+ }
+ }
+
+ return foundStart && to >= from ? new int[] { from, to } : null;
+ }
}
import java.util.ResourceBundle.Control;
import java.util.Set;
-import org.apache.log4j.Logger;
+import jalview.log.JLoggerLog4j;
/**
*
{
private static ResourceBundle rb;
- // BH 2018 switched to org.apache.llog4j.Logger
- private static Logger log = Logger
+ private static JLoggerLog4j log = JLoggerLog4j
.getLogger(MessageManager.class.getCanonicalName());
private static Locale loc;
} catch (Exception e)
{
String msg = "I18N missing: " + loc + "\t" + key;
- logWarning(key, msg);
+ logWarning(key, msg);
}
return value;
}
*/
public static String getStringOrReturn(String keyroot, String name)
{
- String smkey = keyroot + name.toLowerCase().replaceAll(" ", "");
+ String smkey = keyroot
+ + name.toLowerCase(Locale.ROOT).replaceAll(" ", "");
try
{
name = rb.getString(smkey);
} catch (Exception x)
{
- String msg = "I18N missing key with root " + keyroot + ": " + loc + "\t"
- + smkey;
- logWarning(smkey, msg);
+ String msg = "I18N missing key with root " + keyroot + ": " + loc
+ + "\t" + smkey;
+ logWarning(smkey, msg);
}
return name;
}
* @param key
* @param msg
*/
- private static void logWarning(String key, String msg)
+ private static void logWarning(String key, String msg)
{
- if (!reportedMissing.contains(key))
- {
+ if (!reportedMissing.contains(key))
+ {
reportedMissing.add(key);
- log.info(msg);
- }
+ log.info(msg);
+ }
}
}
*/
package jalview.util;
+import java.util.Locale;
+
import java.util.ArrayList;
import java.util.List;
import java.util.StringTokenizer;
return;
}
StringBuilder sb = new StringBuilder(description.length());
- if (description.toUpperCase().indexOf("<HTML>") == -1)
+ if (description.toUpperCase(Locale.ROOT).indexOf("<HTML>") == -1)
{
htmlContent = false;
}
token = token.substring(0, startTag);
}
- if (tag != null && tag.toUpperCase().startsWith("A HREF="))
+ if (tag != null && tag.toUpperCase(Locale.ROOT).startsWith("A HREF="))
{
if (token.length() > 0)
{
public static byte[] getFileBytes(File f)
{
- return /** @j2sNative f && swingjs.JSUtil.getFileBytes$java_io_File(f) || */
+ return /** @j2sNative f && swingjs.JSUtil.getFileAsBytes$O(f) || */
null;
}
public static void getURLCommandArguments()
{
-
- /**
- * Retrieve the first query field as command arguments to Jalview. Include
- * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
- * element to this value.
- *
- * @j2sNative var a =
- * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
- * + "?").split("?")[1].split("#")[0]); a &&
- * (J2S.thisApplet.__Info.args = a.split(" "));
- */
-
+ try {
+ /**
+ * Retrieve the first query field as command arguments to Jalview. Include
+ * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's
+ * __Info.args element to this value.
+ *
+ * @j2sNative var a =
+ * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
+ * + "?").split("?")[1].split("#")[0]); a && (System.out.println("URL arguments detected were "+a)) &&
+ * (J2S.thisApplet.__Info.urlargs = a.split(" "));
+ * (!J2S.thisApplet.__Info.args || J2S.thisApplet.__Info.args == "" || J2S.thisApplet.__Info.args == "??") && (J2S.thisApplet.__Info.args = a) && (System.out.println("URL arguments were passed to J2S main."));
+ */
+ } catch (Throwable t)
+ {
+ }
}
/**
*/
package jalview.util;
+import java.util.Locale;
+
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
}
if (s.length() <= 1)
{
- return s.toUpperCase();
+ return s.toUpperCase(Locale.ROOT);
}
- return s.substring(0, 1).toUpperCase() + s.substring(1).toLowerCase();
+ return s.substring(0, 1).toUpperCase(Locale.ROOT) + s.substring(1).toLowerCase(Locale.ROOT);
}
/**
{
return null;
}
- String tmp2up = text.toUpperCase();
+ String tmp2up = text.toUpperCase(Locale.ROOT);
int startTag = tmp2up.indexOf("<HTML>");
if (startTag > -1)
{
{
text = text.substring(0, endTag);
}
-
+
if (startTag == -1 && (text.contains("<") || text.contains(">")))
{
text = text.replaceAll("<", "<");
}
/**
- * Answers the input string with any occurrences of the 'encodeable' characters
- * replaced by their URL encoding
+ * Answers the input string with any occurrences of the 'encodeable'
+ * characters replaced by their URL encoding
*
* @param s
* @param encodable
}
return enc;
}
+
+ public static int firstCharPosIgnoreCase(String text, String chars)
+ {
+ int min = text.length() + 1;
+ for (char c : chars.toLowerCase().toCharArray())
+ {
+ int i = text.toLowerCase().indexOf(c);
+ if (0 <= i && i < min)
+ {
+ min = i;
+ }
+ }
+ return min < text.length() + 1 ? min : -1;
+ }
}
*/
package jalview.util.matcher;
+import java.util.Locale;
+
import java.util.Objects;
/**
patternType = PatternType.String;
}
- uppercasePattern = pattern == null ? null : pattern.toUpperCase();
+ uppercasePattern = pattern == null ? null : pattern.toUpperCase(Locale.ROOT);
// if we add regex conditions (e.g. matchesPattern), then
// pattern should hold the raw regex, and
boolean matchesString(String compareTo)
{
boolean matched = false;
- String upper = compareTo.toUpperCase().trim();
+ String upper = compareTo.toUpperCase(Locale.ROOT).trim();
switch(condition) {
case Matches:
matched = upper.equals(uppercasePattern);
import jalview.api.FeatureColourI;
import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.MappedFeatures;
-import jalview.datamodel.Mapping;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
Map<String, Float> featureOrder = null;
- protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
- this);
-
protected AlignViewportI av;
+ private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+ this);
+
@Override
public AlignViewportI getViewport()
{
{
firing = Boolean.TRUE;
findAllFeatures(true); // add all new features as visible
- changeSupport.firePropertyChange("changeSupport", null, null);
+ notifyFeaturesChanged();
firing = Boolean.FALSE;
}
}
}
@Override
+ public void notifyFeaturesChanged()
+ {
+ changeSupport.firePropertyChange("changeSupport", null, null);
+ }
+
+ @Override
public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column)
{
/*
* todo: direct lookup of CDS for peptide and vice-versa; for now,
* have to search through an unordered list of mappings for a candidate
*/
- Mapping mapping = null;
+ SequenceToSequenceMapping mapping = null;
SequenceI mapFrom = null;
for (AlignedCodonFrame acf : mappings)
{
- mapping = acf.getMappingForSequence(sequence);
- if (mapping == null || !mapping.getMap().isTripletMap())
+ mapping = acf.getCoveringCodonMapping(ds);
+ if (mapping == null)
{
- continue; // we are only looking for 3:1 or 1:3 mappings
+ continue;
}
SearchResultsI sr = new SearchResults();
- acf.markMappedRegion(ds, pos, sr);
+ mapping.markMappedRegion(ds, pos, sr);
for (SearchResultMatchI match : sr.getResults())
{
int fromRes = match.getStart();
}
}
- return new MappedFeatures(mapping, mapFrom, pos, residue, result);
+ return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue, result);
}
@Override
public class FeaturesDisplayed implements FeaturesDisplayedI
{
- private Set<String> featuresDisplayed = new HashSet<String>();
+ private Set<String> featuresDisplayed = new HashSet<>();
- private Set<String> featuresRegistered = new HashSet<String>();
+ private Set<String> featuresRegistered = new HashSet<>();
public FeaturesDisplayed(FeaturesDisplayedI featuresDisplayed2)
{
}
@Override
+ public void setHidden(String featureType)
+ {
+ featuresDisplayed.remove(featureType);
+ featuresRegistered.add(featureType);
+ }
+
+ @Override
public boolean isRegistered(String type)
{
return featuresRegistered.contains(type);
*/
package jalview.ws;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
throw (new Exception(
"Timed out when communicating with server\nTry again later.\n"));
}
- jalview.bin.Cache.log.debug("Job " + j + " Result state "
+ Console.debug("Job " + j + " Result state "
+ jobs[j].getState() + "(ServerError="
+ jobs[j].isServerError() + ")");
} catch (Exception ex)
.formatMessage("info.server_exception", new Object[]
{ WebServiceName, ex.getMessage() }));
// always output the exception's stack trace to the log
- Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+ Console.warn(WebServiceName + " job(" + jobs[j].jobnum
+ ") Server exception.");
// todo: could limit trace to cause if this is a SOAPFaultException.
ex.printStackTrace();
if (jobs[j].allowedServerExceptions > 0)
{
jobs[j].allowedServerExceptions--;
- Cache.log.debug("Sleeping after a server exception.");
+ Console.debug("Sleeping after a server exception.");
try
{
Thread.sleep(5000);
}
else
{
- Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
+ Console.warn("Dropping job " + j + " " + jobs[j].jobId);
jobs[j].subjobComplete = true;
wsInfo.setStatus(jobs[j].jobnum,
WebserviceInfo.STATE_STOPPED_SERVERERROR);
jobs[j].clearResponse(); // may contain out of date result data
wsInfo.setStatus(jobs[j].jobnum,
WebserviceInfo.STATE_STOPPED_ERROR);
- Cache.log.error("Out of memory when retrieving Job " + j
+ Console.error("Out of memory when retrieving Job " + j
+ " id:" + WsUrl + "/" + jobs[j].jobId, er);
new jalview.gui.OOMWarning(
"retrieving result for " + WebServiceName, er);
Thread.sleep(5000);
} catch (InterruptedException e)
{
- Cache.log.debug("Interrupted sleep waiting for next job poll.",
+ Console.debug("Interrupted sleep waiting for next job poll.",
e);
}
// System.out.println("I'm alive "+alTitle);
}
else
{
- Cache.log.debug(
+ Console.debug(
"WebServiceJob poll loop finished with no jobs created.");
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.appendProgressText(
*/
package jalview.ws;
+import java.util.Locale;
+
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Enumeration;
import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import jalview.analysis.AlignSeq;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
*/
void addSeqId(SequenceI seq, String key)
{
- key = key.toUpperCase();
+ key = key.toUpperCase(Locale.ROOT);
Vector<SequenceI> seqs;
if (seqRefs.containsKey(key))
AlignmentI retrieved = null;
try
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug("Querying " + dbsource.getDbName()
+ Console.debug("Querying " + dbsource.getDbName()
+ " with : '" + queryString.toString() + "'");
}
retrieved = dbsource.getSequenceRecords(queryString.toString());
DBRefEntry upref = uprefs.get(j);
addSeqId(sequence, upref.getAccessionId());
queries.addElement(
- upref.getAccessionId().toUpperCase());
+ upref.getAccessionId().toUpperCase(Locale.ROOT));
}
}
else
{
+ Pattern possibleIds = Pattern.compile("[A-Za-z0-9_]+");
// generate queries from sequence ID string
- StringTokenizer st = new StringTokenizer(sequence.getName(),
- "|");
- while (st.hasMoreTokens())
+ Matcher tokens = possibleIds.matcher(sequence.getName());
+ int p=0;
+ while (tokens.find(p))
{
- String token = st.nextToken();
+ String token = tokens.group();
+ p = tokens.end();
UPEntry[] presp = null;
if (picrClient != null)
{
"Validated ID against PICR... (for what its worth):"
+ token);
addSeqId(sequence, token);
- queries.addElement(token.toUpperCase());
+ queries.addElement(token.toUpperCase(Locale.ROOT));
}
else
{
// System.out.println("Not querying source with
// token="+token+"\n");
addSeqId(sequence, token);
- queries.addElement(token.toUpperCase());
+ queries.addElement(token.toUpperCase(Locale.ROOT));
}
}
}
DBRefEntry ref = entryRefs.get(j);
String accessionId = ref.getAccessionId();
// match up on accessionId
- if (seqRefs.containsKey(accessionId.toUpperCase()))
+ if (seqRefs.containsKey(accessionId.toUpperCase(Locale.ROOT)))
{
Vector<SequenceI> seqs = seqRefs.get(accessionId);
for (int jj = 0; jj < seqs.size(); jj++)
// sequenceMatches now contains the set of all sequences associated with
// the returned db record
final String retrievedSeqString = retrievedSeq.getSequenceAsString();
- String entrySeq = retrievedSeqString.toUpperCase();
+ String entrySeq = retrievedSeqString.toUpperCase(Locale.ROOT);
for (int m = 0; m < sequenceMatches.size(); m++)
{
sequence = sequenceMatches.elementAt(m);
boolean remoteEnclosesLocal = false;
String nonGapped = AlignSeq
.extractGaps("-. ", sequence.getSequenceAsString())
- .toUpperCase();
+ .toUpperCase(Locale.ROOT);
int absStart = entrySeq.indexOf(nonGapped);
if (absStart == -1)
{
String ngAlsq = AlignSeq
.extractGaps("-. ",
alseqs[alsq].getSequenceAsString())
- .toUpperCase();
+ .toUpperCase(Locale.ROOT);
int oldstrt = alseqs[alsq].getStart();
alseqs[alsq].setStart(sequence.getSequenceAsString()
- .toUpperCase().indexOf(ngAlsq) + sequence.getStart());
+ .toUpperCase(Locale.ROOT).indexOf(ngAlsq) + sequence.getStart());
if (oldstrt != alseqs[alsq].getStart())
{
alseqs[alsq].setEnd(
import jalview.ws.dbsources.PfamFull;
import jalview.ws.dbsources.PfamSeed;
import jalview.ws.dbsources.RfamSeed;
+import jalview.ws.dbsources.TDBeacons;
import jalview.ws.dbsources.Uniprot;
import jalview.ws.seqfetcher.ASequenceFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
addDBRefSourceImpl(EmblSource.class);
addDBRefSourceImpl(EmblCdsSource.class);
addDBRefSourceImpl(Uniprot.class);
+ // not a sequence source yet
+ // addDBRefSourceImpl(TDBeacons.class);
addDBRefSourceImpl(Pdb.class);
addDBRefSourceImpl(PfamFull.class);
addDBRefSourceImpl(PfamSeed.class);
import jalview.api.FeatureSettingsModelI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ContactMatrix;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeaturesI;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
@Override
public Regex getAccessionValidator()
{
- return new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+ Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+ validator.setIgnoreCase(true);
+ return validator;
}
/*
@Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
+ return getSequenceRecords(queries, null);
+ }
+ public AlignmentI getSequenceRecords(String queries, String retrievalUrl) throws Exception
+ {
AlignmentI pdbAlignment = null;
String chain = null;
String id = null;
return null;
}
String alphaFoldCif = getAlphaFoldCifDownloadUrl(id);
+ if (retrievalUrl != null)
+ {
+ alphaFoldCif = retrievalUrl;
+ }
try
{
- File tmpFile = File.createTempFile(id, "cif");
+ File tmpFile = File.createTempFile(id, ".cif");
+ Console.debug("Retrieving structure file for "+id+" from "+alphaFoldCif);
UrlDownloadClient.download(alphaFoldCif, tmpFile);
+
+ // may not need this check ?
file = tmpFile.getAbsolutePath();
if (file == null)
{
return null;
}
- // todo get rid of Type and use FileFormatI instead?
- FileFormatI fileFormat = FileFormat.MMCif;
- pdbAlignment = new FormatAdapter().readFile(tmpFile,
- DataSourceType.FILE, fileFormat);
- if (pdbAlignment != null)
- {
- List<SequenceI> toremove = new ArrayList<SequenceI>();
- for (SequenceI pdbcs : pdbAlignment.getSequences())
- {
- String chid = null;
- // Mapping map=null;
- for (PDBEntry pid : pdbcs.getAllPDBEntries())
- {
- if (pid.getFile() == file)
- {
- chid = pid.getChainCode();
-
- }
- }
- if (chain == null || (chid != null && (chid.equals(chain)
- || chid.trim().equals(chain.trim())
- || (chain.trim().length() == 0 && chid.equals("_")))))
- {
- // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
- // TODO: suggest simplify naming to 1qip|A as default name defined
- pdbcs.setName(id + SEPARATOR + pdbcs.getName());
- // Might need to add more metadata to the PDBEntry object
- // like below
- /*
- * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
- * entry.setId(id); if (entry.getProperty() == null)
- * entry.setProperty(new Hashtable());
- * entry.getProperty().put("chains", pdbchain.id + "=" +
- * sq.getStart() + "-" + sq.getEnd());
- * sq.getDatasetSequence().addPDBId(entry);
- */
- // Add PDB DB Refs
- // We make a DBRefEtntry because we have obtained the PDB file from
- // a
- // verifiable source
- // JBPNote - PDB DBRefEntry should also carry the chain and mapping
- // information
- DBRefEntry dbentry = new DBRefEntry(getDbSource(),
- getDbVersion(), (chid == null ? id : id + chid));
- // dbentry.setMap()
- pdbcs.addDBRef(dbentry);
- }
- else
- {
- // mark this sequence to be removed from the alignment
- // - since it's not from the right chain
- toremove.add(pdbcs);
- }
- }
- // now remove marked sequences
- for (SequenceI pdbcs : toremove)
- {
- pdbAlignment.deleteSequence(pdbcs);
- if (pdbcs.getAnnotation() != null)
- {
- for (AlignmentAnnotation aa : pdbcs.getAnnotation())
- {
- pdbAlignment.deleteAnnotation(aa);
- }
- }
- }
- }
+ pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile, id, chain, getDbSource(),getDbVersion());
+
if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
{
// model
File pae = File.createTempFile(id, "pae_json");
String paeURL = getAlphaFoldPaeDownloadUrl(id);
- UrlDownloadClient.download(paeURL, pae);
+
+ if (retrievalUrl!=null) {
+ // manufacture the PAE url from a url like ...-model-vN.cif
+ paeURL = retrievalUrl.replace("model","predicted_aligned_error").replace(".cif",".json");
+ }
+ Console.debug("Downloading pae from " + paeURL
+ + " to " + pae.toString() + "");
+
+ try {
+ UrlDownloadClient.download(paeURL, pae);
if (!importPaeJSONAsContactMatrix(pdbAlignment, pae))
{
- Cache.log.debug("Couln't import contact matrix from " + paeURL
+ Console.warn("Couln't import contact matrix from " + paeURL
+ " (stored in " + pae.toString() + ")");
}
+ } catch (Exception pae_ex) {
+ Console.debug("Couldn't download PAE",pae_ex);
+ }
} catch (Exception ex) // Problem parsing PDB file
{
return true;
}
+ /**
+ * general purpose structure importer - designed to yield alignment useful for transfer of annotation to associated sequences
+ * @param alphaFoldCif
+ * @param tmpFile
+ * @param id
+ * @param chain
+ * @param dbSource
+ * @param dbVersion
+ * @return
+ * @throws Exception
+ */
+ public static AlignmentI importDownloadedStructureFromUrl(String alphaFoldCif,
+ File tmpFile, String id, String chain, String dbSource, String dbVersion) throws Exception
+ {
+ String file = tmpFile.getAbsolutePath();
+ // todo get rid of Type and use FileFormatI instead?
+ FileFormatI fileFormat = FileFormat.MMCif;
+ AlignmentI pdbAlignment = new FormatAdapter().readFile(tmpFile,
+ DataSourceType.FILE, fileFormat);
+ if (pdbAlignment != null)
+ {
+ List<SequenceI> toremove = new ArrayList<SequenceI>();
+ for (SequenceI pdbcs : pdbAlignment.getSequences())
+ {
+ String chid = null;
+ // Mapping map=null;
+ for (PDBEntry pid : pdbcs.getAllPDBEntries())
+ {
+ if (pid.getFile() == file)
+ {
+ chid = pid.getChainCode();
+
+ }
+ }
+ if (chain == null || (chid != null && (chid.equals(chain)
+ || chid.trim().equals(chain.trim())
+ || (chain.trim().length() == 0 && chid.equals("_")))))
+ {
+ // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
+ // TODO: suggest simplify naming to 1qip|A as default name defined
+ pdbcs.setName(id + SEPARATOR + pdbcs.getName());
+ // Might need to add more metadata to the PDBEntry object
+ // like below
+ /*
+ * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
+ * entry.setId(id); if (entry.getProperty() == null)
+ * entry.setProperty(new Hashtable());
+ * entry.getProperty().put("chains", pdbchain.id + "=" +
+ * sq.getStart() + "-" + sq.getEnd());
+ * sq.getDatasetSequence().addPDBId(entry);
+ */
+ // Add PDB DB Refs
+ // We make a DBRefEtntry because we have obtained the PDB file from
+ // a
+ // verifiable source
+ // JBPNote - PDB DBRefEntry should also carry the chain and mapping
+ // information
+ if (dbSource != null)
+ {
+ DBRefEntry dbentry = new DBRefEntry(dbSource,
+
+ dbVersion, (chid == null ? id : id + chid));
+ // dbentry.setMap()
+ pdbcs.addDBRef(dbentry);
+ // update any feature groups
+ List<SequenceFeature> allsf = pdbcs.getFeatures().getAllFeatures();
+ List<SequenceFeature> newsf = new ArrayList<SequenceFeature>();
+ if (allsf!=null && allsf.size()>0)
+ {
+ for (SequenceFeature f:allsf)
+ {
+ if (file.equals(f.getFeatureGroup()))
+ {
+ f = new SequenceFeature(f, f.type, f.begin, f.end, id, f.score);
+ }
+ newsf.add(f);
+ }
+ pdbcs.setSequenceFeatures(newsf);
+ }
+ }
+ }
+ else
+ {
+ // mark this sequence to be removed from the alignment
+ // - since it's not from the right chain
+ toremove.add(pdbcs);
+ }
+ }
+ // now remove marked sequences
+ for (SequenceI pdbcs : toremove)
+ {
+ pdbAlignment.deleteSequence(pdbcs);
+ if (pdbcs.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation aa : pdbcs.getAnnotation())
+ {
+ pdbAlignment.deleteAnnotation(aa);
+ }
+ }
+ }
+ }
+ return pdbAlignment;
+ }
+
/*
* (non-Javadoc)
*
{
return new PDBFeatureSettings();
}
+
}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
-import com.stevesoft.pat.Regex;
-
-public class EmblCdsSource extends EmblXmlSource
+public class EmblCdsSource extends EmblFlatfileSource // was EmblXmlSource
{
public EmblCdsSource()
}
@Override
- public String getAccessionSeparator()
- {
- return null;
- }
-
- @Override
- public Regex getAccessionValidator()
- {
- return new Regex("^[A-Z]+[0-9]+");
- }
-
- @Override
public String getDbSource()
{
return DBRefSource.EMBLCDS;
}
@Override
- public String getDbVersion()
- {
- return "0"; // TODO : this is dynamically set for a returned record - not
- // tied to proxy
- }
-
- @Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
if (queries.indexOf(".") > -1)
return getEmblSequenceRecords(DBRefSource.EMBLCDS, queries);
}
- @Override
- public boolean isValidReference(String accession)
- {
- // most embl CDS refs look like ..
- // TODO: improve EMBLCDS regex
- return (accession == null || accession.length() < 2) ? false
- : getAccessionValidator().search(accession);
- }
-
/**
* cDNA for LDHA_CHICK swissprot sequence
*/
return "EMBL (CDS)";
}
- @Override
- public int getTier()
- {
- return 0;
- }
-
}
--- /dev/null
+package jalview.ws.dbsources;
+
+import java.util.Locale;
+
+import java.io.File;
+import java.io.IOException;
+
+import com.stevesoft.pat.Regex;
+
+import jalview.bin.Console;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.EmblFlatFile;
+import jalview.io.FileParse;
+import jalview.ws.ebi.EBIFetchClient;
+
+/**
+ * A class that does partial parsing of an EMBL flatfile.
+ *
+ * @author gmcarstairs
+ *
+ */
+public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
+{
+ private static final Regex ACCESSION_REGEX = new Regex("^[A-Z]+[0-9]+");
+
+ @Override
+ public String getDbVersion()
+ {
+ return "0";
+ }
+
+ @Override
+ public String getAccessionSeparator()
+ {
+ return null;
+ }
+
+ @Override
+ public Regex getAccessionValidator()
+ {
+ return ACCESSION_REGEX;
+ }
+
+ @Override
+ public boolean isValidReference(String accession)
+ {
+ if (accession == null || accession.length() < 2)
+ {
+ return false;
+ }
+ return getAccessionValidator().search(accession);
+ }
+
+ @Override
+ public AlignmentI getSequenceRecords(String queries) throws Exception
+ {
+ return null;
+ }
+
+ @Override
+ public int getTier()
+ {
+ return 0;
+ }
+
+ protected AlignmentI getEmblSequenceRecords(String dbName, String query)
+ throws Exception
+ {
+ startQuery();
+ EBIFetchClient dbFetch = new EBIFetchClient();
+ File reply;
+ try
+ {
+ reply = dbFetch.fetchDataAsFile(
+ dbName.toLowerCase(Locale.ROOT) + ":" + query.trim(), null, "gz");
+ } catch (Exception e)
+ {
+ stopQuery();
+ throw new Exception(
+ String.format("EBI EMBL retrieval failed for %s:%s",
+ dbName.toLowerCase(Locale.ROOT), query.trim()),
+ e);
+ }
+ return getEmblSequenceRecords(dbName, query, reply);
+ }
+
+ private AlignmentI getEmblSequenceRecords(String dbName, String query,
+ File reply) throws IOException
+ {
+ AlignmentI al = null;
+
+ if (reply != null && reply.exists())
+ {
+ file = reply.getAbsolutePath();
+ FileParse fp = new FileParse(file, DataSourceType.FILE);
+ EmblFlatFile emblParser = new EmblFlatFile(fp, getDbSource());
+ SequenceI[] seqs = emblParser.getSeqsAsArray();
+ if (seqs.length > 0)
+ {
+ al = new Alignment(seqs);
+ }
+
+ if (al == null)
+ {
+ Console.error(
+ "No record found for '" + dbName + ":" + query + "'");
+ }
+ }
+
+ stopQuery();
+ return al;
+ }
+
+ @Override
+ public boolean isDnaCoding()
+ {
+ return true;
+ }
+}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
-import com.stevesoft.pat.Regex;
-
/**
* @author JimP
*
*/
-public class EmblSource extends EmblXmlSource
+public class EmblSource extends EmblFlatfileSource // was EmblXmlSource
{
public EmblSource()
/*
* (non-Javadoc)
*
- * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
- */
- @Override
- public String getAccessionSeparator()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#getAccessionValidator()
- */
- @Override
- public Regex getAccessionValidator()
- {
- return new Regex("^[A-Z]+[0-9]+");
- }
-
- /*
- * (non-Javadoc)
- *
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
@Override
/*
* (non-Javadoc)
*
- * @see jalview.ws.DbSourceProxy#getDbVersion()
- */
- @Override
- public String getDbVersion()
- {
- // TODO Auto-generated method stub
- return "0";
- }
-
- /*
- * (non-Javadoc)
- *
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
@Override
return getEmblSequenceRecords(DBRefSource.EMBL, queries);
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
- */
- @Override
- public boolean isValidReference(String accession)
- {
- // most embl refs look like ..
-
- return (accession == null || accession.length() < 2) ? false
- : getAccessionValidator().search(accession);
-
- }
-
/**
* return LHD_CHICK coding gene
*/
{
return "EMBL"; // getDbSource();
}
-
- @Override
- public int getTier()
- {
- return 0;
- }
}
*/
package jalview.ws.dbsources;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import com.stevesoft.pat.Regex;
+
import jalview.analysis.SequenceIdMatcher;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.util.DnaUtils;
import jalview.util.MapList;
import jalview.util.MappingUtils;
-import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
import jalview.xml.binding.embl.EntryType;
import jalview.xml.binding.embl.EntryType.Feature;
import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
-import jalview.xml.binding.jalview.JalviewModel;
import jalview.xml.binding.embl.ROOT;
import jalview.xml.binding.embl.XrefType;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.stream.FactoryConfigurationError;
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.XMLStreamReader;
-
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
{
+ private static final Regex ACCESSION_REGEX = new Regex("^[A-Z]+[0-9]+");
+
/*
* JAL-1856 Embl returns this text for query not found
*/
try
{
reply = dbFetch.fetchDataAsFile(
- emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
- "xml");
+ emprefx.toLowerCase(Locale.ROOT) + ":" + query.trim(),
+ "display=xml", "xml");
} catch (Exception e)
{
stopQuery();
- throw new Exception(MessageManager.formatMessage(
- "exception.ebiembl_retrieval_failed_on", new String[]
- { emprefx.toLowerCase(), query.trim() }), e);
+ throw new Exception(
+ String.format("EBI EMBL XML retrieval failed for %s:%s",
+ emprefx.toLowerCase(Locale.ROOT), query.trim()),
+ e);
}
return getEmblSequenceRecords(emprefx, query, reply);
}
XMLStreamReader streamReader = XMLInputFactory.newInstance()
.createXMLStreamReader(is);
javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
- JAXBElement<ROOT> rootElement = um.unmarshal(streamReader, ROOT.class);
+ JAXBElement<ROOT> rootElement = um.unmarshal(streamReader,
+ ROOT.class);
ROOT root = rootElement.getValue();
/*
else
{
// final product length truncation check
- int[] cdsRanges = adjustForProteinLength(translationLength,
- exons);
- dnaToProteinMapping = new Mapping(product, cdsRanges,
+ int[] exons2 = adjustForProteinLength(translationLength, exons);
+ dnaToProteinMapping = new Mapping(product, exons2,
new int[]
{ 1, translationLength }, 3, 1);
if (product != null)
proteinSeq = new Sequence(proteinSeqName,
product.getSequenceAsString());
matcher.add(proteinSeq);
+ proteinSeq.setDescription(product.getDescription());
peptides.add(proteinSeq);
}
dnaToProteinMapping.setTo(proteinSeq);
&& dnaToProteinMapping.getTo() != null)
{
DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
- DBRefSource.EMBLCDSProduct, sequenceVersion,
- proteinId);
+ DBRefSource.EMBLCDSProduct, sequenceVersion, proteinId);
dnaToEmblProteinRef.setMap(dnaToProteinMapping);
dnaToProteinMapping.setMappedFromId(proteinId);
dna.addDBRef(dnaToEmblProteinRef);
{
return new int[] {};
}
-
+
try
{
List<int[]> ranges = DnaUtils.parseLocation(location);
return listToArray(ranges);
} catch (ParseException e)
{
- Cache.log.warn(
+ Console.warn(
String.format("Not parsing inexact CDS location %s in ENA %s",
location, accession));
return new int[] {};
return sf;
}
+ @Override
+ public String getAccessionSeparator()
+ {
+ return null;
+ }
+
+ @Override
+ public Regex getAccessionValidator()
+ {
+ return ACCESSION_REGEX;
+ }
+
+ @Override
+ public String getDbVersion()
+ {
+ return "0";
+ }
+
+ @Override
+ public int getTier()
+ {
+ return 0;
+ }
+
+ @Override
+ public boolean isValidReference(String accession)
+ {
+ if (accession == null || accession.length() < 2)
+ {
+ return false;
+ }
+ return getAccessionValidator().search(accession);
+ }
+
/**
* Truncates (if necessary) the exon intervals to match 3 times the length of
- * the protein; also accepts 3 bases longer (for stop codon not included in
- * protein)
+ * the protein (including truncation for stop codon included in exon)
*
* @param proteinLength
* @param exon
}
int expectedCdsLength = proteinLength * 3;
int exonLength = MappingUtils.getLength(Arrays.asList(exon));
-
+
/*
- * if exon length matches protein, or is shorter, or longer by the
- * length of a stop codon (3 bases), then leave it unchanged
+ * if exon length matches protein, or is shorter, then leave it unchanged
*/
- if (expectedCdsLength >= exonLength
- || expectedCdsLength == exonLength - 3)
+ if (expectedCdsLength >= exonLength)
{
return exon;
}
-
+
int origxon[];
int sxpos = -1;
int endxon = 0;
// .println("Truncating final exon interval on region by "
// + (cdspos - cdslength));
}
-
+
/*
* shrink the final exon - reduce end position if forward
* strand, increase it if reverse
break;
}
}
-
+
if (sxpos != -1)
{
// and trim the exon interval set if necessary
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+import java.util.Locale;
+
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.StringUtils;
+import jalview.ws.seqfetcher.DbSourceProxyImpl;
+import jalview.xml.binding.embl.ROOT;
+import jalview.xml.binding.uniprot.DbReferenceType;
+import jalview.xml.binding.uniprot.Entry;
+import jalview.xml.binding.uniprot.FeatureType;
+import jalview.xml.binding.uniprot.LocationType;
+import jalview.xml.binding.uniprot.PositionType;
+import jalview.xml.binding.uniprot.PropertyType;
+
+import java.io.InputStream;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import com.stevesoft.pat.Regex;
+
+/**
+ * This class queries the Uniprot database for sequence data, unmarshals the
+ * returned XML, and converts it to Jalview Sequence records (including attached
+ * database references and sequence features)
+ *
+ * @author JimP
+ *
+ */
+public class TDBeacons extends DbSourceProxyImpl
+{
+ private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
+
+ private static final String BAR_DELIMITER = "|";
+
+ private static final String DEFAULT_THREEDBEACONS_DOMAIN = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/summary/";
+
+ /**
+ * Constructor
+ */
+ public TDBeacons()
+ {
+ super();
+ }
+
+ private String getDomain()
+ {
+ return Cache.getDefault("UNIPROT_DOMAIN", DEFAULT_UNIPROT_DOMAIN);
+ //return Cache.getDefault("3DB_DOMAIN", DEFAULT_THREEDBEACONS_DOMAIN );
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
+ */
+ @Override
+ public String getAccessionSeparator()
+ {
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionValidator()
+ */
+ @Override
+ public Regex getAccessionValidator()
+ {
+ return new Regex("([A-Z]+[0-9]+[A-Z0-9]+|[A-Z0-9]+_[A-Z0-9]+)");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbSource()
+ */
+ @Override
+ public String getDbSource()
+ {
+ return "3d-beacons";// DBRefSource.UNIPROT;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbVersion()
+ */
+ @Override
+ public String getDbVersion()
+ {
+ return "0"; // we really don't know what version we're on.
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
+ */
+ @Override
+ public AlignmentI getSequenceRecords(String queries) throws Exception
+ {
+ startQuery();
+ try
+ {
+ queries = queries.toUpperCase(Locale.ROOT).replaceAll(
+ "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
+ AlignmentI al = null;
+
+ String downloadstring = getDomain() + "/uniprot/" + queries
+ + ".xml";
+// String downloadstring = getDomain() + queries + ".json";
+
+ URL url = new URL(downloadstring);
+ URLConnection urlconn = url.openConnection();
+ InputStream istr = urlconn.getInputStream();
+ List<Entry> entries = getUniprotEntries(istr);
+ if (entries != null)
+ {
+ List<SequenceI> seqs = new ArrayList<>();
+ for (Entry entry : entries)
+ {
+ seqs.add(uniprotEntryToSequence(entry));
+ }
+ al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
+ }
+
+ stopQuery();
+ return al;
+ } catch (Exception e)
+ {
+ throw (e);
+ } finally
+ {
+ stopQuery();
+ }
+ }
+
+ /**
+ * Converts an Entry object (bound from Uniprot XML) to a Jalview Sequence
+ *
+ * @param entry
+ * @return
+ */
+ SequenceI uniprotEntryToSequence(Entry entry)
+ {
+ String id = getUniprotEntryId(entry);
+ /*
+ * Sequence should not include any whitespace, but JAXB leaves these in
+ */
+ String seqString = entry.getSequence().getValue().replaceAll("\\s*",
+ "");
+
+ SequenceI sequence = new Sequence(id,
+ seqString);
+ sequence.setDescription(getUniprotEntryDescription(entry));
+
+ /*
+ * add a 'self' DBRefEntry for each accession
+ */
+ final String dbVersion = getDbVersion();
+ List<DBRefEntry> dbRefs = new ArrayList<>();
+ for (String accessionId : entry.getAccession())
+ {
+ DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
+ accessionId);
+ dbRefs.add(dbRef);
+ }
+
+ /*
+ * add a DBRefEntry for each dbReference element in the XML;
+ * also add a PDBEntry if type="PDB";
+ * also add an EMBLCDS dbref if protein sequence id is given
+ * also add an Ensembl dbref " " " " " "
+ */
+ Vector<PDBEntry> pdbRefs = new Vector<>();
+ for (DbReferenceType dbref : entry.getDbReference())
+ {
+ String type = dbref.getType();
+ DBRefEntry dbr = new DBRefEntry(type,
+ DBRefSource.UNIPROT + ":" + dbVersion, dbref.getId());
+ dbRefs.add(dbr);
+ if ("PDB".equals(type))
+ {
+ pdbRefs.add(new PDBEntry(dbr));
+ }
+ if ("EMBL".equals(type))
+ {
+ /*
+ * e.g. Uniprot accession Q9BXM7 has
+ * <dbReference type="EMBL" id="M19359">
+ * <property type="protein sequence ID" value="AAA40981.1"/>
+ * <property type="molecule type" value="Genomic_DNA"/>
+ * </dbReference>
+ */
+ String cdsId = getProperty(dbref.getProperty(),
+ "protein sequence ID");
+ if (cdsId != null && cdsId.trim().length() > 0)
+ {
+ // remove version
+ String[] vrs = cdsId.split("\\.");
+ String version = vrs.length > 1 ? vrs[1]
+ : DBRefSource.UNIPROT + ":" + dbVersion;
+ dbr = new DBRefEntry(DBRefSource.EMBLCDS, version, vrs[0]);
+ dbRefs.add(dbr);
+ }
+ }
+ if ("Ensembl".equals(type))
+ {
+ /*
+ * e.g. Uniprot accession Q9BXM7 has
+ * <dbReference type="Ensembl" id="ENST00000321556">
+ * <molecule id="Q9BXM7-1"/>
+ * <property type="protein sequence ID" value="ENSP00000364204"/>
+ * <property type="gene ID" value="ENSG00000158828"/>
+ * </dbReference>
+ */
+ String cdsId = getProperty(dbref.getProperty(),
+ "protein sequence ID");
+ if (cdsId != null && cdsId.trim().length() > 0)
+ {
+ dbr = new DBRefEntry(DBRefSource.ENSEMBL,
+ DBRefSource.UNIPROT + ":" + dbVersion, cdsId.trim());
+ dbRefs.add(dbr);
+ }
+ }
+ }
+
+ /*
+ * create features; they have either begin and end, or position, in XML
+ */
+ sequence.setPDBId(pdbRefs);
+ if (entry.getFeature() != null)
+ {
+ for (FeatureType uf : entry.getFeature())
+ {
+ LocationType location = uf.getLocation();
+ int start = 0;
+ int end = 0;
+ if (location.getPosition() != null)
+ {
+ start = location.getPosition().getPosition().intValue();
+ end = start;
+ }
+ else
+ {
+ start = location.getBegin().getPosition().intValue();
+ end = location.getEnd().getPosition().intValue();
+ }
+ SequenceFeature sf = new SequenceFeature(uf.getType(),
+ getDescription(uf), start, end, "Uniprot");
+ sf.setStatus(uf.getStatus());
+ sequence.addSequenceFeature(sf);
+ }
+ }
+ for (DBRefEntry dbr : dbRefs)
+ {
+ sequence.addDBRef(dbr);
+ }
+ return sequence;
+ }
+
+ /**
+ * A helper method that builds a sequence feature description
+ *
+ * @param feature
+ * @return
+ */
+ static String getDescription(FeatureType feature)
+ {
+ String orig = feature.getOriginal();
+ List<String> variants = feature.getVariation();
+ StringBuilder sb = new StringBuilder();
+
+ /*
+ * append variant in standard format if present
+ * e.g. p.Arg59Lys
+ * multiple variants are split over lines using <br>
+ */
+ boolean asHtml = false;
+ if (orig != null && !orig.isEmpty() && variants != null
+ && !variants.isEmpty())
+ {
+ int p = 0;
+ for (String var : variants)
+ {
+ // TODO proper HGVS nomenclature for delins structural variations
+ // http://varnomen.hgvs.org/recommendations/protein/variant/delins/
+ // for now we are pragmatic - any orig/variant sequence longer than
+ // three characters is shown with single-character notation rather than
+ // three-letter notation
+ sb.append("p.");
+ if (orig.length() < 4)
+ {
+ for (int c = 0, clen = orig.length(); c < clen; c++)
+ {
+ char origchar = orig.charAt(c);
+ String orig3 = ResidueProperties.aa2Triplet.get("" + origchar);
+ sb.append(orig3 == null ? origchar
+ : StringUtils.toSentenceCase(orig3));
+ }
+ }
+ else
+ {
+ sb.append(orig);
+ }
+
+ LocationType location = feature.getLocation();
+ PositionType start = location.getPosition() == null
+ ? location.getBegin()
+ : location.getPosition();
+ sb.append(Integer.toString(start.getPosition().intValue()));
+
+ if (var.length() < 4)
+ {
+ for (int c = 0, clen = var.length(); c < clen; c++)
+ {
+ char varchar = var.charAt(c);
+ String var3 = ResidueProperties.aa2Triplet.get("" + varchar);
+
+ sb.append(var3 != null ? StringUtils.toSentenceCase(var3)
+ : "" + varchar);
+ }
+ }
+ else
+ {
+ sb.append(var);
+ }
+ if (++p != variants.size())
+ {
+ sb.append("<br/> ");
+ asHtml = true;
+ }
+ else
+ {
+ sb.append(" ");
+ }
+ }
+ }
+ String description = feature.getDescription();
+ if (description != null)
+ {
+ sb.append(description);
+ }
+ if (asHtml)
+ {
+ sb.insert(0, "<html>");
+ sb.append("</html>");
+ }
+
+ return sb.toString();
+ }
+
+ /**
+ * A helper method that searches the list of properties for one with the given
+ * key, and if found returns the property value, else returns null
+ *
+ * @param properties
+ * @param key
+ * @return
+ */
+ static String getProperty(List<PropertyType> properties, String key)
+ {
+ String value = null;
+ if (properties != null)
+ {
+ for (PropertyType prop : properties)
+ {
+ if (key.equals(prop.getType()))
+ {
+ value = prop.getValue();
+ break;
+ }
+ }
+ }
+ return value;
+ }
+
+ /**
+ * Extracts xml element entry/protein/recommendedName/fullName
+ *
+ * @param entry
+ * @return
+ */
+ static String getUniprotEntryDescription(Entry entry)
+ {
+ String desc = "";
+ if (entry.getProtein() != null
+ && entry.getProtein().getRecommendedName() != null)
+ {
+ // fullName is mandatory if recommendedName is present
+ desc = entry.getProtein().getRecommendedName().getFullName()
+ .getValue();
+ }
+ return desc;
+ }
+
+ /**
+ * Constructs a sequence id by concatenating all entry/name elements with '|'
+ * separator
+ *
+ * @param entry
+ * @return
+ */
+ static String getUniprotEntryId(Entry entry)
+ {
+ StringBuilder name = new StringBuilder(32);
+ for (String n : entry.getName())
+ {
+ if (name.length() > 0)
+ {
+ name.append(BAR_DELIMITER);
+ }
+ name.append(n);
+ }
+ return name.toString();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
+ */
+ @Override
+ public boolean isValidReference(String accession)
+ {
+ // TODO: make the following a standard validator
+ return (accession == null || accession.length() < 2) ? false
+ : getAccessionValidator().search(accession);
+ }
+
+ /**
+ * return LDHA_CHICK uniprot entry
+ */
+ @Override
+ public String getTestQuery()
+ {
+ return "P00340";
+ }
+
+ @Override
+ public String getDbName()
+ {
+ return "Uniprot"; // getDbSource();
+ }
+
+ @Override
+ public int getTier()
+ {
+ return 0;
+ }
+
+ /**
+ * Reads the reply to the EBI Fetch Uniprot data query, unmarshals it to an
+ * Uniprot object, and returns the enclosed Entry objects, or null on any
+ * failure
+ *
+ * @param is
+ * @return
+ */
+ public List<Entry> getUniprotEntries(InputStream is)
+ {
+ List<Entry> entries = null;
+ try
+ {
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.uniprot");
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(is);
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ JAXBElement<jalview.xml.binding.uniprot.Uniprot> uniprotElement =
+ um.unmarshal(streamReader, jalview.xml.binding.uniprot.Uniprot.class);
+ jalview.xml.binding.uniprot.Uniprot uniprot = uniprotElement.getValue();
+
+ if (uniprot != null && !uniprot.getEntry().isEmpty())
+ {
+ entries = uniprot.getEntry();
+ }
+ } catch (JAXBException | XMLStreamException
+ | FactoryConfigurationError e)
+ {
+ e.printStackTrace();
+ }
+ return entries;
+ }
+}
*/
package jalview.ws.dbsources;
+import java.util.Locale;
+
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.schemes.ResidueProperties;
import jalview.util.StringUtils;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
-import jalview.xml.binding.embl.ROOT;
import jalview.xml.binding.uniprot.DbReferenceType;
import jalview.xml.binding.uniprot.Entry;
import jalview.xml.binding.uniprot.FeatureType;
import jalview.xml.binding.uniprot.PropertyType;
import java.io.InputStream;
+import java.net.HttpURLConnection;
import java.net.URL;
-import java.net.URLConnection;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
startQuery();
try
{
- queries = queries.toUpperCase().replaceAll(
+ queries = queries.toUpperCase(Locale.ROOT).replaceAll(
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
AlignmentI al = null;
+ ".xml";
URL url = new URL(downloadstring);
- URLConnection urlconn = url.openConnection();
- InputStream istr = urlconn.getInputStream();
- List<Entry> entries = getUniprotEntries(istr);
- if (entries != null)
+ HttpURLConnection urlconn = (HttpURLConnection)url.openConnection();
+ // anything other than 200 means we don't have data
+ // TODO: JAL-3882 reuse the EnsemblRestClient's fair
+ // use/backoff logic to retry when the server tells us to go away
+ if (urlconn.getResponseCode() == 200)
{
- List<SequenceI> seqs = new ArrayList<>();
- for (Entry entry : entries)
+ InputStream istr = urlconn.getInputStream();
+ List<Entry> entries = getUniprotEntries(istr);
+ if (entries != null)
{
- seqs.add(uniprotEntryToSequence(entry));
+ List<SequenceI> seqs = new ArrayList<>();
+ for (Entry entry : entries)
+ {
+ seqs.add(uniprotEntryToSequence(entry));
+ }
+ al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
}
- al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
}
-
stopQuery();
return al;
+
} catch (Exception e)
{
throw (e);
*/
final String dbVersion = getDbVersion();
List<DBRefEntry> dbRefs = new ArrayList<>();
+ boolean canonical=true;
for (String accessionId : entry.getAccession())
{
DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
- accessionId);
+ accessionId,null,canonical);
+ canonical=false;
dbRefs.add(dbRef);
}
} catch (JAXBException | XMLStreamException
| FactoryConfigurationError e)
{
+ if (e instanceof javax.xml.bind.UnmarshalException && e.getCause()!=null && e.getCause() instanceof XMLStreamException && e.getCause().getMessage().contains("[row,col]:[1,1]"))
+ {
+ // trying to parse an empty stream
+ return null;
+ }
e.printStackTrace();
}
return entries;
*/
package jalview.ws.dbsources;
-import jalview.bin.Cache;
+import java.util.Locale;
+
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.io.DataSourceType;
// TODO: trap HTTP 404 exceptions and return null
String xfamUrl = getURL(queries);
- if (Cache.log != null)
- {
- Cache.log.debug("XFAM URL for retrieval is: " + xfamUrl);
- }
+ Console.debug("XFAM URL for retrieval is: " + xfamUrl);
AlignmentI rcds = new FormatAdapter().readFile(xfamUrl,
DataSourceType.URL, FileFormat.Stockholm);
{
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
// getDbSource(),
- getDbVersion(), queries.trim().toUpperCase()));
+ getDbVersion(), queries.trim().toUpperCase(Locale.ROOT)));
if (!getDbSource().equals(getXfamSource()))
{ // add the specific ref too
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(),
- getDbVersion(), queries.trim().toUpperCase()));
+ getDbVersion(), queries.trim().toUpperCase(Locale.ROOT)));
}
}
stopQuery();
String getURL(String queries)
{
- return getURLPrefix() + "/family/" + queries.trim().toUpperCase()
+ return getURLPrefix() + "/family/" + queries.trim().toUpperCase(Locale.ROOT)
+ getURLSuffix();
}
*/
package jalview.ws.ebi;
+import java.util.Locale;
+
import jalview.datamodel.DBRefSource;
import jalview.util.MessageManager;
import jalview.util.Platform;
* the query formatted as db:query1;query2;query3
* @param format
* the format wanted
- * @param extension
+ * @param ext
* for the temporary file to hold response (without separator)
* @return the file holding the response
* @throws OutOfMemoryError
{
String url = buildUrl(ids, database, format);
InputStream is = null;
+ BufferedReader br = null;
try
{
URL rcall = new URL(url);
Platform.streamToFile(is, outFile);
return null;
}
- BufferedReader br = new BufferedReader(new InputStreamReader(is));
+ br = new BufferedReader(new InputStreamReader(is));
String rtn;
List<String> arl = new ArrayList<>();
while ((rtn = br.readLine()) != null)
{
}
}
+ if (br != null)
+ {
+ try
+ {
+ br.close();
+ } catch (IOException e)
+ {
+ }
+ }
}
return null;
}
if (database.equalsIgnoreCase(DBRefSource.EMBL)
|| database.equalsIgnoreCase(DBRefSource.EMBLCDS))
{
- url = "https://www.ebi.ac.uk/ena/data/view/" + ids.toLowerCase()
- + (format != null ? "&" + format : "");
+ url = "https://www.ebi.ac.uk/ena/browser/api/embl/"
+ + ids.toLowerCase(Locale.ROOT) + "?download=true&gzip=true";
}
else
{
url = "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
- + database.toLowerCase() + "/" + ids.toLowerCase()
+ + database.toLowerCase(Locale.ROOT) + "/" + ids.toLowerCase(Locale.ROOT)
+ (format != null ? "/" + format : "");
}
return url;
*/
package jalview.ws.io.mime;
+import java.util.Locale;
+
import jalview.io.packed.DataProvider.JvDataType;
/**
*/
public static JvDataType getTypeOf(String mimeType)
{
- String mt = mimeType.toLowerCase();
+ String mt = mimeType.toLowerCase(Locale.ROOT);
for (int i = 0; i < typemap.length; i += 2)
{
if (typemap[i].equals(mt))
*/
package jalview.ws.jws1;
+import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
// timeout
} catch (Exception ex)
{
- jalview.bin.Cache.log.error(
+ Console.error(
"Serious! Service location failed\nfor URL :" + WsURL + "\n",
ex);
static private Vector<URL> getDiscoveryURLS()
{
Vector<URL> urls = new Vector<>();
- String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
+ String RootServiceURLs = Cache.getDefault("DISCOVERY_URLS",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
try
}
else
{
- jalview.bin.Cache.log
- .info("Ignoring duplicate url in DISCOVERY_URLS list");
+ Console.info("Ignoring duplicate url in DISCOVERY_URLS list");
}
} catch (Exception ex)
{
- jalview.bin.Cache.log
- .warn("Problem whilst trying to make a URL from '"
+ Console.warn("Problem whilst trying to make a URL from '"
+ ((url != null) ? url : "<null>") + "'");
- jalview.bin.Cache.log.warn(
+ Console.warn(
"This was probably due to a malformed comma separated list"
+ " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
- jalview.bin.Cache.log.debug("Exception was ", ex);
+ Console.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
- jalview.bin.Cache.log.warn(
+ Console.warn(
"Error parsing comma separated list of urls in DISCOVERY_URLS.",
ex);
}
*/
static public void doDiscovery()
{
- jalview.bin.Cache.log
- .debug("(Re)-Initialising the discovery URL list.");
+ Console.debug("(Re)-Initialising the discovery URL list.");
try
{
- reallyDiscoverServices = jalview.bin.Cache
+ reallyDiscoverServices = Cache
.getDefault("DISCOVERY_START", false);
if (reallyDiscoverServices)
{
}
else
{
- jalview.bin.Cache.log.debug("Setting default services");
+ Console.debug("Setting default services");
services = new Hashtable<>();
// Muscle, Clustal and JPred.
ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
ServiceHandles shs = null;
try
{
- jalview.bin.Cache.log.debug("Discovering services using " + location);
+ Console.debug("Discovering services using " + location);
shs = locateWebService(location).getServices();
} catch (org.apache.axis.AxisFault f)
{
}
else
{
- jalview.bin.Cache.log.warn("No Discovery service at " + location);
- jalview.bin.Cache.log.debug("Axis Fault", f);
+ Console.warn("No Discovery service at " + location);
+ Console.debug("Axis Fault", f);
}
} catch (Exception e)
{
- jalview.bin.Cache.log.warn("No Discovery service at " + location);
- jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
+ Console.warn("No Discovery service at " + location);
+ Console.debug("Discovery Service General Exception", e);
}
if ((shs != null) && shs.getServices().length > 0)
{
{
if (!cat.contains(sh[i]))
{
- jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName()
+ Console.debug("A " + sh[i].getAbstractName()
+ " service called " + sh[i].getName() + " exists at "
+ sh[i].getEndpointURL() + "\n");
if (!sscat.containsKey(sh[i].getAbstractName()))
disc_serv = new java.net.URL(sh[i].getEndpointURL());
if (!ServiceURLList.contains(disc_serv))
{
- jalview.bin.Cache.log.debug(
+ Console.debug(
"Adding new discovery service at " + disc_serv);
ServiceURLList.add(disc_serv);
seenNewDiscovery = true;
}
} catch (Exception e)
{
- jalview.bin.Cache.log
- .debug("Ignoring bad discovery service URL "
+ Console.debug("Ignoring bad discovery service URL "
+ sh[i].getEndpointURL(), e);
}
}
int s_url = 0;
if (ServiceURLList == null)
{
- jalview.bin.Cache.log
- .debug("No service endpoints to use for service discovery.");
+ Console.debug("No service endpoints to use for service discovery.");
return;
}
while (s_url < ServiceURLList.size())
}
else
{
- jalview.bin.Cache.log.warn("No services at "
+ Console.warn("No services at "
+ (ServiceURLList.get(s_url))
+ " - check DISCOVERY_URLS property in .jalview_properties");
}
*/
package jalview.ws.jws1;
+import java.util.Locale;
+
import jalview.analysis.AlignSeq;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
Jpred server = locateWebService();
if (server == null)
{
- Cache.log.warn("Couldn't find a Jpred webservice to invoke!");
+ Console.warn("Couldn't find a Jpred webservice to invoke!");
return;
}
SeqCigar[] msf = null;
private String getPredictionName(String webServiceName)
{
- if (webServiceName.toLowerCase()
+ if (webServiceName.toLowerCase(Locale.ROOT)
.indexOf("secondary structure prediction") > -1)
{
return webServiceName;
import jalview.analysis.AlignSeq;
import jalview.analysis.SeqsetUtils;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
JpredResult result = (JpredResult) this.result;
- Cache.log.debug("Parsing output from JNet job.");
+ Console.debug("Parsing output from JNet job.");
// JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt",
// "File");
JPredFile prediction = new JPredFile(result.getPredfile(),
DataSourceType.PASTE);
SequenceI[] preds = prediction.getSeqsAsArray();
- Cache.log.debug("Got prediction profile.");
+ Console.debug("Got prediction profile.");
if ((this.msa != null) && (result.getAligfile() != null))
{
- Cache.log.debug("Getting associated alignment.");
+ Console.debug("Getting associated alignment.");
// we ignore the returned alignment if we only predicted on a single
// sequence
FileFormatI format = new IdentifyFile()
{
job.setSubmitted(true);
job.setSubjobComplete(false);
- Cache.log.info(WsUrl + " Job Id '" + job.getJobId() + "'");
+ Console.info(WsUrl + " Job Id '" + job.getJobId() + "'");
}
}
else
"JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n"
+ e.getMessage() + "\n");
- jalview.bin.Cache.log.warn("Server Exception", e);
+ Console.warn("Server Exception", e);
}
else
{
"info.failed_to_submit_prediction", new String[]
{ e.getMessage(), wsInfo.getProgressText() }));
- jalview.bin.Cache.log
- .debug("Failed Submission of job " + j.getJobnum(), e);
+ Console.debug("Failed Submission of job " + j.getJobnum(), e);
}
j.setAllowedServerExceptions(-1);
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Unexpected exception when processing results for " + altitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
msa = (j.msa != null) ? true : msa;
try
{
- jalview.bin.Cache.log.debug("Parsing output of job " + jn);
+ Console.debug("Parsing output of job " + jn);
jobres = j.getResultSet();
- jalview.bin.Cache.log.debug("Finished parsing output.");
+ Console.debug("Finished parsing output.");
if (jobs.length == 1)
{
res = jobres;
}
} catch (Exception e)
{
- jalview.bin.Cache.log
- .error("JNet Client: JPred Annotation Parse Error", e);
+ Console.error("JNet Client: JPred Annotation Parse Error", e);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.appendProgressText(j.getJobnum(),
}
else
{
- Cache.log.info("Append results onto existing alignment.");
+ Console.info("Append results onto existing alignment.");
}
}
}
*/
package jalview.ws.jws1;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
+ " of " + altitle + "\nJob details\n");
- String jobtitle = WebServiceName.toLowerCase();
+ String jobtitle = WebServiceName.toLowerCase(Locale.ROOT);
if (jobtitle.endsWith("alignment"))
{
if (submitGaps && (!jobtitle.endsWith("realignment")
package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
{
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
- Cache.log.warn(
+ Console.warn(
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Tried to submit an already submitted job " + j.getJobId());
}
return;
&& jobs[j].hasResults())
{
results++;
- // if (Cache.log.isDebugEnabled())
+ // if (Cache.isDebugEnabled())
// {
// System.out.println("Job lob for job
// "+jobs[j].getJobId()+":"+jobs[j].getJobnum());
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Unexpected exception when processing results for " + alTitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
*/
package jalview.ws.jws1;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
.getSupportedDatabases();
} catch (Exception e)
{
- jalview.bin.Cache.log.warn(
+ Console.warn(
"Database list request failed, so disabling SeqSearch Service client "
+ sh.getName() + " at " + sh.getEndpointURL(),
e);
import jalview.analysis.AlignSeq;
import jalview.api.FeatureColourI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
{
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
- Cache.log.warn(
+ Console.warn(
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
SeqSearchWSJob j = (SeqSearchWSJob) job;
if (j.isSubmitted())
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Tried to submit an already submitted job " + j.getJobId());
}
return;
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Unexpected exception when processing results for " + alTitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
package jalview.ws.jws2;
import jalview.api.FeatureColourI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceFeature;
scores = scoremanager.getAnnotationForSequence(seqId);
} catch (Exception q)
{
- Cache.log
- .info("Couldn't recover disorder prediction for sequence "
+ Console.info("Couldn't recover disorder prediction for sequence "
+ seq.getName() + "(Prediction name was " + seqId
+ ")"
+ "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
import jalview.analysis.SeqsetUtils;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
}
if (collectAnnotationResultsFor(rslt))
{
- jalview.bin.Cache.log.debug("Updating result annotation from Job "
+ Console.debug("Updating result annotation from Job "
+ rslt + " at " + service.getUri());
updateResultAnnotation(true);
ap.adjustAnnotationHeight();
*/
package jalview.ws.jws2;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
else
{
jws2Discoverer.addInvalidServiceUrl(jwsserver);
- Cache.log.warn("Ignoring invalid Jws2 service url " + jwsserver);
+ Console.warn("Ignoring invalid Jws2 service url " + jwsserver);
}
} catch (Exception e)
{
e.printStackTrace();
- Cache.log.warn("Exception when discovering Jws2 services.", e);
+ Console.warn("Exception when discovering Jws2 services.", e);
jws2Discoverer.addInvalidServiceUrl(jwsserver);
} catch (Error e)
{
- Cache.log.error("Exception when discovering Jws2 services.", e);
+ Console.error("Exception when discovering Jws2 services.", e);
jws2Discoverer.addInvalidServiceUrl(jwsserver);
}
running = false;
*/
package jalview.ws.jws2;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.List;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+import compbio.metadata.Argument;
import jalview.api.AlignCalcWorkerI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
import jalview.ws.params.WsParamSetI;
import jalview.ws.uimodel.AlignAnalysisUIText;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.List;
-
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
-
-import compbio.metadata.Argument;
-
/**
* provides metadata for a jabaws2 service instance - resolves names, etc.
*
WsParamSetI prset = jobParams.getPreset();
if (prset == null)
{
- paramset = jobParams.isServiceDefaults() ? null
- : JabaParamStore
- .getJabafromJwsArgs(jobParams.getJobParams());
+ paramset =
+ /* JAL-3739 always take values from input form */
+ /* jobParams.isServiceDefaults() ? null : */
+ JabaParamStore.getJabafromJwsArgs(jobParams.getJobParams());
this.preset = null;
}
else
if (service != null
&& !fave.getService().hosturl.equals(service.hosturl))
{
- Cache.log.debug("Changing AACon service to " + service.hosturl
+ Console.debug("Changing AACon service to " + service.hosturl
+ " from " + fave.getService().hosturl);
fave.setService(service);
}
if (!service.serviceType.toString()
.equals(compbio.ws.client.Services.AAConWS.toString()))
{
- Cache.log.warn(
+ Console.warn(
"Ignoring invalid preferred service for AACon calculations (service type was "
+ service.serviceType + ")");
service = null;
package jalview.ws.jws2;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
{
try
{
- Cache.log.debug(
+ Console.debug(
"Waiting around for old discovery thread to finish.");
// wait around until old discoverer dies
Thread.sleep(100);
}
}
aborted = false;
- Cache.log.debug("Old discovery thread has finished.");
+ Console.debug("Old discovery thread has finished.");
}
running = true;
}
if (aborted)
{
- Cache.log.debug(
+ Console.debug(
"Aborting " + qrys.size() + " JABAWS discovery threads.");
for (JabaWsServerQuery squery : qrys)
{
}
else
{
- Cache.log.warn("Ignoring duplicate url " + url + " in "
+ Console.warn("Ignoring duplicate url " + url + " in "
+ JWS2HOSTURLS + " list");
}
} catch (MalformedURLException ex)
{
- Cache.log.warn("Problem whilst trying to make a URL from '"
+ Console.warn("Problem whilst trying to make a URL from '"
+ ((url != null) ? url : "<null>") + "'");
- Cache.log.warn(
+ Console.warn(
"This was probably due to a malformed comma separated list"
+ " in the " + JWS2HOSTURLS
+ " entry of $(HOME)/.jalview_properties)");
- Cache.log.debug("Exception was ", ex);
+ Console.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
- Cache.log.warn("Error parsing comma separated list of urls in "
+ Console.warn("Error parsing comma separated list of urls in "
+ JWS2HOSTURLS + " preference.", ex);
}
return urls;
*/
package jalview.ws.jws2;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentView;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.JvOptionPane;
-import jalview.gui.JvSwingUtils;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
+import java.util.Locale;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import compbio.data.msa.MsaWS;
import compbio.metadata.Argument;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
/**
* DOCUMENT ME!
wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
+ " of " + altitle + "\nJob details\n");
- String jobtitle = WebServiceName.toLowerCase();
+ String jobtitle = WebServiceName.toLowerCase(Locale.ROOT);
if (jobtitle.endsWith("alignment"))
{
if (submitGaps && (!jobtitle.endsWith("realignment")
@Override
public void attachWSMenuEntry(JMenu rmsawsmenu,
- final Jws2Instance service, final AlignFrame alignFrame)
+ final Jws2Instance service, final AlignFrame af)
{
- if (registerAAConWSInstance(rmsawsmenu, service, alignFrame))
+ if (registerAAConWSInstance(rmsawsmenu, service, af))
{
// Alignment dependent analysis calculation WS gui
return;
@Override
public void actionPerformed(ActionEvent e)
{
- AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+ AlignmentView msa = af.gatherSequencesForAlignment();
if (msa != null)
{
- new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
+ new MsaWSClient(service, af.getTitle(), msa, withGaps,
true,
- alignFrame.getViewport().getAlignment().getDataset(),
- alignFrame);
+ af.getViewport().getAlignment().getDataset(),
+ af);
}
}
@Override
public void actionPerformed(ActionEvent e)
{
- AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+ AlignmentView msa = af.gatherSequencesForAlignment();
if (msa != null)
{
- new MsaWSClient(service, null, null, true,
- alignFrame.getTitle(), msa, withGaps, true,
- alignFrame.getViewport().getAlignment().getDataset(),
- alignFrame);
+ startJob(service, af, withGaps, msa);
}
}
final int showToolTipFor = ToolTipManager.sharedInstance()
.getDismissDelay();
- for (final WsParamSetI preset : presets)
+ for (final WsParamSetI preSet : presets)
{
- final JMenuItem methodR = new JMenuItem(preset.getName());
+ final JMenuItem methodR = new JMenuItem(preSet.getName());
final int QUICK_TOOLTIP = 1500;
// JAL-1582 shorten tooltip display time in these menu items as
// they can obscure other options
});
String tooltip = JvSwingUtils.wrapTooltip(true, "<strong>"
- + (preset.isModifiable()
+ + (preSet.isModifiable()
? MessageManager.getString("label.user_preset")
: MessageManager
.getString("label.service_preset"))
- + "</strong><br/>" + preset.getDescription());
+ + "</strong><br/>" + preSet.getDescription());
methodR.setToolTipText(tooltip);
methodR.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- AlignmentView msa = alignFrame
+ AlignmentView msa = af
.gatherSequencesForAlignment();
if (msa != null)
{
- MsaWSClient msac = new MsaWSClient(service, preset,
- alignFrame.getTitle(), msa, false, true,
- alignFrame.getViewport().getAlignment()
+ MsaWSClient msac = new MsaWSClient(service, preSet,
+ af.getTitle(), msa, false, true,
+ af.getViewport().getAlignment()
.getDataset(),
- alignFrame);
+ af);
}
}
}
} while (!finished);
}
+
+ protected void startJob(final Jws2Instance service, final AlignFrame af,
+ final boolean withGaps, AlignmentView msa)
+ {
+ try {
+ new MsaWSClient(service, null, null, true,
+ af.getTitle(), msa, withGaps, true,
+ af.getViewport().getAlignment().getDataset(),
+ af);
+ } catch (Exception e) {
+ JvOptionPane.showMessageDialog(alignFrame, e.getMessage(),
+ MessageManager.getString("label.state_job_error"),
+ JvOptionPane.WARNING_MESSAGE);
+
+ }
+ }
}
package jalview.ws.jws2;
import jalview.analysis.AlignSeq;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
{
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
- Cache.log.warn(
+ Console.warn(
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug(
+ Console.debug(
"Tried to submit an already submitted job " + j.getJobId());
}
return;
} catch (Exception e)
{
- Cache.log.warn(
+ Console.warn(
"Exception when retrieving remaining Job progress data for job "
+ msjob.getJobId() + " on server " + WsUrl);
e.printStackTrace();
}
} while (nunchanged > 0 && nexcept > 0);
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
System.out.println("Job Execution file for job: "
+ msjob.getJobId() + " on server " + WsUrl);
{
// job has failed for some reason - probably due to invalid
// parameters
- Cache.log.debug(
+ Console.debug(
"Results not available for finished job - marking as broken job.",
e);
msjob.jobProgress.append(
msjob.setjobStatus(JobStatus.FAILED);
} catch (Exception e)
{
- Cache.log.error("Couldn't get Alignment for job.", e);
+ Console.error("Couldn't get Alignment for job.", e);
// TODO: Increment count and retry ?
msjob.setjobStatus(JobStatus.UNDEFINED);
}
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Unexpected exception when processing results for " + alTitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
*/
package jalview.ws.jws2;
+import java.util.Locale;
+
import jalview.api.AlignCalcWorkerI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
worker.updateParameters(this.preset, paramset);
}
}
- if (sh.action.toLowerCase().contains("disorder"))
+ if (sh.action.toLowerCase(Locale.ROOT).contains("disorder"))
{
// build IUPred style client. take sequences, returns annotation per
// sequence.
*/
package jalview.ws.jws2.dm;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.ParameterUtils;
-import jalview.ws.params.OptionI;
-
import java.net.MalformedURLException;
import java.net.URL;
import java.util.List;
import compbio.metadata.Option;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.ParameterUtils;
+import jalview.ws.params.OptionI;
public class JabaOption implements jalview.ws.params.OptionI
{
opt.setDefaultValue(selectedItem);
} catch (Exception e)
{
- e.printStackTrace();
- throw new Error(MessageManager.getString(
- "error.implementation_error_cannot_set_jaba_option"));
+ throw new IllegalArgumentException(MessageManager
+ .formatMessage("error.invalid_value_for_option", new String[]
+ { selectedItem, opt.getName() }));
}
}
*/
package jalview.ws.rest;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.io.FileParse;
import jalview.io.packed.DataProvider;
import jalview.io.packed.DataProvider.JvDataType;
{
error = true;
errormessage = "Couldn't parse message from web service.";
- Cache.log.warn("Failed to parse MIME multipart content", me);
+ Console.warn("Failed to parse MIME multipart content", me);
en.consumeContent();
}
return new ParsePackedSet().getAlignment(ds,
: en.getContentEncoding().getValue();
if (en.getContentType() != null)
{
- Cache.log.debug("Result Type: " + en.getContentType().toString());
+ Console.debug("Result Type: " + en.getContentType().toString());
}
else
{
- Cache.log.debug("No Result Type Specified.");
+ Console.debug("No Result Type Specified.");
}
if (enc == null || enc.length() < 1)
{
- Cache.log.debug("Assuming 'Default' Result Encoding.");
+ Console.debug("Assuming 'Default' Result Encoding.");
}
else
{
- Cache.log.debug("Result Encoded as : " + enc);
+ Console.debug("Result Encoded as : " + enc);
}
// attempt to identify file and construct an appropriate DataSource
// identifier for it.
: new InputStreamReader(en.getContent());
} catch (UnsupportedEncodingException e)
{
- Cache.log.error("Can't handle encoding '" + enc
+ Console.error("Can't handle encoding '" + enc
+ "' for response from webservice.", e);
en.consumeContent();
error = true;
*/
package jalview.ws.rest;
+import java.util.Locale;
+
import jalview.ws.params.ArgumentI;
import jalview.ws.params.InvalidArgumentException;
import jalview.ws.params.OptionI;
{
valid = false;
warnings.append("Invalid value for parameter "
- + mtch.group(1).toLowerCase() + " '" + mtch.group(2)
+ + mtch.group(1).toLowerCase(Locale.ROOT) + " '" + mtch.group(2)
+ "' (expected an integer)\n");
}
{
for (RestServiceDescription descr : RestServiceDescription
.parseDescriptions(
- jalview.bin.Cache.getDefault(RSBS_SERVICES,
+ Cache.getDefault(RSBS_SERVICES,
makeShmmrRestClient().service.toString())))
{
services.add(descr.toString());
*/
package jalview.ws.rest;
-import jalview.bin.Cache;
+import java.util.Locale;
+
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+ "</a><br>See Console output for details.";
rj.setAllowedServerExceptions(0);// unrecoverable;
rj.error = true;
- Cache.log.fatal("Unexpected REST Job " + getStage(stg)
+ Console.fatal("Unexpected REST Job " + getStage(stg)
+ "exception for URL " + rj.rsd.postUrl);
throw (he);
} catch (IOException e)
+ "Job. <br>Problematic url was <a href=\""
+ request.getURI() + "\">" + request.getURI()
+ "</a><br>See Console output for details.";
- Cache.log.warn("IO Exception for REST Job " + getStage(stg)
+ Console.warn("IO Exception for REST Job " + getStage(stg)
+ "exception for URL " + rj.rsd.postUrl);
throw (e);
{
case 200:
rj.running = false;
- Cache.log.debug("Processing result set.");
+ Console.debug("Processing result set.");
processResultSet(rj, response, request);
break;
case 202:
{
if (loc.length > 1)
{
- Cache.log.warn("Ignoring additional " + (loc.length - 1)
+ Console.warn("Ignoring additional " + (loc.length - 1)
+ " location(s) provided in response header ( next one is '"
+ loc[1].getValue() + "' )");
}
default:
// Some other response. Probably need to pop up the content in a window.
// TODO: deal with all other HTTP response codes from server.
- Cache.log.warn("Unhandled response status when " + getStage(stg)
+ Console.warn("Unhandled response status when " + getStage(stg)
+ "for " + postUrl + ": " + response.getStatusLine());
rj.error = true;
rj.setAllowedServerExceptions(0);
+ "</a><br/>Filtered response content below:<br/>");
} catch (IOException e)
{
- Cache.log.debug("IOException when consuming unhandled response",
+ Console.debug("IOException when consuming unhandled response",
e);
}
;
*/
String f;
StringBuffer content = new StringBuffer(f = EntityUtils.toString(en));
- f = f.toLowerCase();
+ f = f.toLowerCase(Locale.ROOT);
int body = f.indexOf("<body");
if (body > -1)
{
{
job.setSubjobComplete(true);
job.setAllowedServerExceptions(-1);
- Cache.log.error("Exception when trying to start Rest Job.", ex);
+ Console.error("Exception when trying to start Rest Job.", ex);
}
}
{
// crazy users will see this message
// TODO: finish this! and remove the message below!
- Cache.log.warn("Rest job result parser is currently INCOMPLETE!");
+ Console.warn("Rest job result parser is currently INCOMPLETE!");
int validres = 0;
for (RestJob rj : (RestJob[]) jobs)
{
String ln = null;
try
{
- Cache.log.debug("Parsing data for job " + rj.getJobId());
+ Console.debug("Parsing data for job " + rj.getJobId());
rj.parseResultSet();
if (rj.hasResults())
{
validres++;
}
- Cache.log.debug("Finished parsing data for job " + rj.getJobId());
+ Console.debug("Finished parsing data for job " + rj.getJobId());
} catch (Error ex)
{
- Cache.log.warn(
+ Console.warn(
"Failed to finish parsing data for job " + rj.getJobId());
ex.printStackTrace();
} catch (Exception ex)
{
- Cache.log.warn(
+ Console.warn(
"Failed to finish parsing data for job " + rj.getJobId());
ex.printStackTrace();
} finally
{
// TODO: decide if multiple multiple alignments returned by
// non-vseparable services are allowed.
- Cache.log.warn(
+ Console.warn(
"dealing with multiple alignment products returned by non-vertically separable service.");
}
// recover reference to last alignment created for this rest frame
}
else
{
- Cache.log.warn(
+ Console.warn(
"Couldn't resolve original sequence for new sequence.");
}
}
grass = groupNames.get(alan[nrj][an].groupRef.getName());
if (grass == null)
{
- Cache.log.error(
+ Console.error(
"Couldn't relocate group referemce for group "
+ alan[nrj][an].groupRef.getName());
}
{
// TODO: process each newick file, lifting over sequence refs to
// current alignment, if necessary.
- Cache.log.error(
+ Console.error(
"Tree recovery from restjob not yet implemented.");
}
}
package jalview.ws.seqfetcher;
import jalview.api.FeatureSettingsModelI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
return true;
}
}
- Cache.log.warn("isFetchable doesn't know about '" + source + "'");
+ Console.warn("isFetchable doesn't know about '" + source + "'");
return false;
}
*/
package jalview.ws.sifts;
+import java.util.Locale;
+
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
}
String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
- + pdbId.toLowerCase() + ".xml.gz";
+ + pdbId.toLowerCase(Locale.ROOT) + ".xml.gz";
File siftsFile = new File(siftsFileName);
if (siftsFile.exists())
{
BackupFiles.moveFileToFile(siftsFile, oldSiftsFile);
try
{
- siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ siftsFile = downloadSiftsFile(pdbId.toLowerCase(Locale.ROOT));
oldSiftsFile.delete();
return siftsFile;
} catch (IOException e)
}
try
{
- siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ siftsFile = downloadSiftsFile(pdbId.toLowerCase(Locale.ROOT));
} catch (IOException e)
{
throw new SiftsException(e.getMessage());
public static boolean deleteSiftsFileByPDBId(String pdbId)
{
File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
- + pdbId.toLowerCase() + ".xml.gz");
+ + pdbId.toLowerCase(Locale.ROOT) + ".xml.gz");
if (siftsFile.exists())
{
return siftsFile.delete();
for (MapRegion mapRegion : mapRegions)
{
accessions
- .add(mapRegion.getDb().getDbAccessionId().toLowerCase());
+ .add(mapRegion.getDb().getDbAccessionId().toLowerCase(Locale.ROOT));
}
}
}
HashSet<String> dbRefAccessionIdsString = new HashSet<String>();
for (DBRefEntry dbref : seq.getDBRefs())
{
- dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase());
+ dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase(Locale.ROOT));
}
- dbRefAccessionIdsString.add(sourceDBRef.getAccessionId().toLowerCase());
+ dbRefAccessionIdsString.add(sourceDBRef.getAccessionId().toLowerCase(Locale.ROOT));
curDBRefAccessionIdsString = dbRefAccessionIdsString;
curSourceDBRef = sourceDBRef.getAccessionId();
{
boolean isStrictMatch = true;
return isStrictMatch ? curSourceDBRef.equalsIgnoreCase(accession)
- : curDBRefAccessionIdsString.contains(accession.toLowerCase());
+ : curDBRefAccessionIdsString.contains(accession.toLowerCase(Locale.ROOT));
}
private boolean isFoundInSiftsEntry(String accessionId)
{
Set<String> siftsDBRefs = getAllMappingAccession();
return accessionId != null
- && siftsDBRefs.contains(accessionId.toLowerCase());
+ && siftsDBRefs.contains(accessionId.toLowerCase(Locale.ROOT));
}
/**
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="alcodon" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="alcodMap" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
- * </sequence>
- * <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="alcodon" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="alcodMap" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the alcodon property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alcodon property.
+ * This is why there is not a <CODE>set</CODE> method for the alcodon property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAlcodon().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link AlcodonFrame.Alcodon }
*
/**
* Gets the value of the alcodMap property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alcodMap property.
+ * This is why there is not a <CODE>set</CODE> method for the alcodMap property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAlcodMap().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link AlcodonFrame.AlcodMap }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
- * </sequence>
- * <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
* Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
*
*
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="thresholdLine" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="property" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" />
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="thresholdLine" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="property" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" /&gt;
+ * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the annotationElement property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the annotationElement property.
+ * This is why there is not a <CODE>set</CODE> method for the annotationElement property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAnnotationElement().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link AnnotationElement }
*
/**
* Gets the value of the property property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the property property.
+ * This is why there is not a <CODE>set</CODE> method for the property property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getProperty().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Annotation.Property }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for AnnotationColourScheme complex type.
+ * <p>Java class for AnnotationColourScheme complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="AnnotationColourScheme">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="AnnotationColourScheme"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="secondaryStructure" minOccurs="0">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <length value="1"/>
- * </restriction>
- * </simpleType>
- * </element>
- * <element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/>
- * </sequence>
- * <attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="secondaryStructure" minOccurs="0"&gt;
+ * &lt;simpleType&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;length value="1"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/simpleType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for DoubleMatrix complex type.
+ * <p>Java class for DoubleMatrix complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="DoubleMatrix">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="row" type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="D" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
- * <element name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
- * </sequence>
- * <attribute name="rows" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="columns" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="DoubleMatrix"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="row" type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="D" type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt;
+ * &lt;element name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="rows" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="columns" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the row property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the row property.
+ * This is why there is not a <CODE>set</CODE> method for the row property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getRow().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link DoubleVector }
*
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for DoubleVector complex type.
+ * <p>Java class for DoubleVector complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="DoubleVector">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="v" type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="DoubleVector"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="v" type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the v property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the v property.
+ * This is why there is not a <CODE>set</CODE> method for the v property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getV().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Double }
*
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for feature complex type.
+ * <p>Java class for feature complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="feature">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="otherData" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="feature"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="otherData" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the otherData property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the otherData property.
+ * This is why there is not a <CODE>set</CODE> method for the otherData property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getOtherData().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Feature.OtherData }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for FeatureMatcher complex type.
+ * <p>Java class for FeatureMatcher complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="FeatureMatcher">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="condition" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * </sequence>
- * <attribute name="by" type="{www.jalview.org/colours}FilterBy" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="FeatureMatcher"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;element name="condition" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="by" type="{www.jalview.org/colours}FilterBy" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the attributeName property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAttributeName().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
* A feature match condition, which may be simple or compound
*
- * <p>Java class for FeatureMatcherSet complex type.
+ * <p>Java class for FeatureMatcherSet complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="FeatureMatcherSet">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <choice>
- * <element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/>
- * <element name="compoundMatcher">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
- * </sequence>
- * <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </choice>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="FeatureMatcherSet"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;choice&gt;
+ * &lt;element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/&gt;
+ * &lt;element name="compoundMatcher"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/choice&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
- * </sequence>
- * <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the matcherSet property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the matcherSet property.
+ * This is why there is not a <CODE>set</CODE> method for the matcherSet property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getMatcherSet().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link FeatureMatcherSet }
*
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for FilterBy.
+ * <p>Java class for FilterBy.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- * <p>
- * <pre>
- * <simpleType name="FilterBy">
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="byLabel"/>
- * <enumeration value="byScore"/>
- * <enumeration value="byAttribute"/>
- * </restriction>
- * </simpleType>
- * </pre>
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <pre>
+ * &lt;simpleType name="FilterBy"&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;enumeration value="byLabel"/&gt;
+ * &lt;enumeration value="byScore"/&gt;
+ * &lt;enumeration value="byAttribute"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/simpleType&gt;
+ * </pre>
*
*/
@XmlType(name = "FilterBy", namespace = "www.jalview.org/colours")
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for JalviewModel complex type.
+ * <p>Java class for JalviewModel complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="JalviewModel">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
- * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
- * <sequence>
- * <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * </sequence>
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
- * </sequence>
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="tree" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence minOccurs="0">
- * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="sequencePoint" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="axis" maxOccurs="3" minOccurs="3">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="seqPointMin">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="seqPointMax">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attGroup ref="{www.jalview.org}SimilarityParams"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="FeatureSettings" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="setting" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="group" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="JalviewModel"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt;
+ * &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org}pdbentry"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;simpleContent&gt;
+ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/simpleContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
+ * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
+ * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence minOccurs="0"&gt;
+ * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="seqPointMin"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="seqPointMax"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="FeatureSettings" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the jSeq property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the jSeq property.
+ * This is why there is not a <CODE>set</CODE> method for the jSeq property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getJSeq().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq }
*
/**
* Gets the value of the jGroup property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the jGroup property.
+ * This is why there is not a <CODE>set</CODE> method for the jGroup property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getJGroup().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JGroup }
*
/**
* Gets the value of the viewport property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the viewport property.
+ * This is why there is not a <CODE>set</CODE> method for the viewport property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getViewport().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.Viewport }
*
/**
* Gets the value of the userColours property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the userColours property.
+ * This is why there is not a <CODE>set</CODE> method for the userColours property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getUserColours().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.UserColours }
*
/**
* Gets the value of the tree property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the tree property.
+ * This is why there is not a <CODE>set</CODE> method for the tree property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getTree().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.Tree }
*
/**
* Gets the value of the pcaViewer property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
+ * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getPcaViewer().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.PcaViewer }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="setting" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="group" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the setting property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the setting property.
+ * This is why there is not a <CODE>set</CODE> method for the setting property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSetting().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.FeatureSettings.Setting }
*
/**
* Gets the value of the group property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the group property.
+ * This is why there is not a <CODE>set</CODE> method for the group property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getGroup().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.FeatureSettings.Group }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the attributeName property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAttributeName().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * </sequence>
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
+ * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the seq property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the seq property.
+ * This is why there is not a <CODE>set</CODE> method for the seq property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSeq().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org}pdbentry"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;simpleContent&gt;
+ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/simpleContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the features property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the features property.
+ * This is why there is not a <CODE>set</CODE> method for the features property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getFeatures().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Feature }
*
/**
* Gets the value of the pdbids property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the pdbids property.
+ * This is why there is not a <CODE>set</CODE> method for the pdbids property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getPdbids().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq.Pdbids }
*
/**
* Gets the value of the hiddenSequences property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
+ * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getHiddenSequences().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
/**
* Gets the value of the rnaViewer property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
+ * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getRnaViewer().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq.RnaViewer }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org}pdbentry"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;simpleContent&gt;
+ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/simpleContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the structureState property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the structureState property.
+ * This is why there is not a <CODE>set</CODE> method for the structureState property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getStructureState().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq.Pdbids.StructureState }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;simpleContent&gt;
+ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/simpleContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the secondaryStructure property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
+ * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSecondaryStructure().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="sequencePoint" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="axis" maxOccurs="3" minOccurs="3">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="seqPointMin">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="seqPointMax">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attGroup ref="{www.jalview.org}SimilarityParams"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="seqPointMin"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="seqPointMax"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the sequencePoint property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
+ * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSequencePoint().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.PcaViewer.SequencePoint }
*
/**
* Gets the value of the axis property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the axis property.
+ * This is why there is not a <CODE>set</CODE> method for the axis property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAxis().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.PcaViewer.Axis }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence minOccurs="0">
- * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence minOccurs="0"&gt;
+ * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
- * </sequence>
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
+ * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the hiddenColumns property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
+ * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getHiddenColumns().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.Viewport.HiddenColumns }
*
/**
* Gets the value of the calcIdParam property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
+ * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getCalcIdParam().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.Viewport.CalcIdParam }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
+ * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for JalviewUserColours complex type.
+ * <p>Java class for JalviewUserColours complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="JalviewUserColours">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="colour" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * </sequence>
- * <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="filter" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
- * </sequence>
- * <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="JalviewUserColours"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="colour" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="filter" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the colour property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the colour property.
+ * This is why there is not a <CODE>set</CODE> method for the colour property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getColour().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewUserColours.Colour }
*
/**
* Gets the value of the filter property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the filter property.
+ * This is why there is not a <CODE>set</CODE> method for the filter property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getFilter().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewUserColours.Filter }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * </sequence>
- * <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the attributeName property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAttributeName().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
- * </sequence>
- * <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
* This effectively represents a java.util.MapList object
*
*
- * <p>Java class for mapListType complex type.
+ * <p>Java class for mapListType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="mapListType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="mapListFrom" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="mapListTo" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
- * <attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="mapListType"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="mapListFrom" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="mapListTo" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
+ * &lt;attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the mapListFrom property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the mapListFrom property.
+ * This is why there is not a <CODE>set</CODE> method for the mapListFrom property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getMapListFrom().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link MapListType.MapListFrom }
*
/**
* Gets the value of the mapListTo property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the mapListTo property.
+ * This is why there is not a <CODE>set</CODE> method for the mapListTo property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getMapListTo().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link MapListType.MapListTo }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
* to the sequence set (which will mean they are then added to the alignment too).
*
*
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.vamsas.ac.uk/jalview/version2}mapListType">
- * <sequence>
- * <choice minOccurs="0">
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/>
- * <element name="dseqFor">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * </restriction>
- * </simpleType>
- * </element>
- * </choice>
- * </sequence>
- * <attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.vamsas.ac.uk/jalview/version2}mapListType"&gt;
+ * &lt;sequence&gt;
+ * &lt;choice minOccurs="0"&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/&gt;
+ * &lt;element name="dseqFor"&gt;
+ * &lt;simpleType&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;/restriction&gt;
+ * &lt;/simpleType&gt;
+ * &lt;/element&gt;
+ * &lt;/choice&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for NoValueColour.
+ * <p>Java class for NoValueColour.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- * <p>
- * <pre>
- * <simpleType name="NoValueColour">
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="None"/>
- * <enumeration value="Min"/>
- * <enumeration value="Max"/>
- * </restriction>
- * </simpleType>
- * </pre>
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <pre>
+ * &lt;simpleType name="NoValueColour"&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;enumeration value="None"/&gt;
+ * &lt;enumeration value="Min"/&gt;
+ * &lt;enumeration value="Max"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/simpleType&gt;
+ * </pre>
*
*/
@XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours")
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
* This object contains factory methods for each
* Java content interface and Java element interface
* generated in the jalview.xml.binding.jalview package.
- * <p>An ObjectFactory allows you to programatically
+ * <p>An ObjectFactory allows you to programatically
* construct new instances of the Java representation
* for XML content. The Java representation of XML
* content can consist of schema derived interfaces
@XmlRegistry
public class ObjectFactory {
- private final static QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
private final static QName _JalviewModel_QNAME = new QName("www.jalview.org", "JalviewModel");
private final static QName _JalviewUserColours_QNAME = new QName("www.jalview.org/colours", "JalviewUserColours");
+ private final static QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
/**
* Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview
}
/**
- * Create an instance of {@link AlcodonFrame }
- *
- */
- public AlcodonFrame createAlcodonFrame() {
- return new AlcodonFrame();
- }
-
- /**
* Create an instance of {@link MapListType }
*
*/
}
/**
+ * Create an instance of {@link AlcodonFrame }
+ *
+ */
+ public AlcodonFrame createAlcodonFrame() {
+ return new AlcodonFrame();
+ }
+
+ /**
* Create an instance of {@link Annotation }
*
*/
}
/**
- * Create an instance of {@link DoubleMatrix }
- *
- */
- public DoubleMatrix createDoubleMatrix() {
- return new DoubleMatrix();
- }
-
- /**
* Create an instance of {@link AnnotationColourScheme }
*
*/
}
/**
- * Create an instance of {@link AlcodonFrame.Alcodon }
- *
- */
- public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() {
- return new AlcodonFrame.Alcodon();
- }
-
- /**
- * Create an instance of {@link AlcodonFrame.AlcodMap }
- *
- */
- public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() {
- return new AlcodonFrame.AlcodMap();
- }
-
- /**
- * Create an instance of {@link AnnotationElement }
+ * Create an instance of {@link DoubleMatrix }
*
*/
- public AnnotationElement createAnnotationElement() {
- return new AnnotationElement();
+ public DoubleMatrix createDoubleMatrix() {
+ return new DoubleMatrix();
}
/**
}
/**
+ * Create an instance of {@link AlcodonFrame.Alcodon }
+ *
+ */
+ public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() {
+ return new AlcodonFrame.Alcodon();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame.AlcodMap }
+ *
+ */
+ public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() {
+ return new AlcodonFrame.AlcodMap();
+ }
+
+ /**
+ * Create an instance of {@link AnnotationElement }
+ *
+ */
+ public AnnotationElement createAnnotationElement() {
+ return new AnnotationElement();
+ }
+
+ /**
* Create an instance of {@link Annotation.ThresholdLine }
*
*/
}
/**
- * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}}
- *
- */
- @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
- public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(WebServiceParameterSet value) {
- return new JAXBElement<WebServiceParameterSet>(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}}
+ * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
*
+ * @param value
+ * Java instance representing xml element's value.
+ * @return
+ * the new instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
*/
@XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value) {
}
/**
- * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}}
+ * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
*
+ * @param value
+ * Java instance representing xml element's value.
+ * @return
+ * the new instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
*/
@XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours")
public JAXBElement<JalviewUserColours> createJalviewUserColours(JalviewUserColours value) {
return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value);
}
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
+ *
+ * @param value
+ * Java instance representing xml element's value.
+ * @return
+ * the new instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
+ */
+ @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
+ public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(WebServiceParameterSet value) {
+ return new JAXBElement<WebServiceParameterSet>(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
+ }
+
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
* The results of a PCA calculation
*
*
- * <p>Java class for PcaDataType complex type.
+ * <p>Java class for PcaDataType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="PcaDataType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="pairwiseMatrix" type="{www.jalview.org}DoubleMatrix"/>
- * <element name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/>
- * <element name="eigenMatrix" type="{www.jalview.org}DoubleMatrix"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="PcaDataType"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="pairwiseMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
+ * &lt;element name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
+ * &lt;element name="eigenMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for pdbentry complex type.
+ * <p>Java class for pdbentry complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="pdbentry">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence maxOccurs="unbounded" minOccurs="0">
- * <element name="property" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="pdbentry"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;element name="property" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the property property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the property property.
+ * This is why there is not a <CODE>set</CODE> method for the property property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getProperty().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Pdbentry.Property }
*
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType">
- * <sequence>
- * <element name="DBRef" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
- * </sequence>
- * <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="DBRef" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the dbRef property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the dbRef property.
+ * This is why there is not a <CODE>set</CODE> method for the dbRef property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getDBRef().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Sequence.DBRef }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
- * </sequence>
- * <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
protected String accessionId;
@XmlAttribute(name = "locus")
protected Boolean locus;
+ @XmlAttribute(name = "canonical")
+ protected Boolean canonical;
/**
* Gets the value of the mapping property.
this.locus = value;
}
+ /**
+ * Gets the value of the canonical property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isCanonical() {
+ if (canonical == null) {
+ return false;
+ } else {
+ return canonical;
+ }
+ }
+
+ /**
+ * Sets the value of the canonical property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setCanonical(Boolean value) {
+ this.canonical = value;
+ }
+
}
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * <attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the sequence property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequence property.
+ * This is why there is not a <CODE>set</CODE> method for the sequence property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSequence().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Sequence }
*
/**
* Gets the value of the annotation property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the annotation property.
+ * This is why there is not a <CODE>set</CODE> method for the annotation property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAnnotation().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Annotation }
*
/**
* Gets the value of the sequenceSetProperties property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequenceSetProperties property.
+ * This is why there is not a <CODE>set</CODE> method for the sequenceSetProperties property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSequenceSetProperties().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link SequenceSet.SequenceSetProperties }
*
/**
* Gets the value of the alcodonFrame property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alcodonFrame property.
+ * This is why there is not a <CODE>set</CODE> method for the alcodonFrame property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAlcodonFrame().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link AlcodonFrame }
*
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for SequenceType complex type.
+ * <p>Java class for SequenceType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="SequenceType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * </sequence>
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="SequenceType"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for ThresholdType.
+ * <p>Java class for ThresholdType.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- * <p>
- * <pre>
- * <simpleType name="ThresholdType">
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="NONE"/>
- * <enumeration value="ABOVE"/>
- * <enumeration value="BELOW"/>
- * </restriction>
- * </simpleType>
- * </pre>
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <pre>
+ * &lt;simpleType name="ThresholdType"&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;enumeration value="NONE"/&gt;
+ * &lt;enumeration value="ABOVE"/&gt;
+ * &lt;enumeration value="BELOW"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/simpleType&gt;
+ * </pre>
*
*/
@XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours")
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for VAMSAS complex type.
+ * <p>Java class for VAMSAS complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="VAMSAS">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="VAMSAS"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the tree property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the tree property.
+ * This is why there is not a <CODE>set</CODE> method for the tree property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getTree().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
* Gets the value of the sequenceSet property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequenceSet property.
+ * This is why there is not a <CODE>set</CODE> method for the sequenceSet property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSequenceSet().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link SequenceSet }
*
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
/**
- * <p>Java class for WebServiceParameterSet complex type.
+ * <p>Java class for WebServiceParameterSet complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="WebServiceParameterSet">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/>
- * <element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * </sequence>
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="WebServiceParameterSet"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/&gt;
+ * &lt;element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the serviceURL property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the serviceURL property.
+ * This is why there is not a <CODE>set</CODE> method for the serviceURL property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getServiceURL().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.06.07 at 02:21:15 PM BST
+// Generated on: 2021.08.30 at 11:05:22 AM BST
//
@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
public String pdbid = "";
- public PDBChain(String thePdbid, String theId)
+ String tfacName = "Temperature Factor";
+
+
+ public PDBChain(String thePdbid, String theId, String tempFactorColumnName)
{
this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase();
this.id = theId;
+ if (tempFactorColumnName!=null && tempFactorColumnName.length()>0)
+ {
+ tfacName = tempFactorColumnName;
+ }
+ }
+
+ /**
+ * import chain data assuming Temperature Factor is in the Temperature Factor column
+ * @param thePdbid
+ * @param theId
+ */
+ public PDBChain(String thePdbid, String theId)
+ {
+ this(thePdbid,theId, null);
}
/**
* @param seq
* @param status
* The Status of the transferred annotation
+ *
+ * @param altPDBID the group id for the features on the destination sequence (e.g. the official accession ID)
*/
public void transferRESNUMFeatures(SequenceI seq,
- String status)
+ String status, String altPDBID)
{
+ if (altPDBID==null)
+ {
+ altPDBID = pdbid;
+ }
SequenceI sq = seq;
while (sq != null && sq.getDatasetSequence() != null)
{
int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
.elementAt(0).alignmentMapping;
SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
- feature.getFeatureGroup(), feature.getScore());
+ altPDBID, feature.getScore());
tx.setStatus(status
+ ((tx.getStatus() == null || tx.getStatus().length() == 0)
? ""
min = Math.min(min, annots[i].value);
resAnnotation.setElementAt(null, i);
}
-
AlignmentAnnotation tfactorann = new AlignmentAnnotation(
- "Temperature Factor", "Temperature Factor for " + pdbid + id,
+ tfacName, tfacName + " for " + pdbid + id,
annots, min, max, AlignmentAnnotation.LINE_GRAPH);
+
+ tfactorann.setCalcId(getClass().getName());
+
tfactorann.setSequenceRef(sequence);
sequence.addAlignmentAnnotation(tfactorann);
}
}
+
/**
* Colour start/end of bonds by charge
* <ul>
for (AlignmentAnnotation ana : shadow.getAnnotation())
{
- List<AlignmentAnnotation> transfer = sq
- .getAlignmentAnnotations(ana.getCalcId(), ana.label);
+ // match on calcId, label and description so annotations from
+ // different structures are preserved
+ List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
+ ana.getCalcId(), ana.label, ana.description);
if (transfer == null || transfer.size() == 0)
{
ana = new AlignmentAnnotation(ana);
{
for (AlignmentAnnotation ana : sequence.getAnnotation())
{
+ // match on calcId, label and description so annotations from
+ // different structures are preserved
List<AlignmentAnnotation> transfer = dsq
- .getAlignmentAnnotations(ana.getCalcId(), ana.label);
+ .getAlignmentAnnotations(ana.getCalcId(), ana.label,
+ ana.description);
if (transfer == null || transfer.size() == 0)
{
ana = new AlignmentAnnotation(ana);
tmpchain.atoms.addElement(tmpatom);
} else
{
+ // PDBfile never handles alphafold models
tmpchain = new PDBChain(getId(), tmpatom.chain);
getChains().add(tmpchain);
tmpchain.atoms.addElement(tmpatom);
-Notes
-=====
+java2script/SwingJS Notes
+=========================
+
+updated 12/31/2020 -- full support for 64-bit long
+updated 12/6/2020 -- note about restrictions on long, including BitSet and Scanner
+updated 3/21/2020 -- adds note about HashMap, Hashtable, and HashSet iterator ordering
+updated 3/20/2020 -- adds note about interning, new String("xxx"), and "xxx"
+updated 2/26/2020 -- adds Graphics.setClip issue
+updated 12/22/19 -- additional issues
+updated 11/03/19 -- adds information about File.exists() and points to src/javajs/async
+updated 10/26/19 -- adds information about File.createTempFile()
+updated 8/16/19 -- minor typos and added summary paragraph
+updated 7/19/19 -- clarification that AWT and Swing classes are supported directly
+updated 5/13/19 -- Mandarin U+79D8 reserved character; Missing Math methods; int and long
+updated 5/10/19 -- adds a section on static issues in multi-(duplicate)-applet pages
+updated 1/4/19 -- nio
+updated 9/15/18 -- adds integer 1/0 == Infinity
+updated 7/24/18 -- most classes replaced with https://github.com/frohoff/jdk8u-jdk
+updated 6/5/17 -- reserved package name "window"
+updated 3/11/17 -- myClass.getField
+updated 3/7/17 -- overloading of JSplitPane.setDividerLocation
+updated 3/2/17 -- more indication of classes not implemented (KeyListener)
---IMPORTANT CHARACTER SET NOTE---
-It is critical that all development work in Java2Script
-be done in UTF-8. This means:
+It is critical that all development work in Java2Script be done in UTF-8. This means:
- making sure your Eclipse project is set up for UTF-8 (not the Eclipse default?)
- making sure your server can serve up UTF-8 by default for any browser-loaded files
Note that the DOCTYPE tag is critical for some browsers to switch into HTML5 mode. (MSIE?)
-
-
In particular, the Mandarin character 秘 (mi; "secret") is used extensively throughout
the SwingJS class files to distinguish j2s-specific fields and methods that must not
ever be shadowed or overridden by subclasses. For example, we see in java.lang.Thread.java:
----------------------------------
-updated 12/6/2020 -- note about restrictions on long, including BitSet and Scanner
-updated 3/21/2020 -- adds note about HashMap, Hashtable, and HashSet iterator ordering
-updated 3/20/2020 -- adds note about interning, new String("xxx"), and "xxx"
-updated 2/26/2020 -- adds Graphics.setClip issue
-updated 12/22/19 -- additional issues
-updated 11/03/19 -- adds information about File.exists() and points to src/javajs/async
-updated 10/26/19 -- adds information about File.createTempFile()
-updated 8/16/19 -- minor typos and added summary paragraph
-updated 7/19/19 -- clarification that AWT and Swing classes are supported directly
-updated 5/13/19 -- Mandarin U+79D8 reserved character; Missing Math methods; int and long
-updated 5/10/19 -- adds a section on static issues in multi-(duplicate)-applet pages
-updated 1/4/19 -- nio
-updated 9/15/18 -- adds integer 1/0 == Infinity
-updated 7/24/18 -- most classes replaced with https://github.com/frohoff/jdk8u-jdk
-updated 6/5/17 -- reserved package name "window"
-updated 3/11/17 -- myClass.getField
-updated 3/7/17 -- overloading of JSplitPane.setDividerLocation
-updated 3/2/17 -- more indication of classes not implemented (KeyListener)
=============================================================================
SwingJS and OpenJDK 8+
and for all practical purposes it will appear that Java is running.
+The goal of java2script/SwingJS is NOT to reproduce Java byte code processing in a
+browser. We leave that task and its own issues to others. Here, instead, we have a
+working JavaScript version of the Java classes along with runtime assistance in the
+j2sClazz.js library. This design has several advantages:
+
+ 1) It leads to much smaller downloads, since the class loader can dynamically load
+ code at the class level.
+
+ 2) It allow the browser to use its own optimizations and features, not to ignore those.
+ This leads to huge performance gains and in many cases much simpler coding.
+
+ 3) It allows for in-browser debugging and analysis.
+
+ 4) It allows for code switching between Java and JavaScript. Working Java code
+ can be annotated (@j2sNative, @j2sAlias, @j2sIgnore) in a fashion that
+ allows the code to run slightly differently in a Java than a JavaScript environment.
+ For example:
+
+ int delayMS = /** @j2sNative 10 ||*/2;
+
+ will read "var delayMS = 10 || 2;" (i.e. 10) in JavaScript but read by the Java
+ compiler as "int delayMS = 2".
+
+ 5) Just generally, it allows for a much more integrated environment. JavaScript on
+ the page can call into any SwingJS program, and, likewise, any SwingJS code can
+ access anything on the page.
+
Method and Field Disambiguation
-------------------------------
-SwingJS has no problem with the overloading of methods, for example:
+This is no problem. SwingJS has no problem with the overloading of methods, for example:
public void print(int b);
public void print(float b);
Clazz.newMeth(C$, 'c$$S', function (text) {...});
-Field disambiguation involves prepending. In Java, a class and its subclass
-can both have the same field name, such as
+Field disambiguation involves prepending.
+
+In Java, a class and its subclass can both have the same field name, such as
boolean visible;
since JavaScript does not have the "super" keyword.
-
-
Parameterless methods such as toString() are appended with "$" to become toString$().
The one exception to this rule is private methods, which are saved in (truly) private
array in the class (and are not accessible by reflection). Private parameterless
This renaming of methods has a few consequences, which are discussed more fully below.
See particularly the section on "qualified field and method names", where it is described
how you can use packages or classes or interfaces with ".api.js" in them to represent JavaScript
-objects for which all method names are to be left unqualified. Note that it is not
-possible to cherry-pick methods to be unqualified; only full packages, classes or
-interfaces can hold this status.
+objects for which all method names are to be left unqualified, and how individual methods
+can have more than one name using @j2sAlias.
The swingjs.api.js package in particular contains a number of useful interfaces that
you can import into your project for JavaScript-specific capabilities.
some refactoring of the Java to make it more efficient in both Java and JavaScript.
"for" loops need to be more carefully crafted; use of "new" and "instanceof" need to be
minimized in critical areas. Note that method overloading -- that is, the same method name
-with different parameters, such as read(int) and read(byte) -- is no longer any problem.
-
+with different parameters, such as read(int) and read(byte) -- is no longer any problem.
Threads
-------
The key is to create a state-based run() that can be exited and re-entered in JavaScript.
+The javajs.async package can be added to any Java program to provide Java+JavaScript asynchronous
+classes, including AsyncColorChooser, AsyncDialog, AsyncFileChooser, and AsyncSwingWorker. All
+of these classes work just as well in Java as in JavaScript. There is no need to run them
+only when in JavaScript.
Static fields
-------------
The SwingJS library is the swingjs/ package. There are interfaces that may be of assistance
in swingjs/api, but other than that, it is not recommended that developers access classes in
-this package. The "public" nature of their methods is really an internal necessity.
+this package. The "public" nature of their methods is really an internal necessity. Most access
+to this package in working Java should be via the swingjs.api.JSUtilI interface.
In addition to swingjs/, though, there are several useful classes in the javajs/ package
that could be very useful. This package is a stand-alone package that can be
Fortunately, they are not common, and those that are present in Java (for example, in calculating
checksums in ZIP file creation) are at a low enough level that most developers do not utilize them
or do not even have access to them. All native calls in Java classes have been replaced by
-Java equivalents.
+Java or JavaScript equivalents.
Swing GUI Peers and UIClasses
-----------------------------
One of the biggest adaptations introduced in SwingJS is in the area of the graphical
-user interface. The issue here is complex but workable. In Java there are two background
-concepts -- the Component "peer" (one per "heavy-weight" component, such as a Frame) and the
-component "uiClass" (one per component, such as JButton or JTextField).
+user interface. Basically, what we have is a Java Swing "LookAndFeel" customized for HTML.
+
+The issue here is complex but workable. In Java there are two background concepts -- the
+Component "peer" (one per "heavy-weight" component, such as a Frame) and the
+component "uiClass" (one per component, such as BasicButtonUI or BasicTextFieldUI).
Peers are native objects of the operating system. These are the virtual buttons and text areas
-that the user is interacting with at a very base level. Their events are being passed on to
-Java or the browser by the operating system. UI classes provide a consistent "look and feel"
-for these native objects, rendering them onto the native window canvas and handling all
-user-generated events. They paint the borders, the backgrounds, the highlights, of every
-control you see in Java. There is one-to-one correspondence of Swing classes and UI classes.
-Setting the Look and Feel for a project amounts to selecting the directory from which to draw
-these UI classes. The UI classes can be found in the javax.swing.plaf ("platform look and feel")
-package.
+that the user is interacting with at a very base level. They are chunks of low-level code that
+paint the screen to give the illusion that you really are pressing a button or typing text
+ot the screen. Their events are being passed on to Java or the browser by the operating system.
+
+UI classes provide a consistent "look and feel" for these native objects, rendering them onto
+the native window canvas and handling all user-generated events. They paint the borders,
+the backgrounds, the highlights, of every control you see in Java. There is one-to-one
+correspondence of Swing classes and UI classes. Setting the Look and Feel for a project amounts
+to selecting the directory from which to draw these UI classes. Java's UI class interfaces can
+be found in the javax.swing.plaf ("platform look and feel") package. Individual look and feel
+implementations are found in sun.plaf.basic, sun.plaf.metal, and other such specialized packages.
Early on in the development of SwingJS, we decided not to fully reproduce the painfully detailed
bit-by-bit painting of controls as is done in Java. Instead, we felt it was wiser to utilize the standard
design choice posed a huge headache for Swing class developers.
For SwingJS, we decided from the beginning NOT to allow this mixed-mode programming and
-instead to require that all components be Swing components.
-
-However, this is no longer an issue. All AWT components in SwingJS are now subclasses of
-javax.swing.JComponent. So far, we have found no problem with this.
+instead to require that all components be Swing components. However, this is not really an
+issue. We have reconfigured the class relationships a bit. In SwingJS, all AWT components
+are now subclasses of javax.swing.JComponent. While this might seem error prone, so far we have
+found no problem with this arrangement. It's a little surprising to me that the original developers
+of Swing did not think of this.
The a2s Adapter Package
The solution turned out to be simple: Write a package (a2s) that recreates the interface for
non-Swing components as subclasses of Swing components. Thus, a2s.Button subclasses javax.swing.JButton
but also accepts all of the methods of java.awt.Button. This works amazingly well, with a few
-special adaptations to the core javax.swing to be "AWT-aware." All AWT components now subclass
-a2s components, which in turn subclass JComponents. So no changes in code are necessary. We have
-successfully transpiled over 500 applets using this strategy. (Kind of surprising, actually, that
-the original Java developers did not see that option. But we have a hindsight advantage here.)
+special adaptations to the core javax.swing to be "AWT-aware."
+Then, to tie it all togeter, all AWT components such as java.awt.Button now subclass their respective
+a2s components, which in turn subclass JComponents. So no changes in code are necessary. We have
+successfully transpiled over 500 applets using this strategy.
Working with Files
==================
Simple String file names are not optimal for passing information about
-read files within SwingJS applications.
+files read by SwingJS applications. That is because just peeking at a file
+in SwingJS will load its entire byte[] data.
-All work with files should either use Path or File objects exclusively.
+Optimally, all work with files should either use Path or File objects exclusively.
These objects, after a file is read or checked for existence, will already
-contain the file byte[] data. Doing something like this:
-
-File f = File("./test.dat");
-boolean isOK = f.exists();
-
-will load f with its byte[] data, if the file exists.
-
-But if after that, we use:
-
-File f2 = new File(f.getAbsolutePath());
-
-f2 will not contain that data. Such copying should be done as:
-
-File f2 = new File(f);
-
-in which case, the byte[] data will be transferred.
-
+contain the file byte[] data. The string name can be used alone, since SwingJS will
+cache the files itself and not reload them -- just as the browser normally does.
SwingJS uses the following criteria to determine if File.exists() returns true:
Temporary files can be created in SwingJS. SwingJS will maintain a pseudo-filesystem for files
created with File.createTempFile(). This is useful in that closure of writing to a temporary file
-does not generate a pseudo-download to the user's machine.
+does not generate a pseudo-download to the user's machine. Temporary files will be placed in the
+"/TEMP/" directory, as seen from the running Java program. Any file written to this directory will
+simply be stored in memory; files written to any other directory, when closed, will appear to the
+user as a download, often involving a "What do you want to do with this file" dialog.
+
+
+See below for details relating to each of the subjects below:
UNIMPLEMENTED CLASSES BY DESIGN
TODO LIST FOR UNIMPLEMENTED CLASSES
===================================
-JEditorPane (minimal implementation) - DONE 12/2018; some issues still
-JSplitPane - DONE 8/2018
-JTabbedPane - DONE 10/2018
-JTree - done 12/2019
+none as of 2020.12.31. Source code for classes and methods missing
+from Java 8 or from Java 9+ can be inserted by any developer along
+with their running code source, and they should run.
MINOR ISSUES--required some rewriting/refactoring by Bob and Udo
See below for a full discussion.
-Restrictions on long
-Restriction on BitSet and Scanner
+primitive type restrictions - int, long, and float
HashMap, Hashtable, and HashSet iterator ordering
interning, new String("xxx") vs "xxx"
Names with "$" and "_"
-positive integers do not add to give negative numbers
ArrayIndexOutOfBounds
java.awt.Color
native methods
"window" and other reserved JavaScript names
reserved field and method names
qualified field and method names
-missing Math methods
Component.getGraphics(), Graphics.dispose()
Graphics.setClip()
threads
modal dialogs
image loading
-BigDecimal not fully implemented
no format internationalization
-no winding rules
+Graphics2D: missing winding rules
text-related field implementation
Formatter/Regex limitations
-integer 1/0 == Infinity
========================================================================
Table row/col sorter needs checking after removal of java.text.Collator references
-I had to move all of SunHints class to RenderingHints, or the
-two classes could not be loaded. Shouldn't be a problem, I think. The sun classes are
-not accessible to developers in Java anyway, since they are generally package private.
-
==========================================================================
//////////////////////////////////////////////////////////////////////////////
MINOR ISSUES--requiring some rewriting/refactoring outside of SwingJS
=====================================================================
-restrictions on long
---------------------
+primitive restrictions - int, long, and float
+---------------------------------------------
-Java's 64-bit long type is not supported in JavaScript. There is no Int64Array in JavaScript,
-and 0x20000000000000 + 1 evaluates to 0x20000000000000, not 0x20000000000001.
-(Likewise, -0x20000000000000 - 1 is left unchanged.)
+int
-The largest "integer" value in JavaScript is 9007199254740991 (9.007199254740991E13, or 0x1FFFFFFFFFFFFFF).
-Effectively, you get to use only 53 bits of the long, not 64. Trying to set a long larger than
-0x1FFFFFFFFFFFFFF or smaller than -0x1FFFFFFFFFFFFFF will result in a NumberFormatException.
+For performance reasons, int addition and multiplication do not by default overflow to
+negative values. Instead, they just get bigger. Java code that relies on overflow to
+negative values should be surrounded by ()|0 -- an OR with integer 0:
-The transpiler handles conversion to long the same as Java for all cases other than from double.
-For small double values, there is no problem, and, in fact, this is a known trick used to round
-doubles and floats toward zero:
+int bigI, bigJ;
+...
-double d;
-d = (long) 3.8;
-assert(d == 3);
-d = (long) -3.8;
-assert(d == -3);
+bigI = (bigI + bigJ)|0;
-SwingJS will evaluate (long) d as 0 for d > 9007199254740991
-or d < -9007199254740991, same as Java returns for Double.NaN.
-So, in Java we have:
+bigI = (bigI + 1)|0; //instead of bigI++
- assert(((long) Double.NaN) == 0);
- assert(((int) Double.NaN) == 0);
- assert(((long) Float.NaN) == 0);
- assert(((int) Float.NaN) == 0);
-and also, in JavaScript only, we also have:
+Thus, in Java, the following is true:
- double d = 0x2000000000000L;
- assert(((long) d) == 0);
+ 2000000000 + 2000000000 == -294967296
+But in SwingJS, that will be 4000000000. So, for example, the following
+strategy will fail in SwingJS:
-restrictions on BitSet and Scanner
-----------------------------------
+ int newLength = lineBuf.length * 2;
+ if (newLength < 0) {
+ newLength = Integer.MAX_VALUE;
+ }
+
+This is because, generally, "-1" in JavaScript is not 0xFFFFFFFF. The simple ()|0 takes
+caes of this:
-Because of the issue of long being only 53 bits, any time a method returns a long value, considerations must
-be made as to whether this will work in JavaScript. In particular, BitSet and Scanner have issues.
+ int newLength = (lineBuf.length * 2)|0;
+ if (newLength < 0) {
+ newLength = Integer.MAX_VALUE;
+ }
-In SwingJS, java.util.BitSet has been implemented as a 32-bit integer-based bitset. This was no problem in
-Java 6, but starting with Java 7, a method was added to BitSet that allows for the extraction of the
-underlying long[] word data. This is not work in JavaScript. Instead, SwingJS java.util.Bitset.toLongArray() will deliver
-32-bit int[] data.
+JavaScript does process bitwise operators & | ^ ~ properly for int values. There is no issue using
+these operations.
-SwingJS Scanner has hasNextLong() and nextLong(), and although it will scan through long numbers,
-Scanner will choke on long numbers greater than the JavaScript 53-bit limit. hasNextLong() will
-return false, and nextLong() will throw an InputMismatchException triggered by the NumberFormatException
-thrown by Long.parseLong().
+Note that int 1/0 in Java throws "java.lang.ArithmeticException: / by zero", but in JavaScript is just Infinity.
+
+Importantly, the JavaScript Int32Array does behave properly. From the Firefox developer console:
+
+>> x = new Int32Array(1)
+<- Int32Array(1) [ 0 ]
+>> x[0] = 4000000000
+<- 4000000000
+>> x[0]
+<- -294967296
+
+Notice that, perhaps unexpectedly, the following two constructs produce
+different results in JavaScript:
+
+x = new Int32Array(1);
+b = x[0] = 4000000000;
+
+(b will be 4000000000)
+
+and
+
+x = new Int32Array(1);
+x[0] = 4000000000;
+b = x[0];
+
+(b will be -294967296)
+
+
+SwingJS leverages array typing to handle all byte and short arithmetic so as
+to ensure that any byte or short operation in JavaScript does give the same
+result in Java.
+
+long
+
+Java's 64-bit long type is fully supported, starting with java2script 3.3.1 (2020.12.31)
+The transpiler handles all conversions to and from long appropriately. See the discussion
+at https://github.com/BobHanson/java2script/issues/202 for how this is done.
+
+float
+
+SwingJS does not distinguish between float and double. Everything is double.
HashMap, Hashtable, and HashSet iterator ordering
whenever all keys are strictly of JavaScript typeof "string". If any key is introduced that is not a string, the
implementation falls back to using hash codes, the same as Java.
-Note strings created using new String("xxxx") are NOT typeof "string"; they are typeof "object".
-
The result is significantly faster performance (3-12 x faster) than originally, and up to 3 x faster
-performance in JavaScript than in Java itself. Right. Faster than Java.
+performance in JavaScript than in Java itself. That is not a misprint. Faster than Java.
The JavaScript Map implementation is implemented UNLESS the constructor used is the one that
specifies both initial capacity and load factor in their constructor. Thus,
methods that return new String(), and those classes that do that would cause a JavaScript error
if implicitly stringified if new String() returned a JavaScript String object.
-This is fine in JavaScript
+This is fine in JavaScript:
test1 = function() { return { toString:function(){ return "OK" } } }
"testing" + new test1()
assert(new String("xxx") != "xxx");
assert(new String("xxx") != new String("xxx"));
-But the following two fail to assert true:
+But the following two fail to assert true in SwingJS:
assert("xxx" != "xx" + a);
assert("xxx" != "xx" + a.toString());
-because in JavaScript, both of these right-side expressions evaluate to a simple "interned" string.
+because, in JavaScript, both of these right-side expressions evaluate to a simple "interned" string.
In Java, however, these assertions are true because Java implicitly "boxes" String
concatentaion as a String object, not a literal.
My recommendation, if you need to use IdentityHashMap with strings is to always use an explicit String.intern()
for any keys -- unless you really want to keep every string as separate keys even if they are the same sequence,
-in which case, use new String(). This will work in Java and in JavaScript.
+in which case, use new String(). This will work in Java and in JavaScript.
Be aware when working with strings that come from SwingJS and are being used by other JavaScript modules
that those that are String objects will return "object" for the JavaScript typeof operator, not "string".
unless you are certain that the string is being returned is a raw JavaScript string.
+
Names with "$" and "_"
----------------------
creating the fully qualified JavaScript name.
-positive integers do not add to give negative numbers
------------------------------------------------------
-
-In Java, the following is true:
-
- 2000000000 + 2000000000 == -294967296
-
-But in SwingJS, that will be 4000000000. So, for example, the following
-strategy will fail in SwingJS:
-
- int newLength = lineBuf.length * 2;
- if (newLength < 0) {
- newLength = Integer.MAX_VALUE;
- }
-
-"-1" in JavaScript is not 0xFFFFFFFF.
-
-And one must take care to not compare a negative number with a 32-bit mask. So
-
-(b & 0xFF000000) == 0xFF000000
-
-is true in Java for (int) b = -1, but is false in JavaScript, because 0xFF000000 is 4278190080,
-while (-1 & 0xFF000000) is, strangely enough, -16777216, and, in fact,
-
-(0xFF000000 & 0xFF000000) != 0xFF000000
-
-because -16777216 is not 4278190080.
-
-The fix is that one must compare similar operations:
-
-if ((b & 0xFF000000) == (0xFF000000 & 0xFF000000)) .....
-
-Importantly, the JavaScript Int32Array does behave properly. From
-the Firefox developer console:
-
->> x = new Int32Array(1)
-<- Int32Array(1) [ 0 ]
->> x[0] = 4000000000
-<- 4000000000
->> x[0]
-<- -294967296
-
-Notice that, perhaps unexpectedly, the following two constructs produce
-different results in JavaScript:
-
-x = new Int32Array(1);
-b = x[0] = 4000000000;
-
-(b will be 4000000000)
-
-and
-
-x = new Int32Array(1);
-x[0] = 4000000000;
-b = x[0];
-
-(b will be -294967296)
-
-
-SwingJS leverages array typing to handle all byte and short arithmetic so as
-to ensure that any byte or short operation in JavaScript does give the same
-result in Java. The design decision to not also do this with integer math was
-a trade-off between performance and handling edge cases.
-
-
ArrayIndexOutOfBounds
---------------------
will work in Java but not in JavaScript. Code should not depend upon this sort
of trap anyway, if you ask me.
+
Throwable vs Error vs Exception
-------------------------------
Error and Exception as well. So if you want to be sure to catch any JavaScript
error, use try{}catch (Throwable t){}, not try{}catch (Exception e){}.
-j
-ava.awt.Color
+java.awt.Color
--------------
ColorSpace: only "support" CS_sRGB.
javax.swing.JOptionPane dialogs
-------------------------------
-For this action to work, the parentComponent must implement
+For a full discussion of modal dialogs, see the javajs.asyc.AsyncDialog.java discussion.
+
+For this action to work, the parent component must implement
propertyChangeListener, and any call to JOptionPanel should allow for
an asynchronous response, meaning that there is no actionable code following the
call to the dialog opening.
-For full compatibility, The calling method must not continue beyond this
-call.
+For full compatibility, The calling method must not continue beyond this call.
-All of the standard Java events associated with Components are also
-available.
+All of the standard Java events associated with Components are also available.
Certain fall back mechanisms are possible, where onReturn does not exist, but
only for the following cases:
*/
Note that if you follow that directly with a {...} block, then
- the javadoc code will run in JavaScript, and the {...} code will run in Java.
+ only the javadoc code will run in JavaScript, and only the {...} code will run in Java.
key Focus
No reserved top-level JavaScript name is allowed for a package name. So, for example,
one must rename packages such as "window" or "document" to names such as "win" or "doc".
+
reserved field and method names
-------------------------------
would be if you use that character followed by certain English words in certain classes. For example
\u79D8canvas for JComponents (in java.awt.JSComponent) and \u79D8byte (in java.io.File).
+
qualified field and method names
--------------------------------
parameters, such as write(int) and write(double), must not have the same name in JavaScript. (In this
case, we will have write$I and write$D.) However, in certain cases it may be desirable to leave the
method names unqualified. In particular, when an interface actually represents a JavaScript object,
-the transpiler can leave a method name unqualified. The default situation for this is a class name
-includes ".api.js" (case-sensitive). This means that any method in any class in a package js within
-a package api, or any private interface js that has an outer interface api, will have all-unqualified
-methods. An example of this is swingjs.plaf.JSComboPopupList, which needs to communicate with a jQuery
+the transpiler can leave a method name unqualified.
+
+You can implement a simple name for a method using the @j2sAlias annoation in the javadoc for the
+method involved. For example:
+
+
+/**
+ * @j2sAlias read
+ *
+ */
+public void read(byte[] buf, int pos, int len) {...}
+
+will allow the method to be accesible either as "read" or "read$BA$I$I" in JavaScript.
+
+
+The default situation for this is a class name includes ".api.js" (case-sensitive).
+This means that any method in any class in a package js within a package api, or any private interface js
+that has an outer interface api, will have all-unqualified methods. An example of this is
+swingjs.plaf.JSComboPopupList, which needs to communicate with a jQuery
object directly using the following interface:
private interface api {
Notice that all these variants of j2sCB() will call the same method in JavaScript by design.
-missing Math methods
---------------------
-
-java.lang.Math is worked out, but some methods are missing, either because they
-involve long integer value that are inaccessible in JavaScript, or because I just
-didn't implement them. This is a result of continued Java development.
-It is easy enough to add these methods if you have the source. They go into j2sClazz.js,
-which is combined with other initial libraries into swingjs2.js by build_site.xml
-
-
Component.getGraphics(), Graphics.dispose()
-------------------------------------------
Use of component.getGraphics() is discouraged in Java and in SwingJS.
Specifically in SwingJS, any call to component.getGraphics() or
BufferedImage.createGraphics() or Graphics.create(...) should be matched with graphics.dispose(),
-particularly when it is called outside the context of a paint(Graphics)
-call from the system.
+particularly when it is called outside the context of a paint(Graphics) call from the system.
If you see your graphics scrolling down the page with each repaint,
look for where you have used Component.getGraphics() and not Graphics.dispose().
...
Graphics.setClip(oldClip);
-If you need to do something like this, you must schedule the paints
-to not have overlapping clip needs.
+If you need to do something like this, you must schedule the paints to not have overlapping clip needs.
MAJOR ISSUES--for Bob and Udo within SwingJS
java.awt.Toolkit
java.awt.GraphicsEnvironment
-
-
+
which are created using Class.forName are implemented using classes in the swingjs package.
-AWTAccessor is not implemented.
+sun.awt.AWTAccessor is not implemented.
AWT component peers and component "ui" user interfaces
References to such objects have been removed, but clearly there must be
some connection to similar DOM objects, even for "light-weight" components.
-
MAJOR ISSUES--to be resolved by implementers
============================================
}
}
+
image loading
-------------
- All image loading in SwingJS is synchronous. A MediaTracker call will immediately return "complete".
BigInteger and BigDecimal
-------------------------
-java.math.BigInteger is fully supported; java.math.BigDecimal is roughed
-in and not fully tested (07/2019).
+java.math.BigInteger and java.math.BigDecimal are fully supported.
-Both classes present significant issues for JavaScript, as they are based in
-Java's 64-bit long for all their operations. Here is the JavaDoc note I added
-to BigInteger:
-
- * SwingJS note: Because of the limitations of JavaScript with regard
- * to long-integer bit storage as a double, this implementation drops
- * the integer storage bit length to 24, giving 48 for long and leaving
- * the last 16 bits clear for the exponent of the double number. This should
- * not affect performance significantly. It does increase the storage
- * size by about 33%. By bringing an "int" to 3 bytes, we can easily construct
- * and use byte[] data intended for the original BitSet.
-
-"Easily" may be a bit strong there. This was a serious challenge.
-
-BigDecimal seems to run normally, but in order to do that, my hack involves
-reducing the size of an integer that is allowed to be stored as such and not
-in byte[] as a BigInteger. I'm sure there is a performance hit, but it does work.
no format internationalization
------------------------------
-For now, just en for number and date formatters
+For now, just "en" for number and date formatters
-no winding rules
-----------------
- When filling a graphic, only nonzero winding rule is implemented in HTML5 Canvas2D.
+missing winding rules
+---------------------
+
+When filling a graphic, only nonzero winding rule is implemented in HTML5 Canvas2D.
key value even after SwingUtilities.invokeLater() is called. Thus, key pressed actions may need
to be recorded after a key released event instead.
+
Formatter/Regex limitations
---------------------------
java.util.Formatter will function correctly for all standard %... patterns.
-integer 1/0 == Infinity
------------------------
+In addition, JavaScript does not implement some of the more arcane POSIX {...} formats.
+From java.util.regex.Pattern.java, we find the listing of conversions SwingJS does use:
+
+ "\\p{javaWhitespace}","\\s",
+ "\\p{javaDigit}","\\d",
+ "\\p{Lower}", "[a-z]",
+ "\\p{Upper}", "[A-Z]",
+ "\\p{ASCII}", "[\u0000-\u007F]",
+ "\\p{Alpha}", "[A-Za-z]",
+ "\\p{Digit}", "[0-9]",
+ "\\p{Alnum}", "[A-Za-z0-9]",
+ "\\p{Punct}", "[!\"#$%&'\\(\\)\\*\\+,-./:;<=>?@\\[\\\\\\]^_`{\\|}~]",
+ "\\p{Graph}", "[A-Za-z0-9]!\"#$%&'\\(\\)\\*\\+,-./:;<=>?@\\[\\\\\\]^_`{\\|}~]",
+ "\\p{Print}", "[A-Za-z0-9]!\"#$%&'\\(\\)\\*\\+,-./:;<=>?@\\[\\\\\\]^_`{\\|}~]",
+ "\\p{Blank}", "[ \t]",
+ "\\p{Cntrl}", "[\u0000-\u001F\u007F]",
+ "\\p{XDigit}", "[0-9a-fA-F]",
+ "\\p{Space}", "[ \t\n\u000B\f\r]",
+ "\\p{javaLowerCase}", "[a-z]",
+ "\\p{javaUpperCase}", "[A-Z]",
+ "\\p{Sc}", "[\u0024\u00A2\u00A3\u00A4\u00A5\u058F\u060B\u07FE\u07FF\u09F2\u09F3\u09FB\u0AF1\u0BF9\u0E3F\u20A0\u20A1\u20A2\u20A3\u20A4\u20A5\u20A6\u20A7\u20A8\u20A9\u20AA\u20AB\u20AC\u20AD\u20AE\u20AF\u20B0\u20B1\u20B2\u20B3\u20B4\u20B5\u20B6\u20B7\u20B8\u20B9\u20BA\u20BB\u20BC\u20BD\u20BE\u20BF\uA838\uFDFC\uFE69\uFF04\uFFE0\uFFE1\uFFE5\uFFE6]"
+
+Java's \Q \E quoting is handled appropriately.
-1/0 in Java throws "java.lang.ArithmeticException: / by zero", but in JavaScript is just Infinity.
-
+Additional Issues
+-----------------
+
+Method reflection is limited. Fields and methods do not retain public or default characteristics.
+(This could be easily adapted, though.) Interfaces do not expose their methods, as the transpiler does not
+actually transpile the interfaces themselves unless they contain default methods.
+And method reflection only includes annotated methods.
+
+java.util.concurrent is not fully elaborated. This package is rewritten to not actually use the
+memory handling capabilities of concurrency, which JavaScript does not have access to.
+
+System.getProperties() just returns a minimal set of properties.
Summary
may or may not be present with the JAR or class files. Use class files at your own risk.
Bob Hanson
-2019.08.16
-
-
-Additional Issues
------------------
-
-Annotation is working for classes, methods, and fields (12/22/19). Method reflection, however,
-is limited. Interfaces do not expose their methods, as the transpiler does not actually transpile
-the interfaces themselves. And method reflection only includes annotated methods.
-
-java.util.concurrent is not fully elaborated. This package is rewritten to not actually use the
-memory handling capabilities of concurrency, which JavaScript does not have access to.
-
-System.getProperties() just returns a minimal set of properties.
-20201222130550
+20210728172208
--- /dev/null
+This is sources/net.sf.j2s.java.core/dist/DEV_NOTES.txt
+
+_j2sclasslist.txt
+
+the list of .js files concatenated into coreswingjs.js and minified to coreswingjs.z.js
+
+
+SwingJS-site.zip
+
+the full site directory for SwingJS including all files not in the test/ directory.
--- /dev/null
+java/applet/Applet.js
+java/applet/AppletContext.js
+java/applet/AppletStub.js
+java/applet/JSApplet.js
+java/awt/ActiveEvent.js
+java/awt/Adjustable.js
+java/awt/AWTEvent.js
+java/awt/AWTEventMulticaster.js
+java/awt/AWTKeyStroke.js
+java/awt/BasicStroke.js
+java/awt/BorderLayout.js
+java/awt/Button.js
+java/awt/Color.js
+java/awt/color/ColorSpace.js
+java/awt/Component.js
+java/awt/ComponentOrientation.js
+java/awt/ContainerOrderFocusTraversalPolicy.js
+java/awt/Container.js
+java/awt/Cursor.js
+java/awt/DefaultFocusTraversalPolicy.js
+java/awt/DefaultKeyboardFocusManager.js
+java/awt/Dialog.js
+java/awt/Dimension.js
+java/awt/dnd/peer/DropTargetPeer.js
+java/awt/event/ActionListener.js
+java/awt/event/AdjustmentEvent.js
+java/awt/event/AdjustmentListener.js
+java/awt/event/AWTEventListener.js
+java/awt/event/ComponentAdapter.js
+java/awt/event/ComponentEvent.js
+java/awt/event/ComponentListener.js
+java/awt/event/ContainerListener.js
+java/awt/event/FocusEvent.js
+java/awt/event/FocusListener.js
+java/awt/event/HierarchyBoundsListener.js
+java/awt/event/HierarchyListener.js
+java/awt/event/InputEvent.js
+java/awt/event/InputMethodListener.js
+java/awt/event/InvocationEvent.js
+java/awt/event/ItemEvent.js
+java/awt/event/ItemListener.js
+java/awt/event/KeyListener.js
+java/awt/event/MouseEvent.js
+java/awt/event/MouseListener.js
+java/awt/event/MouseMotionListener.js
+java/awt/event/MouseWheelListener.js
+java/awt/event/TextListener.js
+java/awt/event/WindowAdapter.js
+java/awt/event/WindowEvent.js
+java/awt/event/WindowFocusListener.js
+java/awt/event/WindowListener.js
+java/awt/event/WindowStateListener.js
+java/awt/EventDispatchThread.js
+java/awt/EventFilter.js
+java/awt/EventQueue.js
+java/awt/EventQueueItem.js
+java/awt/FlowLayout.js
+java/awt/FocusTraversalPolicy.js
+java/awt/Font.js
+java/awt/font/FontRenderContext.js
+java/awt/FontMetrics.js
+java/awt/Frame.js
+java/awt/geom/AffineTransform.js
+java/awt/geom/Dimension2D.js
+java/awt/geom/Path2D.js
+java/awt/geom/PathIterator.js
+java/awt/geom/Point2D.js
+java/awt/geom/Rectangle2D.js
+java/awt/geom/RectangularShape.js
+java/awt/geom/RectIterator.js
+java/awt/GraphicsCallback.js
+java/awt/GraphicsConfiguration.js
+java/awt/GraphicsDevice.js
+java/awt/GraphicsEnvironment.js
+java/awt/Image.js
+java/awt/image/ImageObserver.js
+java/awt/Insets.js
+java/awt/ItemSelectable.js
+java/awt/JSComponent.js
+java/awt/JSDialog.js
+java/awt/JSFrame.js
+java/awt/JSPanel.js
+java/awt/KeyboardFocusManager.js
+java/awt/KeyEventDispatcher.js
+java/awt/KeyEventPostProcessor.js
+java/awt/Label.js
+java/awt/LayoutManager.js
+java/awt/LayoutManager2.js
+java/awt/LightweightDispatcher.js
+java/awt/Paint.js
+java/awt/Panel.js
+java/awt/peer/ComponentPeer.js
+java/awt/peer/ContainerPeer.js
+java/awt/peer/FramePeer.js
+java/awt/peer/KeyboardFocusManagerPeer.js
+java/awt/peer/LightweightPeer.js
+java/awt/peer/WindowPeer.js
+java/awt/Point.js
+java/awt/Queue.js
+java/awt/Rectangle.js
+java/awt/RenderingHints.js
+java/awt/Scrollbar.js
+java/awt/ScrollPane.js
+java/awt/Shape.js
+java/awt/Stroke.js
+java/awt/TextArea.js
+java/awt/TextComponent.js
+java/awt/TextField.js
+java/awt/Toolkit.js
+java/awt/Transparency.js
+java/awt/Window.js
+java/beans/ChangeListenerMap.js
+java/beans/PropertyChangeEvent.js
+java/beans/PropertyChangeListener.js
+java/beans/PropertyChangeSupport.js
+java/lang/AbstractStringBuilder.js
+java/lang/Class.js
+java/lang/Enum.js
+java/lang/Iterable.js
+java/lang/reflect/Constructor.js
+java/lang/reflect/Method.js
+java/lang/StringBuffer.js
+java/lang/StringBuilder.js
+java/lang/Thread.js
+java/lang/ThreadGroup.js
+java/math/RoundingMode.js
+java/net/URL.js
+java/net/URLStreamHandlerFactory.js
+java/net/HttpURLConnection.js
+java/net/URLStreamHandler.js
+javax/net/ssl/HttpsUrlConnection.js
+java/text/CharacterIterator.js
+java/text/DecimalFormat.js
+java/text/DecimalFormatSymbols.js
+java/text/DigitList.js
+java/text/FieldPosition.js
+java/text/Format.js
+java/text/NumberFormat.js
+java/util/AbstractCollection.js
+java/util/AbstractList.js
+java/util/AbstractMap.js
+java/util/AbstractSequentialList.js
+java/util/AbstractSet.js
+java/util/ArrayList.js
+java/util/Arrays.js
+java/util/Collection.js
+java/util/Collections.js
+java/util/Comparator.js
+java/util/Deque.js
+java/util/Dictionary.js
+java/util/Enumeration.js
+java/util/EventListener.js
+java/util/EventObject.js
+java/util/HashMap.js
+java/util/HashSet.js
+java/util/Hashtable.js
+java/util/IdentityHashMap.js
+java/util/Iterator.js
+java/util/LinkedHashMap.js
+java/util/LinkedList.js
+java/util/List.js
+java/util/ListResourceBundle.js
+java/util/Locale.js
+java/util/Map.js
+java/util/Objects.js
+java/util/Queue.js
+java/util/Random.js
+java/util/RandomAccess.js
+java/util/ResourceBundle.js
+java/util/Set.js
+java/util/TimSort.js
+java/util/Vector.js
+javajs/api/JSFunction.js
+javajs/util/AjaxURLConnection.js
+javajs/util/AjaxURLStreamHandlerFactory.js
+javajs/util/AU.js
+javajs/util/JSThread.js
+javajs/util/Lst.js
+javajs/util/PT.js
+javajs/util/Rdr.js
+javajs/util/SB.js
+javax/swing/AbstractAction.js
+javax/swing/AbstractButton.js
+javax/swing/AbstractListModel.js
+javax/swing/Action.js
+javax/swing/ActionMap.js
+javax/swing/AncestorNotifier.js
+javax/swing/ArrayTable.js
+javax/swing/border/AbstractBorder.js
+javax/swing/border/BevelBorder.js
+javax/swing/border/Border.js
+javax/swing/border/CompoundBorder.js
+javax/swing/border/EmptyBorder.js
+javax/swing/border/EtchedBorder.js
+javax/swing/border/LineBorder.js
+javax/swing/border/TitledBorder.js
+javax/swing/BorderFactory.js
+javax/swing/BoundedRangeModel.js
+javax/swing/BoxLayout.js
+javax/swing/ButtonGroup.js
+javax/swing/ButtonModel.js
+javax/swing/ClientPropertyKey.js
+javax/swing/ComboBoxModel.js
+javax/swing/DefaultBoundedRangeModel.js
+javax/swing/DefaultButtonModel.js
+javax/swing/DefaultComboBoxModel.js
+javax/swing/DefaultSingleSelectionModel.js
+javax/swing/DropMode.js
+javax/swing/event/AncestorEvent.js
+javax/swing/event/AncestorListener.js
+javax/swing/event/CaretEvent.js
+javax/swing/event/CaretListener.js
+javax/swing/event/ChangeEvent.js
+javax/swing/event/ChangeListener.js
+javax/swing/event/DocumentEvent.js
+javax/swing/event/DocumentListener.js
+javax/swing/event/EventListenerList.js
+javax/swing/event/ListDataEvent.js
+javax/swing/event/ListDataListener.js
+javax/swing/event/UndoableEditEvent.js
+javax/swing/event/UndoableEditListener.js
+javax/swing/FocusManager.js
+javax/swing/InternalFrameFocusTraversalPolicy.js
+javax/swing/LayoutComparator.js
+javax/swing/LayoutFocusTraversalPolicy.js
+javax/swing/SortingFocusTraversalPolicy.js
+javax/swing/SwingContainerOrderFocusTraversalPolicy.js
+javax/swing/SwingDefaultFocusTraversalPolicy.js
+javax/swing/Icon.js
+javax/swing/ImageIcon.js
+javax/swing/InputMap.js
+javax/swing/JApplet.js
+javax/swing/JButton.js
+javax/swing/JCheckBox.js
+javax/swing/JCheckBoxMenuItem.js
+javax/swing/JComboBox.js
+javax/swing/JComponent.js
+javax/swing/JFrame.js
+javax/swing/JLabel.js
+javax/swing/JLayeredPane.js
+javax/swing/JMenu.js
+javax/swing/JMenuBar.js
+javax/swing/JMenuItem.js
+javax/swing/JPanel.js
+javax/swing/JPopupMenu.js
+javax/swing/JRadioButtonMenuItem.js
+javax/swing/JRootPane.js
+javax/swing/JScrollBar.js
+javax/swing/JScrollPane.js
+javax/swing/JSeparator.js
+javax/swing/JTextArea.js
+javax/swing/JTextField.js
+javax/swing/JToggleButton.js
+javax/swing/JViewport.js
+javax/swing/KeyboardManager.js
+javax/swing/KeyStroke.js
+javax/swing/ListModel.js
+javax/swing/LookAndFeel.js
+javax/swing/MenuElement.js
+javax/swing/MutableComboBoxModel.js
+javax/swing/plaf/ActionMapUIResource.js
+javax/swing/plaf/basic/BasicBorders.js
+javax/swing/plaf/BorderUIResource.js
+javax/swing/plaf/ColorUIResource.js
+javax/swing/plaf/ComponentUI.js
+javax/swing/plaf/DimensionUIResource.js
+javax/swing/plaf/FontUIResource.js
+javax/swing/plaf/InputMapUIResource.js
+javax/swing/plaf/InsetsUIResource.js
+javax/swing/plaf/UIResource.js
+javax/swing/RepaintManager.js
+javax/swing/RootPaneContainer.js
+javax/swing/Scrollable.js
+javax/swing/ScrollPaneConstants.js
+javax/swing/ScrollPaneLayout.js
+javax/swing/SingleSelectionModel.js
+javax/swing/SizeRequirements.js
+javax/swing/SwingConstants.js
+javax/swing/SwingPaintEventDispatcher.js
+javax/swing/SwingUtilities.js
+javax/swing/text/AbstractDocument.js
+javax/swing/text/AttributeSet.js
+javax/swing/text/Caret.js
+javax/swing/text/DefaultCaret.js
+javax/swing/text/DefaultEditorKit.js
+javax/swing/text/Document.js
+javax/swing/text/EditorKit.js
+javax/swing/text/Element.js
+javax/swing/text/GapContent.js
+javax/swing/text/GapVector.js
+javax/swing/text/JTextComponent.js
+javax/swing/text/MutableAttributeSet.js
+javax/swing/text/PlainDocument.js
+javax/swing/text/PlainView.js
+javax/swing/text/Position.js
+javax/swing/text/Segment.js
+javax/swing/text/SegmentCache.js
+javax/swing/text/SimpleAttributeSet.js
+javax/swing/text/Style.js
+javax/swing/text/StyleConstants.js
+javax/swing/text/StyleContext.js
+javax/swing/text/TabExpander.js
+javax/swing/text/TextAction.js
+javax/swing/text/Utilities.js
+javax/swing/text/View.js
+javax/swing/tree/TreeNode.js
+javax/swing/UIDefaults.js
+javax/swing/UIManager.js
+javax/swing/undo/AbstractUndoableEdit.js
+javax/swing/undo/CompoundEdit.js
+javax/swing/undo/UndoableEdit.js
+javax/swing/ViewportLayout.js
+javax/swing/WindowConstants.js
+sun/awt/AppContext.js
+sun/awt/AWTAutoShutdown.js
+sun/awt/CausedFocusEvent.js
+sun/awt/ComponentFactory.js
+sun/awt/KeyboardFocusManagerPeerProvider.js
+sun/awt/MostRecentKeyValue.js
+sun/awt/MostRecentThreadAppContext.js
+sun/awt/PaintEventDispatcher.js
+sun/awt/PostEventQueue.js
+sun/awt/RequestFocusController.js
+sun/awt/SunToolkit.js
+sun/awt/WindowClosingListener.js
+sun/awt/WindowClosingSupport.js
+sun/awt/image/DataStealer.js
+sun/awt/image/IntegerComponentRaster.js
+sun/awt/image/IntegerInterleavedRaster.js
+sun/awt/image/SunWritableRaster.js
+sun/font/FontDesignMetrics.js
+sun/swing/DefaultLookup.js
+sun/swing/SwingLazyValue.js
+sun/text/resources/FormatData.js
+sun/text/resources/en/FormatData_en.js
+sun/util/resources/LocaleData.js
+sun/util/locale/BaseLocale.js
+sun/util/locale/LocaleUtils.js
+sun/util/locale/provider/LocaleProviderAdapter.js
+sun/util/locale/provider/LocaleDataMetaInfo.js
+swingjs/a2s/A2SContainer.js
+swingjs/a2s/A2SEvent.js
+swingjs/a2s/A2SListener.js
+swingjs/a2s/Applet.js
+swingjs/a2s/Button.js
+swingjs/a2s/Label.js
+swingjs/a2s/Panel.js
+swingjs/a2s/Scrollbar.js
+swingjs/a2s/ScrollPane.js
+swingjs/a2s/TextArea.js
+swingjs/a2s/TextField.js
+swingjs/api/Interface.js
+swingjs/api/js/DOMNode.js
+swingjs/api/js/HTML5CanvasContext2D.js
+swingjs/api/js/JSInterface.js
+swingjs/jquery/JQueryUI.js
+swingjs/JSApp.js
+swingjs/JSAppletThread.js
+swingjs/JSAppletViewer.js
+swingjs/JSFocusPeer.js
+swingjs/JSFontMetrics.js
+swingjs/JSFrameViewer.js
+swingjs/JSGraphics2D.js
+swingjs/JSGraphicsConfiguration.js
+swingjs/JSGraphicsEnvironment.js
+swingjs/JSImage.js
+swingjs/JSImagekit.js
+swingjs/JSMouse.js
+swingjs/JSNullComponentPeer.js
+swingjs/JSScreenDevice.js
+swingjs/JSThreadGroup.js
+swingjs/JSToolkit.js
+swingjs/JSUtil.js
+swingjs/plaf/ButtonListener.js
+swingjs/plaf/DefaultMenuLayout.js
+swingjs/plaf/HTML5LookAndFeel.js
+swingjs/plaf/JSAppletUI.js
+swingjs/plaf/JSButtonUI.js
+swingjs/plaf/JSCheckBoxMenuItemUI.js
+swingjs/plaf/JSCheckBoxUI.js
+swingjs/plaf/JSComboBoxUI.js
+swingjs/plaf/JSComponentUI.js
+swingjs/plaf/JSEventHandler.js
+swingjs/plaf/JSFrameUI.js
+swingjs/plaf/JSGraphicsUtils.js
+swingjs/plaf/JSLabelUI.js
+swingjs/plaf/JSLayeredPaneUI.js
+swingjs/plaf/JSLightweightUI.js
+swingjs/plaf/JSMenuBarUI.js
+swingjs/plaf/JSMenuItemUI.js
+swingjs/plaf/JSMenuUI.js
+swingjs/plaf/JSPanelUI.js
+swingjs/plaf/JSPopupMenuSeparatorUI.js
+swingjs/plaf/JSPopupMenuUI.js
+swingjs/plaf/JSRadioButtonMenuItemUI.js
+swingjs/plaf/JSRadioButtonUI.js
+swingjs/plaf/JSRootPaneUI.js
+swingjs/plaf/JSScrollBarUI.js
+swingjs/plaf/JSScrollPaneUI.js
+swingjs/plaf/JSSeparatorUI.js
+swingjs/plaf/JSSliderUI.js
+swingjs/plaf/JSTextAreaUI.js
+swingjs/plaf/JSTextFieldUI.js
+swingjs/plaf/JSTextUI.js
+swingjs/plaf/JSTextViewUI.js
+swingjs/plaf/JSViewportUI.js
+swingjs/plaf/JSWindowUI.js
+swingjs/plaf/LazyActionMap.js
+swingjs/plaf/Resizer.js
+swingjs/plaf/TextListener.js
+
+
--- /dev/null
+java2script/SwingJS Notes
+=========================
+
+updated 12/31/2020 -- full support for 64-bit long
+updated 12/6/2020 -- note about restrictions on long, including BitSet and Scanner
+updated 3/21/2020 -- adds note about HashMap, Hashtable, and HashSet iterator ordering
+updated 3/20/2020 -- adds note about interning, new String("xxx"), and "xxx"
+updated 2/26/2020 -- adds Graphics.setClip issue
+updated 12/22/19 -- additional issues
+updated 11/03/19 -- adds information about File.exists() and points to src/javajs/async
+updated 10/26/19 -- adds information about File.createTempFile()
+updated 8/16/19 -- minor typos and added summary paragraph
+updated 7/19/19 -- clarification that AWT and Swing classes are supported directly
+updated 5/13/19 -- Mandarin U+79D8 reserved character; Missing Math methods; int and long
+updated 5/10/19 -- adds a section on static issues in multi-(duplicate)-applet pages
+updated 1/4/19 -- nio
+updated 9/15/18 -- adds integer 1/0 == Infinity
+updated 7/24/18 -- most classes replaced with https://github.com/frohoff/jdk8u-jdk
+updated 6/5/17 -- reserved package name "window"
+updated 3/11/17 -- myClass.getField
+updated 3/7/17 -- overloading of JSplitPane.setDividerLocation
+updated 3/2/17 -- more indication of classes not implemented (KeyListener)
+
+---IMPORTANT CHARACTER SET NOTE---
+
+It is critical that all development work in Java2Script be done in UTF-8. This means:
+
+- making sure your Eclipse project is set up for UTF-8 (not the Eclipse default?)
+- making sure your server can serve up UTF-8 by default for any browser-loaded files
+- making sure you don't edit a Java2Script class file or one of the site .js files
+ using a non-UTF-8 editor. It may replace non-Latin characters with "?" or garbage.
+- making sure that your web pages are delivered with proper headings indicating HTML5 and UTF-8
+
+<!DOCTYPE html>
+<html>
+<head>
+<meta charset="utf-8">
+
+Note that the DOCTYPE tag is critical for some browsers to switch into HTML5 mode. (MSIE?)
+
+
+In particular, the Mandarin character 秘 (mi; "secret") is used extensively throughout
+the SwingJS class files to distinguish j2s-specific fields and methods that must not
+ever be shadowed or overridden by subclasses. For example, we see in java.lang.Thread.java:
+
+ public static JSThread 秘thisThread;
+
+----------------------------------
+
+
+
+=============================================================================
+SwingJS and OpenJDK 8+
+=============================================================================
+
+SwingJS implements a wide range of the Java language in JavaScript. The base
+version for this implementation is OpenJDK8. some classes are implemented using
+older source code, and there are some missing methods. For the most part, this is
+no real problem. You can add or modify any java class just be adding it as source
+in your project. Or (preferably) you can contact me, and I can get it into the
+distribution. Or (even more preferably) you can do that via a patch submission.
+
+=================
+DESIGN PHILOSOPHY
+=================
+
+The java2script/SwingJS design goal is to recreate a recognizable, easily debuggable
+equivalent in JavaScript for as much of Java as practical. This means, for example,
+that one can call in JavaScript
+
+ new java.util.Hashtable()
+
+and for all practical purposes it will appear that Java is running.
+
+The goal of java2script/SwingJS is NOT to reproduce Java byte code processing in a
+browser. We leave that task and its own issues to others. Here, instead, we have a
+working JavaScript version of the Java classes along with runtime assistance in the
+j2sClazz.js library. This design has several advantages:
+
+ 1) It leads to much smaller downloads, since the class loader can dynamically load
+ code at the class level.
+
+ 2) It allow the browser to use its own optimizations and features, not to ignore those.
+ This leads to huge performance gains and in many cases much simpler coding.
+
+ 3) It allows for in-browser debugging and analysis.
+
+ 4) It allows for code switching between Java and JavaScript. Working Java code
+ can be annotated (@j2sNative, @j2sAlias, @j2sIgnore) in a fashion that
+ allows the code to run slightly differently in a Java than a JavaScript environment.
+ For example:
+
+ int delayMS = /** @j2sNative 10 ||*/2;
+
+ will read "var delayMS = 10 || 2;" (i.e. 10) in JavaScript but read by the Java
+ compiler as "int delayMS = 2".
+
+ 5) Just generally, it allows for a much more integrated environment. JavaScript on
+ the page can call into any SwingJS program, and, likewise, any SwingJS code can
+ access anything on the page.
+
+
+Method and Field Disambiguation
+-------------------------------
+
+This is no problem. SwingJS has no problem with the overloading of methods, for example:
+
+ public void print(int b);
+ public void print(float b);
+
+JavaScript does not allow overloading of methods, and the common practice in
+Java of naming a field the same as a method -- isAllowed and isAllowed() -- is
+not possible in JavaScript. As a result, SwingJS implements "fully-qualified"
+method names using "$" parameter type separation. Thus, these methods in SwingJS
+will be referred to as print$I and print$F. The rules for this encoding are
+relatively simple:
+
+1. The seven primitive types in Java are encoded $I (int), $L (long), $F (float),
+$D (double), $B (byte) $Z (boolean), and $H (short).
+
+2. String and Object are encoded as $S and $O, respectively.
+
+3. "java_lang_" is dropped for all other classes in the java.lang package (as in Java).
+ For example: $StringBuffer, not $java_lang_StringBuffer
+
+4. All other classes are encoded as
+
+ "$" + Class.getName().replace(".","_")
+
+For example, in Java we see:
+
+ public void equals(Object o) {...}
+
+Whereas in SwingJS we have:
+
+ Clazz.newMeth(C$, 'equals$O', function (o) {...}
+
+And
+
+ this.getContentPane().add(bar, "North");
+
+becomes
+
+ this.getContentPane$().add$java_awt_Component$O(bar, "North");
+
+5. Arrays are indicated with appended "A" for each level. So
+
+ setDataVector(Object[][] dataVector, Object[] columnIdentifiers)
+
+becomes
+
+ setDataVector$OAA$OA(dataVector, columnIdentifiers)
+
+(It is recognized that this design does introduce a bit of ambiguity, in that
+ in principal there could be user class named XA and X in the same package,
+ and methods a(X[]) and a(XA) in the same class that cannot be distinguished.
+ The benefit of this simple system, however, triumphed over the unlikelyhood
+ of that scenario.) The transpiler could be set to flag this possibility.
+
+6. Constructors are prepended with "c$". So
+
+ public JLabel(String text) {...}
+
+becomes:
+
+ Clazz.newMeth(C$, 'c$$S', function (text) {...});
+
+Field disambiguation involves prepending.
+
+In Java, a class and its subclass can both have the same field name, such as
+
+ boolean visible;
+
+When this happens, it is called "shadowing", and though not recommended, Java allows
+it. The Java2Script transpiler will prepend such shadowing fields with "$" so that the
+subclass instance has both "visible" (for use in its methods inherited from its
+superclass) and "$visible" (for its own methods). Thus, we might see in Java:
+
+ this.visible = super.visible;
+
+while in SwingJS we will see:
+
+ this.$visible=this.visible;
+
+since JavaScript does not have the "super" keyword.
+
+Parameterless methods such as toString() are appended with "$" to become toString$().
+The one exception to this rule is private methods, which are saved in (truly) private
+array in the class (and are not accessible by reflection). Private parameterless
+methods retain their simple Java name, since they cannot conflict with field names.
+
+This renaming of methods has a few consequences, which are discussed more fully below.
+See particularly the section on "qualified field and method names", where it is described
+how you can use packages or classes or interfaces with ".api.js" in them to represent JavaScript
+objects for which all method names are to be left unqualified, and how individual methods
+can have more than one name using @j2sAlias.
+
+The swingjs.api.js package in particular contains a number of useful interfaces that
+you can import into your project for JavaScript-specific capabilities.
+
+
+Applet vs. Application
+----------------------
+
+One of the very cool aspects of SwingJS is that it doesn't particularly matter if a browser-based
+Java app is an "applet" or an "application". We don't need JNLP (Java Network Launch Protocol)
+because now we can just start up any Java application in a browser just as easily as any applet.
+The associative array that passes information to the SwingJS applet (information that formerly
+might have been part of the APPLET tag, such as width, height, and codebase, always referred to
+in our writing as "the Info array") allows the option to specify the JApplet/Applet "code"
+class or the application "main" class. Either one will run just fine.
+
+
+Performance
+-----------
+
+Obviously, there are limitations. One is performance, but we have seen reproducible
+performance at 1/6 - 1/3 the speed of Java. Achieving this performance may require
+some refactoring of the Java to make it more efficient in both Java and JavaScript.
+"for" loops need to be more carefully crafted; use of "new" and "instanceof" need to be
+minimized in critical areas. Note that method overloading -- that is, the same method name
+with different parameters, such as read(int) and read(byte) -- is no longer any problem.
+
+Threads
+-------
+
+Although there is only a single thread in JavaScript, meaning Thread.wait(), Thread.sleep(int) and
+Thread.notify() cannot be reproduced, we have found that this is not a serious limitation.
+For example, javax.swing.Timer() works perfectly in JavaScript. All it means is that threads
+that use sleep(int) or notify() must be refactored to allow Timer-like callbacks. That is,
+they must allow full exit and re-entry of Thread.run(), not the typical while/sleep motif.
+
+The key is to create a state-based run() that can be exited and re-entered in JavaScript.
+
+The javajs.async package can be added to any Java program to provide Java+JavaScript asynchronous
+classes, including AsyncColorChooser, AsyncDialog, AsyncFileChooser, and AsyncSwingWorker. All
+of these classes work just as well in Java as in JavaScript. There is no need to run them
+only when in JavaScript.
+
+Static fields
+-------------
+
+Final static primitive "constant" fields (String, boolean, int, etc.) such as
+
+static final int TEST = 3;
+static final String MY_STRING = "my " + "string";
+
+are converted to their primitive form automatically by the Eclipse Java compiler
+and do not appear in the JavaScript by their names.
+
+Other static fields are properties of their class and can be used as expected.
+
+Note, however, that SwingJS runs all "Java" code on a page in a common "jvm"
+(like older versions of Java). So, like the older Java schema, the JavaScript
+equivalents of both applets and applications will share all of their static
+fields and methods. This includes java.lang.System.
+
+Basically, SwingJS implementations of Java run in a browser page-based sandbox
+instead of an applet-specific one.
+
+In general, this is no problem. But if we are to implement pages with
+multiple applets present, we must be sure to only have static references
+that are "final" or specifically meant to be shared in a JavaScript
+environment only (since they will not be shared in Java).
+
+A simple solution, if static non-constant references are needed, is to attach the
+field to Thread.currentThread.threadGroup(), which is an applet-specific reference.
+Be sure, if you do this, that you use explicit setters and getters:
+
+For example,
+
+private static String myvar;
+
+...
+
+public void setMyVar(String x) {
+ ThreadGroup g = Thread.currentThread().threadGroup();
+ /**
+ * @j2sNative g._myvar = x;
+ *
+ */
+ {
+ myvar = x;
+ }
+}
+
+public String getMyVar() {
+ ThreadGroup g = Thread.currentThread().threadGroup();
+ /**
+ * @j2sNative return g._myvar || null;
+ *
+ */
+ {
+ return myvar;
+ }
+}
+
+ in Java will get and set x the same in JavaScript and in Java.
+
+
+A convenient way to do this in general is to supply a singleton class with
+explicitly private-only constructors and then refer to it in Java and in JavaScript
+instead of using static field, referring to myclass.getIntance().xxx instead of
+myclass.xxx in Java (and JavaScript).
+
+This was done extensively in the Jalview project. See jalview.bin.Instance.
+
+
+Helper Packages -- swingjs/ and javajs/
+---------------------------------------
+
+The SwingJS library is the swingjs/ package. There are interfaces that may be of assistance
+in swingjs/api, but other than that, it is not recommended that developers access classes in
+this package. The "public" nature of their methods is really an internal necessity. Most access
+to this package in working Java should be via the swingjs.api.JSUtilI interface.
+
+In addition to swingjs/, though, there are several useful classes in the javajs/ package
+that could be very useful. This package is a stand-alone package that can be
+cloned in any Java project that also would be great to have in any JavaScript project
+-- SwingJS-related or not. Functionality ranges from reading and writing various file
+formats, including PDF, BMP, PNG, GIF, JPG, JSON, ZIP, and CompoundDocument formats.
+
+A variety of highly efficient three- and four-dimensional point, vector, matrix, and
+quaternion classes are included, as they were developed for JSmol and inherited from that
+project.
+
+Of particular interest should be javajs/async/, which includes
+
+javajs.async.Async
+javajs.async.AsyncColorChooser
+javajs.async.AsyncDialog
+javajs.async.AsyncFileChooser
+
+See javajs.async.Async JavaDoc comments for a full description of
+these useful classes.
+
+
+Modal Dialogs
+-------------
+
+Although true modal dialogs are not possible with only one thread, a functional equivalent --
+asynchronous modal dialogs -- is relatively easy to set up. All the JOptionPane dialogs will
+return PropertyChangeEvents to signal that they have been disposed of and containing the results.
+See below and classes in the javajs.async package.
+
+
+Native calls
+------------
+
+Native calls in Java are calls to operating system methods that are not in Java. JavaScript
+has no access to these, of course, and they must all be replaced by JavaScript equivalents.
+Fortunately, they are not common, and those that are present in Java (for example, in calculating
+checksums in ZIP file creation) are at a low enough level that most developers do not utilize them
+or do not even have access to them. All native calls in Java classes have been replaced by
+Java or JavaScript equivalents.
+
+
+Swing GUI Peers and UIClasses
+-----------------------------
+
+One of the biggest adaptations introduced in SwingJS is in the area of the graphical
+user interface. Basically, what we have is a Java Swing "LookAndFeel" customized for HTML.
+
+The issue here is complex but workable. In Java there are two background concepts -- the
+Component "peer" (one per "heavy-weight" component, such as a Frame) and the
+component "uiClass" (one per component, such as BasicButtonUI or BasicTextFieldUI).
+
+Peers are native objects of the operating system. These are the virtual buttons and text areas
+that the user is interacting with at a very base level. They are chunks of low-level code that
+paint the screen to give the illusion that you really are pressing a button or typing text
+ot the screen. Their events are being passed on to Java or the browser by the operating system.
+
+UI classes provide a consistent "look and feel" for these native objects, rendering them onto
+the native window canvas and handling all user-generated events. They paint the borders,
+the backgrounds, the highlights, of every control you see in Java. There is one-to-one
+correspondence of Swing classes and UI classes. Setting the Look and Feel for a project amounts
+to selecting the directory from which to draw these UI classes. Java's UI class interfaces can
+be found in the javax.swing.plaf ("platform look and feel") package. Individual look and feel
+implementations are found in sun.plaf.basic, sun.plaf.metal, and other such specialized packages.
+
+Early on in the development of SwingJS, we decided not to fully reproduce the painfully detailed
+bit-by-bit painting of controls as is done in Java. Instead, we felt it was wiser to utilize the standard
+HTML5 UI capabilities as much as possible, using DIV, and INPUT especially, with extensive use
+of CSS and sometimes jQuery (menus, and sliders, for example). Thus, we have created a new
+set of UIs -- the "HTML5 Look and Feel". These classes can be found in swingjs.plaf. Besides being
+more adaptable, this approach allows far more versatility to SwingJS developers, allowing them
+to modify the GUI to suit their needs if desired.
+
+In SwingJS, since we have no access to native peers except through the browser DOM,
+it seemed logical to merge the peer and UI idea. So instead of having one peer per heavy-weight control and
+one UI class instance for each control type, we just have one UI class instance per control, and
+that UI class instance is what is being referred to when a "peer" is notified.
+
+In some ways this is a throw back to when all of Swing's components were subclasses of
+specific AWT components such as Button and List. These "heavy-weight components" all had their
+own individual native peers and thus automatically took on the look and feel provided by the OS.
+Later Swing versions implemented full look and feel for all peers, leaving only JDialog, JFrame,
+and a few other classes to have native peers. But in SwingJS we have again a 1:1 map of component
+and UI class/peer instance.
+
+The origin of most issues (read "bugs") in relation to the GUI will probably be found in the
+swingjs.plaf JSxxxxUI.java code.
+
+
+Swing-only Components -- no longer an issue
+-------------------------------------------
+
+Swing was introduced into Java well after the Java Abstract Window Toolkit (AWT) was well
+established. As such, its designers chose to allow AWT controls such as Button and List to be used
+alongside their Swing counterparts JButton and JList. Reading the code, it is clear that this
+design choice posed a huge headache for Swing class developers.
+
+For SwingJS, we decided from the beginning NOT to allow this mixed-mode programming and
+instead to require that all components be Swing components. However, this is not really an
+issue. We have reconfigured the class relationships a bit. In SwingJS, all AWT components
+are now subclasses of javax.swing.JComponent. While this might seem error prone, so far we have
+found no problem with this arrangement. It's a little surprising to me that the original developers
+of Swing did not think of this.
+
+
+The a2s Adapter Package
+-----------------------
+
+Originally, we thought that we would restrict ourselves to JApplets only. That is, only
+Swing-based applets. But as we worked, we discovered that there are a lot of great
+applets out there that are pre-Swing pure-AWT java.applet.Applet applets. Our problem was
+that we also wanted it to be possible to quickly adapt these applets to JavaScript as well.
+
+The solution turned out to be simple: Write a package (a2s) that recreates the interface for
+non-Swing components as subclasses of Swing components. Thus, a2s.Button subclasses javax.swing.JButton
+but also accepts all of the methods of java.awt.Button. This works amazingly well, with a few
+special adaptations to the core javax.swing to be "AWT-aware."
+
+Then, to tie it all togeter, all AWT components such as java.awt.Button now subclass their respective
+a2s components, which in turn subclass JComponents. So no changes in code are necessary. We have
+successfully transpiled over 500 applets using this strategy.
+
+Working with Files
+==================
+
+Simple String file names are not optimal for passing information about
+files read by SwingJS applications. That is because just peeking at a file
+in SwingJS will load its entire byte[] data.
+
+Optimally, all work with files should either use Path or File objects exclusively.
+These objects, after a file is read or checked for existence, will already
+contain the file byte[] data. The string name can be used alone, since SwingJS will
+cache the files itself and not reload them -- just as the browser normally does.
+
+SwingJS uses the following criteria to determine if File.exists() returns true:
+
+(1) if this File object has been used directly to read data, or
+(2) if reading data using this File object is successful.
+
+Note that you cannot check to see if a file exists before input or if it
+was actually written or if it already exists prior to writing in SwingJS.
+
+Thus, you should check each use of file.exists() carefully, and if necessary, provide a J2sNative
+block that gives an appropriate "OK" message, for example:
+
+(/** @j2sNative 1 ? false : */ outputfile.exits())
+
+or
+
+(/** @j2sNative 1 ? true : */ inputfile.exits())
+
+Temporary files can be created in SwingJS. SwingJS will maintain a pseudo-filesystem for files
+created with File.createTempFile(). This is useful in that closure of writing to a temporary file
+does not generate a pseudo-download to the user's machine. Temporary files will be placed in the
+"/TEMP/" directory, as seen from the running Java program. Any file written to this directory will
+simply be stored in memory; files written to any other directory, when closed, will appear to the
+user as a download, often involving a "What do you want to do with this file" dialog.
+
+
+See below for details relating to each of the subjects below:
+
+
+UNIMPLEMENTED CLASSES BY DESIGN
+===============================
+
+The SwingJS implementation of the following classes are present
+in a way that gracefully bypasses their functionality:
+
+accessibility
+security
+serialization
+
+
+
+TODO LIST FOR UNIMPLEMENTED CLASSES
+===================================
+
+none as of 2020.12.31. Source code for classes and methods missing
+from Java 8 or from Java 9+ can be inserted by any developer along
+with their running code source, and they should run.
+
+
+MINOR ISSUES--required some rewriting/refactoring by Bob and Udo
+================================================================
+
+Thread.currentThread() == dispatchThread
+
+
+MINOR ISSUES--requiring some rewriting/refactoring outside of SwingJS
+=====================================================================
+
+See below for a full discussion.
+
+primitive type restrictions - int, long, and float
+HashMap, Hashtable, and HashSet iterator ordering
+interning, new String("xxx") vs "xxx"
+Names with "$" and "_"
+ArrayIndexOutOfBounds
+java.awt.Color
+native methods
+javax.swing.JFileDialog
+key focus
+LookAndFeel and UI Classes
+System.exit(0) does not stop all processes
+list cell renderers must be JComponents
+myClass.getField not implemented
+"window" and other reserved JavaScript names
+reserved field and method names
+qualified field and method names
+Component.getGraphics(), Graphics.dispose()
+Graphics.setClip()
+
+MAJOR ISSUES--for Bob and Udo within SwingJS
+============================================
+
+fonts
+OS-dependent classes
+AWT component peers
+some aspects of reflection
+
+MAJOR ISSUES--to be resolved by implementers
+============================================
+
+fonts
+threads
+modal dialogs
+image loading
+no format internationalization
+Graphics2D: missing winding rules
+text-related field implementation
+Formatter/Regex limitations
+
+========================================================================
+
+DISCUSS
+=======
+
+Table row/col sorter needs checking after removal of java.text.Collator references
+
+==========================================================================
+
+//////////////////////////////////////////////////////////////////////////////
+
+UNIMPLEMENTED CLASSES
+=====================
+
+accessibility
+-------------
+
+All Accessibility handling has been commented out to save the download footprint.
+This removes the need for sun.misc.SharedSecrets as well.
+Nothing says we could not implement accessibility. We just didn't.
+
+
+security
+--------
+
+All JavaScript security is handled by the browser natively.
+Thus, Java security checking is no longer necessary, and
+java.security.AccessController has been simplified to work without
+native security checking.
+
+Note that private methods in a class are REALLY private.
+
+
+serialization
+-------------
+
+All serialization has been removed. It was never very useful for Swing anyway,
+because one needs exactly the same Java version to save and restore serialized objects.
+
+
+keyboard accelerators and mnemonics
+-----------------------------------
+
+This work was completed in the spring of 2019. Note that in a browser, some
+key strokes, particularly CTRL-keys, are not available. Bummer.
+
+
+MINOR ISSUES--required some rewriting/refactoring by Bob and Udo
+================================================================
+
+
+Thread.currentThread() == dispatchThread
+----------------------------------------
+
+changed to JSToolkit.isDispatchThread()
+
+
+MINOR ISSUES--requiring some rewriting/refactoring outside of SwingJS
+=====================================================================
+
+primitive restrictions - int, long, and float
+---------------------------------------------
+
+int
+
+For performance reasons, int addition and multiplication do not by default overflow to
+negative values. Instead, they just get bigger. Java code that relies on overflow to
+negative values should be surrounded by ()|0 -- an OR with integer 0:
+
+
+int bigI, bigJ;
+...
+
+bigI = (bigI + bigJ)|0;
+
+bigI = (bigI + 1)|0; //instead of bigI++
+
+
+Thus, in Java, the following is true:
+
+ 2000000000 + 2000000000 == -294967296
+
+But in SwingJS, that will be 4000000000. So, for example, the following
+strategy will fail in SwingJS:
+
+ int newLength = lineBuf.length * 2;
+ if (newLength < 0) {
+ newLength = Integer.MAX_VALUE;
+ }
+
+This is because, generally, "-1" in JavaScript is not 0xFFFFFFFF. The simple ()|0 takes
+caes of this:
+
+ int newLength = (lineBuf.length * 2)|0;
+ if (newLength < 0) {
+ newLength = Integer.MAX_VALUE;
+ }
+
+JavaScript does process bitwise operators & | ^ ~ properly for int values. There is no issue using
+these operations.
+
+Note that int 1/0 in Java throws "java.lang.ArithmeticException: / by zero", but in JavaScript is just Infinity.
+
+Importantly, the JavaScript Int32Array does behave properly. From the Firefox developer console:
+
+>> x = new Int32Array(1)
+<- Int32Array(1) [ 0 ]
+>> x[0] = 4000000000
+<- 4000000000
+>> x[0]
+<- -294967296
+
+Notice that, perhaps unexpectedly, the following two constructs produce
+different results in JavaScript:
+
+x = new Int32Array(1);
+b = x[0] = 4000000000;
+
+(b will be 4000000000)
+
+and
+
+x = new Int32Array(1);
+x[0] = 4000000000;
+b = x[0];
+
+(b will be -294967296)
+
+
+SwingJS leverages array typing to handle all byte and short arithmetic so as
+to ensure that any byte or short operation in JavaScript does give the same
+result in Java.
+
+long
+
+Java's 64-bit long type is fully supported, starting with java2script 3.3.1 (2020.12.31)
+The transpiler handles all conversions to and from long appropriately. See the discussion
+at https://github.com/BobHanson/java2script/issues/202 for how this is done.
+
+float
+
+SwingJS does not distinguish between float and double. Everything is double.
+
+
+HashMap, Hashtable, and HashSet iterator ordering
+-------------------------------------------------
+
+In Java, iterators for HashMap, Hashtable, and HashSet do not guarantee any particular order.
+From the HashMap documentation for Java 8:
+
+ This class makes no guarantees as to the order of the map; in particular, it does not
+ guarantee that the order will remain constant over time.
+
+Likewise, for HashSet (because it is simply a convenience method for HashMap<Object,PRESENT>:
+
+ [HashSet] makes no guarantees as to the iteration order of the set.
+
+JavaScript's Map object is different. It is basically a LinkedHashMap, so it guarantees iteration
+in order of object addition.
+
+Starting with java2script 3.2.9.v1, these classes use the JavaScript Map object rather than hash codes
+whenever all keys are strictly of JavaScript typeof "string". If any key is introduced that is not a string, the
+implementation falls back to using hash codes, the same as Java.
+
+The result is significantly faster performance (3-12 x faster) than originally, and up to 3 x faster
+performance in JavaScript than in Java itself. That is not a misprint. Faster than Java.
+
+The JavaScript Map implementation is implemented UNLESS the constructor used is the one that
+specifies both initial capacity and load factor in their constructor. Thus,
+
+new Hashtable()
+new HashMap()
+new HashMap(16)
+new HashSet()
+
+all use the JavaScript Map. But
+
+new Hashtable(11, 0.75f)
+new HashMap(16, 0.75f)
+new HashSet(16, 0.75f)
+
+do not.
+
+This design allows for opting out of the JavaScript Map use in order to retain the exact behavior of
+iterators in JavaScript as in Java.
+
+
+interning, new String("xxx") vs "xxx"
+-------------------------------------
+
+Note that the following are true in JavaScript:
+
+typeof new String("xxxx") == "object"
+typeof "xxxx" == "string"
+var s = "x";typeof ("xxx" + s) == "string"
+
+There is no equivalence to this behavior in Java, where a String is a String is a String.
+
+Be aware that SwingJS does not always create a JavaScript String object using JavaScript's
+new String(...) constructor. It only does this for Java new String("xxxx") or new String(new String()).
+
+In all other cases, new String(...) (in Java) results in a simple "xxxx" string in JavaScript.
+That is, it will be JavaScript typeof "string", not typeof "object".
+
+The reason for this design is that several classes in the Java core use toString()
+methods that return new String(), and those classes that do that would cause a JavaScript error
+if implicitly stringified if new String() returned a JavaScript String object.
+
+This is fine in JavaScript:
+
+test1 = function() { return { toString:function(){ return "OK" } } }
+"testing" + new test1()
+>> "testingOK"
+
+But for whatever reason in JavaScript:
+
+test2 = function() { return { toString:function(){ return new String("OK") } } }
+"testing" + new test2()
+>> Uncaught TypeError: Cannot convert object to primitive value
+
+The lesson here is never to use
+
+ return new String("...");
+
+in a Java toString() method. In Java it will be fine; in JavaScript it will also be fine as long as
+that method is never called in JavaScript implicitly in the context of string concatenation.
+
+A note about interning. Consider the following six Java constructions, where we have a == "x";
+
+"xxx"
+"xx" + "x"
+new String("xxx").intern()
+
+new String("xxx")
+"xx" + a.toString()
+"xx" + a
+
+All six of these will return java.lang.String for .getClass().getName().
+However, the first three are String literals, while the last three are String objects.
+Thus:
+ "xxx" == "xxx"
+ "xxx" == "xx" + "x"
+ "xxx" == new String("xxx").intern()
+
+but none of the other three are equivalent to "xxx" or each other:
+
+ "xxx" != new String("xxx")
+ "xxx" != "xx" + a.toString()
+ "xxx" != "xx" + a
+ new String("xxx") != new String("xxx")
+ "xx" + a != new String("xxx")
+
+etc.
+
+As in Java, in SwingJS, all of the following Java assertions pass as true:
+
+ assert("xxx" == "xx" + "x");
+ assert("xxx" == ("xx" + a).intern());
+ assert("xxx" === new String("xxx").intern());
+
+and both of these do as well:
+
+ assert(new String("xxx") != "xxx");
+ assert(new String("xxx") != new String("xxx"));
+
+But the following two fail to assert true in SwingJS:
+
+ assert("xxx" != "xx" + a);
+ assert("xxx" != "xx" + a.toString());
+
+because, in JavaScript, both of these right-side expressions evaluate to a simple "interned" string.
+
+In Java, however, these assertions are true because Java implicitly "boxes" String
+concatentaion as a String object, not a literal.
+
+Most of us know not to generally use == with Strings unless they are explicitly interned.
+Where this problem may arise, though, is in IdentityHashMap, which compares objects using
+System.identityHashCode(), which is not the same for different objects or their string literal equivalents.
+
+My recommendation, if you need to use IdentityHashMap with strings is to always use an explicit String.intern()
+for any keys -- unless you really want to keep every string as separate keys even if they are the same sequence,
+in which case, use new String(). This will work in Java and in JavaScript.
+
+Be aware when working with strings that come from SwingJS and are being used by other JavaScript modules
+that those that are String objects will return "object" for the JavaScript typeof operator, not "string".
+
+The easy way to ensure this is no problem is to concatenate strings with "" to force immediate interning:
+
+ var x = aJavaObject.getString() + "";
+
+unless you are certain that the string is being returned is a raw JavaScript string.
+
+
+Names with "$" and "_"
+----------------------
+
+For the most part, this should be no problem.
+
+Note that the use of $ and _ in Java field names has always been discouraged:
+[https://docs.oracle.com/javase/tutorial/java/nutsandbolts/variables.html]
+
+ You may find some situations where auto-generated names will contain the dollar sign,
+ but your variable names should always avoid using it. A similar convention
+ exists for the underscore character; while it's technically legal to begin your
+ variable's name with "_", this practice is discouraged.
+
+Some impacts of transpiling method names with full qualification:
+
+1) SwingJS will introduce fields that start with $ or _. These will not conflict
+ if the above convention is followed.
+
+2) Fields that have the same Java name as a method are not an issue.
+
+3) Fields that have a Java name with $ that matches a transpiled method name,
+ such as toString$, will need to be refactored in Java to not have that name collision.
+
+4) Fields in a subclass that have the same name as private fields in a superclass
+ represent a name collision, because the superclass method needs to call its private
+ field even if invoked from a subclass. The solution was to modify the subclass field
+ name using one or more prepended $.
+
+5) Use of Class.getDeclaredMethods() reflection will return Method objects having the transpiled
+ name, not the Java name. This could require some j2sNative adjustment
+ to strip the $... parameters from the name if that is needed.
+
+6) Use of Method.getParameterTypes() should work fine, provided class names
+ do not contain "_". This is because the transpiler converts "." to "_" when
+ creating the fully qualified JavaScript name.
+
+
+ArrayIndexOutOfBounds
+---------------------
+
+You cannot implicitly throw an ArrayIndexOutOfBoundsException in JavaScript.
+JavaScript will simply return "undefined", not throw an Exception. So:
+
+boolean notAGoodIdeaIsOutOfBounds(String[] sa, int i) {
+ try {
+ return (sa[i] == sa[i]);
+ } catch (ArrayIndexOutOfBoundsException e) {
+ return false;
+ }
+}
+
+will work in Java but not in JavaScript. Code should not depend upon this sort
+of trap anyway, if you ask me.
+
+
+Throwable vs Error vs Exception
+-------------------------------
+
+True JavaScript errors are trapped as Throwable, whereas you can still trap
+Error and Exception as well. So if you want to be sure to catch any JavaScript
+error, use try{}catch (Throwable t){}, not try{}catch (Exception e){}.
+
+java.awt.Color
+--------------
+
+ColorSpace: only "support" CS_sRGB.
+
+ TODO -- any volunteers??
+
+
+javax.swing.JFileDialog
+-----------------------
+
+HTML5 cannot expose a file reading directory structure. But you certainly
+can still do file reading and writing. It just works a little differently.
+It's a simple modification:
+
+ b = new JButton("FileOpenDialog");
+ b.addActionListener(new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ JFileChooser fc = new JFileChooser();
+ Test_Dialog.this.onDialogReturn(fc.showOpenDialog(Test_Dialog.this));
+ // Java will wait until the dialog is closed, then enter the onDialogReturn method.
+ // JavaScript will exit with NaN immediately, and then call back with its actual value
+ // asynchronously.
+ }
+
+ });
+
+ public void onDialogReturn(int value) {
+ if (value != Math.floor(value))
+ return; // in JavaScript, this will be NaN, indicating the dialog has been opened
+ // If we are here, the dialog has closed, in both Java and JavaScript.
+ System.out.println("int value is " + value);
+ }
+
+
+ @Override
+ public void propertyChange(PropertyChangeEvent event) {
+ Object val = event.getNewValue();
+ String name = event.getPropertyName();
+ System.out.println(name);
+ switch (event.getSource().getClass().getName()) {
+ case "javax.swing.JOptionPane":
+ switch (name) {
+ case "inputValue":
+ onDialogReturn(val);
+ return;
+ case "value":
+ if (val instanceof Integer)
+ onDialogReturn(((Integer) val).intValue());
+ else
+ onDialogReturn(val);
+ return;
+ }
+ break;
+ case "javax.swing.ColorChooserDialog":
+ switch (name) {
+ case "SelectedColor":
+ onDialogReturn(val);
+ return;
+ }
+ break;
+ case "javax.swing.JFileChooser":
+ switch (name) {
+ case "SelectedFile":
+ File file = (File) val;
+ byte[] array = (val == null ? null : /** @j2sNative file.秘bytes || */
+ null);
+ onDialogReturn("fileName is '" + file.getName() + "'\n\n" + new String(array));
+ return;
+ }
+ break;
+ }
+ System.out.println(
+ event.getSource().getClass().getName() + " " + event.getPropertyName() + ": " + event.getNewValue());
+ }
+
+
+Developers are encouraged to create a separate class that handles general calls to JFileDialog.
+An example class can be found in the SwingJS distribution as
+
+/sources/net.sf.j2s.java.core/src/javajs/async/AsyncFileChooser.java.
+
+
+javax.swing.JOptionPane dialogs
+-------------------------------
+
+For a full discussion of modal dialogs, see the javajs.asyc.AsyncDialog.java discussion.
+
+For this action to work, the parent component must implement
+propertyChangeListener, and any call to JOptionPanel should allow for
+an asynchronous response, meaning that there is no actionable code following the
+call to the dialog opening.
+
+In addition, for compatibility with the Java version, implementation should
+wrap the call to getConfirmDialog or getOptionDialog in a method call to
+handle the Java:
+
+onDialogReturn(JOptionPane.showConfirmDialog(parentFrame,
+messageOrMessagePanel, "title", JOptionPane.OK_CANCEL_OPTION));
+
+Then parentFrame.propertyChange(event) should also call onDialogReturn.
+
+This will then work in both Java and JavaScript.
+
+Note that there is an int and an Object version of onDialogReturn().
+
+
+In JavaScript:
+
+The initial return from JOptionPane.showConfirmDialog and showMessageDialog
+will be (SwingJS) JDialog.ASYNCHRONOUS_INTEGER (NaN), testable as an impossible
+Java int value using ret != -(-ret) if the parent implements PropertyChangeListener, or -1
+(CLOSE_OPTION) if not.
+
+For showOptionDialog (which returns Object) or showInputDialog (which returns
+String), the initial return will be (SwingJS) JDialog.ASYNCHRONOUS_OBJECT, testable as
+((Object) ret) instanceof javax.swing.plaf.UIResource if the parent implements
+PropertyChangeListeneer, or null if not.
+
+The second return will be the desired return.
+
+In Java:
+
+The initial return will be the one and only modal final return.
+
+
+
+For full compatibility, The calling method must not continue beyond this call.
+
+All of the standard Java events associated with Components are also available.
+
+Certain fall back mechanisms are possible, where onReturn does not exist, but
+only for the following cases:
+
+
+For showMessageDialog, for WARNING_MESSAGE and ERROR_MESSAGE, a simple
+JavaScript alert() is used, returning 0 (OK_OPTION) or -1 (CLOSED_OPTION).
+
+For showInputDialog, if the message is a string, a simple JavaScript prompt()
+with input box is used, returning the entered string or null.
+
+For showConfirmDialog, a simple JavaScript confirm() is used, in which case:
+
+for YES_NO_OPTION: YES_OPTION or NO_OPTION
+
+for YES_NO_CANCEL_OPTION: YES_OPTION or CANCEL_OPTION
+
+for OK_CANCEL_OPTION or any other: OK_OPTION or CANCEL_OPTION
+
+Note that you should implement a response for CLOSED_OPTION for
+showConfirmDialog. For other dialogs, a null return indicates the dialog was
+closed, just as for Java.
+
+Developers are encouraged to create a separate class that handles general calls.
+An example class can be found in the SwingJS distribution as src/javajs/async/AsyncDialog.java.
+Very simple modifications to the Java allows asynchronous operation using AsyncDialog. Here
+is a simple "do you want to close this frame" example, where you can see that what we have
+done is to set the reply into an ActionListener that is defined in the constructor of
+the AsyncDisplay object:
+
+// Original:
+//
+// private void promptQuit() {
+// int sel = JOptionPane.showConfirmDialog(null, PROMPT_EXIT, NAME, JOptionPane.YES_NO_OPTION);
+// switch (sel) {
+// case JOptionPane.YES_OPTION:
+// resultsTab.clean();
+// seqs.dispose();
+// if (fromMain) {
+// System.exit(0);
+// }
+// break;
+// }
+// }
+
+ private void promptQuitAsync() {
+ new AsyncDialog(new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ int sel = ((AsyncDialog)e.getSource()).getOption();
+ switch (sel) {
+ case JOptionPane.YES_OPTION:
+ resultsTab.clean();
+ seqs.dispose();
+ if (fromMain) {
+ System.exit(0);
+ }
+ break;
+ }
+ }}).showConfirmDialog(null, PROMPT_EXIT, NAME, JOptionPane.YES_NO_OPTION);
+ }
+
+Very simple!
+
+
+native methods
+--------------
+
+The J2S compiler ignores all static native method declarations.
+Anything of this nature needs to be implemented in JavaScript if it is needed,
+using j2sNative blocks:
+
+/**
+ * @j2sNative
+ *
+ * var putYourJavaScriptCodeHere
+ *
+ */
+
+ Note that if you follow that directly with a {...} block, then
+ only the javadoc code will run in JavaScript, and only the {...} code will run in Java.
+
+
+key Focus
+---------
+
+As of June, 2019, the keyboard focus manager is fully implemented.
+The one catch is that JTextPane and JTextArea, which already consume
+VK_TAB in Java, cannot use CTRL-TAB to continue a tabbing cycle around
+the components in a window. Instead, CTRL-TAB is absorbed by the browser.
+
+
+LookAndFeel and UI Classes
+--------------------------
+
+SwingJS implements the native browser look and feel as swingjs.plaf.HTML5LookAndFeel.
+There are small differences between all look and feels -- MacOS, Windows, SwingJS.
+
+Expert developers know how to coerce changes in the UI by subclassing the UI for a
+component. This probably will not work in SwingJS.
+
+Note that LookAndFeel in Java usually determines canvas size in a Frame because
+different operating systems (Mac OS vs Windows vs HTML5) will have
+different edge sizes on their frames. If you want to ensure a component size,
+use getContentPane().setPreferredSize().
+
+
+System.exit(0) does not stop all processes
+------------------------------------------
+
+Although System.ext(int) has been implemented in JavaScript, it just closes the
+frames, stops all pending javax.swing.Timer objects in the queue, and runs any
+threads added using Runtime.getRuntime().addShutdownHook(Thread).
+It may not stop all "threads." So don't rely on that.
+Applications are responsible for shutting down prior to executing System.exit(0).
+
+
+myClass.getField not implemented
+--------------------------------
+
+java.lang.reflect.Field is implemented minimally. It is not
+certain that Field.getDeclaringClass() will work. If you just want a
+value of a field, you can do this:
+
+/**
+ *@j2sNative
+ *
+ * return myClass[name]
+ */
+
+But that is not a java.lang.reflection.Field object.
+
+
+"window" and other reserved JavaScript names
+--------------------------------------------
+
+No reserved top-level JavaScript name is allowed for a package name. So, for example,
+one must rename packages such as "window" or "document" to names such as "win" or "doc".
+
+
+reserved field and method names
+-------------------------------
+
+In order to minimize the chance of added SwingJS field and method names colliding with ones
+developers might use in subclassing Java classes, we have added U+79D8 (first character of Mandarin
+"secret") to the characters already disrecommended by Java documentation ("$" and "_"). The only problem
+would be if you use that character followed by certain English words in certain classes. For example
+\u79D8canvas for JComponents (in java.awt.JSComponent) and \u79D8byte (in java.io.File).
+
+
+qualified field and method names
+--------------------------------
+
+Method names in SwingJS are fully qualified, meaning two methods with the same Java name but different
+parameters, such as write(int) and write(double), must not have the same name in JavaScript. (In this
+case, we will have write$I and write$D.) However, in certain cases it may be desirable to leave the
+method names unqualified. In particular, when an interface actually represents a JavaScript object,
+the transpiler can leave a method name unqualified.
+
+You can implement a simple name for a method using the @j2sAlias annoation in the javadoc for the
+method involved. For example:
+
+
+/**
+ * @j2sAlias read
+ *
+ */
+public void read(byte[] buf, int pos, int len) {...}
+
+will allow the method to be accesible either as "read" or "read$BA$I$I" in JavaScript.
+
+
+The default situation for this is a class name includes ".api.js" (case-sensitive).
+This means that any method in any class in a package js within a package api, or any private interface js
+that has an outer interface api, will have all-unqualified methods. An example of this is
+swingjs.plaf.JSComboPopupList, which needs to communicate with a jQuery
+object directly using the following interface:
+
+ private interface api {
+
+ interface js extends JQueryObject {
+
+ abstract js j2sCB(Object options);
+
+ abstract Object[] j2sCB(String method);
+
+ abstract Object[] j2sCB(String method, Object o);
+
+ abstract Object[] j2sCB(String method, int i);
+
+ abstract int j2sCB(String OPTION, String name);
+
+ }
+ }
+
+Notice that all these variants of j2sCB() will call the same method in JavaScript by design.
+
+
+Component.getGraphics(), Graphics.dispose()
+-------------------------------------------
+
+Use of component.getGraphics() is discouraged in Java and in SwingJS.
+Specifically in SwingJS, any call to component.getGraphics() or
+BufferedImage.createGraphics() or Graphics.create(...) should be matched with graphics.dispose(),
+particularly when it is called outside the context of a paint(Graphics) call from the system.
+
+If you see your graphics scrolling down the page with each repaint,
+look for where you have used Component.getGraphics() and not Graphics.dispose().
+For example, this will definitely NOT work in SwingJS:
+
+ this.paint(getGraphics())
+
+and really should not work in Java, either, as it is technically a resource memory leak.
+
+Instead, if you really do not want to use repaint(), use this:
+
+ Graphics g = getGraphics();
+ paint(g);
+ g.dispose();
+
+
+
+Graphics.setClip()
+------------------
+
+The HTML5 canvas.clip() method is permanent. You can only reset the clip using
+save/restore. This is different from Java, where you can temporarily change it using
+
+ Shape oldClip = Graphics.getClip();
+ Graphics.setClip(newClip);
+ ...
+ Graphics.setClip(oldClip);
+
+If you need to do something like this, you must schedule the paints to not have overlapping clip needs.
+
+
+MAJOR ISSUES--for Bob and Udo within SwingJS
+============================================
+
+fonts
+-----
+
+Fonts and FontMetrics will all be handled in JavaScript. Font matching will
+not be exact, and composite (drawn) fonts will not be supported.
+
+SwingJS handles calls such as font.getFontMetrics(g).stringWidth("xxx") by
+creating a <div> containing that text, placing it in an obscure location on
+the page, and reading div.getBoundingClientRect(). This is a VERY precise
+value, but can be a pixel or two off from what Java reports for the same font.
+
+
+OS-dependent classes
+--------------------
+
+Static classes such as:
+
+ java.awt.Toolkit
+ java.awt.GraphicsEnvironment
+
+which are created using Class.forName are implemented using classes in the swingjs package.
+
+sun.awt.AWTAccessor is not implemented.
+
+
+AWT component peers and component "ui" user interfaces
+------------------------------------------------------
+
+ComponentPeer is a class that represents a native AWT component.
+Components with such peers are called "heavy-weight" components.
+They are expected to do the dirty work of graphics drawing.
+
+Java Swing implements peers only for JApplet, JDialog, JFrame, and JWindow.
+References to such objects have been removed, but clearly there must be
+some connection to similar DOM objects, even for "light-weight" components.
+
+
+MAJOR ISSUES--to be resolved by implementers
+============================================
+
+fonts
+-----
+
+Glyph/composite/outline fonts are not supported.
+
+
+
+threads
+-------
+
+Thread locking and synchronization are not relevant to JavaScript.
+Thus, anything requiring "notify.." or "waitFor.." could be a serious issue.
+
+All threading must be "faked" in JavaScript. Specifically not available is:
+
+ Thread.sleep()
+
+javax.swing.AbstractButton#doClick(pressTime) will not work, as it requires Thread.sleep();
+
+However, java.lang.Thread itself is implemented and used extensively.
+
+Methods thread.start() and thread.run() both work fine.
+
+For simple applications that use Thread.sleep() just to have a delay, as in a frame rate, for
+example, one can use javax.swing.Timer instead. That is fully implemented.
+
+Likewise, java.util.Timer can be replaced with no loss of performance with javax.Swing.Timer.
+Note that java.util.TimerTask is implemented, but it can also be replaced by an implementation of Runnable.
+
+task = new TimerTask(){....};
+t = new java.util.Timer();
+t.schedule(task, 0, 1);
+
+becomes
+
+task = new TimerTask(){....}; // or task = new Runnable() {...}
+t = new javax.swing.Timer(1, new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ task.run();
+ }
+};
+t.setInitialDelay(0); // not particularly necessary
+t.start();
+
+In addition, SwingJS provides swingjs.JSThread, which can be subclassed
+if desired. This class allows simple
+
+ while(!interrupted()){
+ wait()
+ ...
+ }
+
+action through an asynchronous function run1(mode). For example:
+
+ protected void run1(int mode) {
+ try {
+ while (true)
+ switch (mode) {
+ case INIT:
+ // once-through stuff here
+ mode = LOOP;
+ break;
+ case LOOP:
+ if (!doDispatch || isInterrupted()) {
+ mode = DONE;
+ } else {
+ Runnable r = new Runnable() {
+ public void run() {
+ // put the loop code here
+ }
+ };
+ dispatchAndReturn(r);
+ if (isJS)
+ return;
+ }
+ break;
+ // add more cases as needed
+ case DONE:
+ // finish up here
+ if (isInterrupted())
+ return;
+ // or here
+ break;
+ }
+ } finally {
+ // stuff here to be executed after each loop in JS or at the end in Java
+ }
+ }
+
+
+image loading
+-------------
+- All image loading in SwingJS is synchronous. A MediaTracker call will immediately return "complete".
+ However, it still may take one system clock tick to fully load images. Thus, it is recommended that
+ images be preloaded in the static block of the applet if it is necessary that they be available in init().
+ This is only an issue if you are trying to access the pixel buffer of the image in JavaScript.
+
+- Applet.getImage(path, name) will return null if the image does not exist.
+
+- BufferedImage: only "support" imageType RGB and ARGB
+
+ -BH: This is a temporary edit, just to get us started. Certainly GRAY will be needed
+
+
+BigInteger and BigDecimal
+-------------------------
+
+java.math.BigInteger and java.math.BigDecimal are fully supported.
+
+
+no format internationalization
+------------------------------
+
+For now, just "en" for number and date formatters
+
+
+missing winding rules
+---------------------
+
+When filling a graphic, only nonzero winding rule is implemented in HTML5 Canvas2D.
+
+
+
+text-related field implementation
+---------------------------------
+
+Text fields are:
+
+JTextField (JavaScript <input type="text">)
+JTextArea (JavaScript <textarea>)
+JTextPane (JavaScript <div>)
+JEditorPane (JavaScript <div>)
+
+For the initial implementation, we don't implement infinite undo/redo, and the abstract
+document model is much less elaborate. Only PlainDocument (in the form of JSPlainDocument)
+is implemented. The Document returned by JTextField.getDocument() is a javax.swing.text.Document.
+
+All scrolling is handled by HTML5. javax.swing.AutoScroller is not implemented.
+public static methods .stop, .isRunning, .processMouseDragged require true Java threading
+and so are not implmented. javax.swing.text.View and its subclasses are not implemented.
+
+The JS document model does not allow two text fields to address the same underlying document.
+
+JavaScript is slightly different from Java in that the field value is changed asynchronously after
+the keypressed event, so Java actions that are keyed to KEY_PRESSED may not pick up the new
+key value even after SwingUtilities.invokeLater() is called. Thus, key pressed actions may need
+to be recorded after a key released event instead.
+
+
+Formatter/Regex limitations
+---------------------------
+
+Some browsers cannot process Regex "look-behind" process such as (?<=\W)
+java.util.regex.Matcher and Pattern use JavaScript's RegExp object rather than
+the native Java object. These are not identical. Only flags /igm are supported.
+Matcher.start(groupID) is not supported.
+
+java.util.Formatter will function correctly for all standard %... patterns.
+
+In addition, JavaScript does not implement some of the more arcane POSIX {...} formats.
+From java.util.regex.Pattern.java, we find the listing of conversions SwingJS does use:
+
+ "\\p{javaWhitespace}","\\s",
+ "\\p{javaDigit}","\\d",
+ "\\p{Lower}", "[a-z]",
+ "\\p{Upper}", "[A-Z]",
+ "\\p{ASCII}", "[\u0000-\u007F]",
+ "\\p{Alpha}", "[A-Za-z]",
+ "\\p{Digit}", "[0-9]",
+ "\\p{Alnum}", "[A-Za-z0-9]",
+ "\\p{Punct}", "[!\"#$%&'\\(\\)\\*\\+,-./:;<=>?@\\[\\\\\\]^_`{\\|}~]",
+ "\\p{Graph}", "[A-Za-z0-9]!\"#$%&'\\(\\)\\*\\+,-./:;<=>?@\\[\\\\\\]^_`{\\|}~]",
+ "\\p{Print}", "[A-Za-z0-9]!\"#$%&'\\(\\)\\*\\+,-./:;<=>?@\\[\\\\\\]^_`{\\|}~]",
+ "\\p{Blank}", "[ \t]",
+ "\\p{Cntrl}", "[\u0000-\u001F\u007F]",
+ "\\p{XDigit}", "[0-9a-fA-F]",
+ "\\p{Space}", "[ \t\n\u000B\f\r]",
+ "\\p{javaLowerCase}", "[a-z]",
+ "\\p{javaUpperCase}", "[A-Z]",
+ "\\p{Sc}", "[\u0024\u00A2\u00A3\u00A4\u00A5\u058F\u060B\u07FE\u07FF\u09F2\u09F3\u09FB\u0AF1\u0BF9\u0E3F\u20A0\u20A1\u20A2\u20A3\u20A4\u20A5\u20A6\u20A7\u20A8\u20A9\u20AA\u20AB\u20AC\u20AD\u20AE\u20AF\u20B0\u20B1\u20B2\u20B3\u20B4\u20B5\u20B6\u20B7\u20B8\u20B9\u20BA\u20BB\u20BC\u20BD\u20BE\u20BF\uA838\uFDFC\uFE69\uFF04\uFFE0\uFFE1\uFFE5\uFFE6]"
+
+Java's \Q \E quoting is handled appropriately.
+
+Additional Issues
+-----------------
+
+Method reflection is limited. Fields and methods do not retain public or default characteristics.
+(This could be easily adapted, though.) Interfaces do not expose their methods, as the transpiler does not
+actually transpile the interfaces themselves unless they contain default methods.
+And method reflection only includes annotated methods.
+
+java.util.concurrent is not fully elaborated. This package is rewritten to not actually use the
+memory handling capabilities of concurrency, which JavaScript does not have access to.
+
+System.getProperties() just returns a minimal set of properties.
+
+
+Summary
+-------
+
+These are all the known limitations of SwingJS. We have not found any of these limitations
+to be show-stoppers. The primary issue for newcomers to SwingJS is having the source code.
+You must check that source code for all your library jar files is available or, if you
+choose, you will need to decompile those classes. We have used decompilation on some projects,
+and it works just fine. So, technically, all we really need are JAR/class files. But the
+source is by far superior. It's generally prettier, and it has the license information that
+may or may not be present with the JAR or class files. Use class files at your own risk.
+
+Bob Hanson
+
+
--- /dev/null
+20210208070817
--- /dev/null
+This is sources/net.sf.j2s.java.core/dist/DEV_NOTES.txt
+
+_j2sclasslist.txt
+
+the list of .js files concatenated into coreswingjs.js and minified to coreswingjs.z.js
+
+
+SwingJS-site.zip
+
+the full site directory for SwingJS including all files not in the test/ directory.
--- /dev/null
+java/applet/Applet.js
+java/applet/AppletContext.js
+java/applet/AppletStub.js
+java/applet/JSApplet.js
+java/awt/ActiveEvent.js
+java/awt/Adjustable.js
+java/awt/AWTEvent.js
+java/awt/AWTEventMulticaster.js
+java/awt/AWTKeyStroke.js
+java/awt/BasicStroke.js
+java/awt/BorderLayout.js
+java/awt/Button.js
+java/awt/Color.js
+java/awt/color/ColorSpace.js
+java/awt/Component.js
+java/awt/ComponentOrientation.js
+java/awt/ContainerOrderFocusTraversalPolicy.js
+java/awt/Container.js
+java/awt/Cursor.js
+java/awt/DefaultFocusTraversalPolicy.js
+java/awt/DefaultKeyboardFocusManager.js
+java/awt/Dialog.js
+java/awt/Dimension.js
+java/awt/dnd/peer/DropTargetPeer.js
+java/awt/event/ActionListener.js
+java/awt/event/AdjustmentEvent.js
+java/awt/event/AdjustmentListener.js
+java/awt/event/AWTEventListener.js
+java/awt/event/ComponentAdapter.js
+java/awt/event/ComponentEvent.js
+java/awt/event/ComponentListener.js
+java/awt/event/ContainerListener.js
+java/awt/event/FocusEvent.js
+java/awt/event/FocusListener.js
+java/awt/event/HierarchyBoundsListener.js
+java/awt/event/HierarchyListener.js
+java/awt/event/InputEvent.js
+java/awt/event/InputMethodListener.js
+java/awt/event/InvocationEvent.js
+java/awt/event/ItemEvent.js
+java/awt/event/ItemListener.js
+java/awt/event/KeyListener.js
+java/awt/event/MouseEvent.js
+java/awt/event/MouseListener.js
+java/awt/event/MouseMotionListener.js
+java/awt/event/MouseWheelListener.js
+java/awt/event/TextListener.js
+java/awt/event/WindowAdapter.js
+java/awt/event/WindowEvent.js
+java/awt/event/WindowFocusListener.js
+java/awt/event/WindowListener.js
+java/awt/event/WindowStateListener.js
+java/awt/EventDispatchThread.js
+java/awt/EventFilter.js
+java/awt/EventQueue.js
+java/awt/EventQueueItem.js
+java/awt/FlowLayout.js
+java/awt/FocusTraversalPolicy.js
+java/awt/Font.js
+java/awt/font/FontRenderContext.js
+java/awt/FontMetrics.js
+java/awt/Frame.js
+java/awt/geom/AffineTransform.js
+java/awt/geom/Dimension2D.js
+java/awt/geom/Path2D.js
+java/awt/geom/PathIterator.js
+java/awt/geom/Point2D.js
+java/awt/geom/Rectangle2D.js
+java/awt/geom/RectangularShape.js
+java/awt/geom/RectIterator.js
+java/awt/GraphicsCallback.js
+java/awt/GraphicsConfiguration.js
+java/awt/GraphicsDevice.js
+java/awt/GraphicsEnvironment.js
+java/awt/Image.js
+java/awt/image/ImageObserver.js
+java/awt/Insets.js
+java/awt/ItemSelectable.js
+java/awt/JSComponent.js
+java/awt/JSDialog.js
+java/awt/JSFrame.js
+java/awt/JSPanel.js
+java/awt/KeyboardFocusManager.js
+java/awt/KeyEventDispatcher.js
+java/awt/KeyEventPostProcessor.js
+java/awt/Label.js
+java/awt/LayoutManager.js
+java/awt/LayoutManager2.js
+java/awt/LightweightDispatcher.js
+java/awt/Paint.js
+java/awt/Panel.js
+java/awt/peer/ComponentPeer.js
+java/awt/peer/ContainerPeer.js
+java/awt/peer/FramePeer.js
+java/awt/peer/KeyboardFocusManagerPeer.js
+java/awt/peer/LightweightPeer.js
+java/awt/peer/WindowPeer.js
+java/awt/Point.js
+java/awt/Queue.js
+java/awt/Rectangle.js
+java/awt/RenderingHints.js
+java/awt/Scrollbar.js
+java/awt/ScrollPane.js
+java/awt/Shape.js
+java/awt/Stroke.js
+java/awt/TextArea.js
+java/awt/TextComponent.js
+java/awt/TextField.js
+java/awt/Toolkit.js
+java/awt/Transparency.js
+java/awt/Window.js
+java/beans/ChangeListenerMap.js
+java/beans/PropertyChangeEvent.js
+java/beans/PropertyChangeListener.js
+java/beans/PropertyChangeSupport.js
+java/lang/AbstractStringBuilder.js
+java/lang/Class.js
+java/lang/Enum.js
+java/lang/Iterable.js
+java/lang/reflect/Constructor.js
+java/lang/reflect/Method.js
+java/lang/StringBuffer.js
+java/lang/StringBuilder.js
+java/lang/Thread.js
+java/lang/ThreadGroup.js
+java/math/RoundingMode.js
+java/net/URL.js
+java/net/URLStreamHandlerFactory.js
+java/net/HttpURLConnection.js
+java/net/URLStreamHandler.js
+javax/net/ssl/HttpsUrlConnection.js
+java/text/CharacterIterator.js
+java/text/DecimalFormat.js
+java/text/DecimalFormatSymbols.js
+java/text/DigitList.js
+java/text/FieldPosition.js
+java/text/Format.js
+java/text/NumberFormat.js
+java/util/AbstractCollection.js
+java/util/AbstractList.js
+java/util/AbstractMap.js
+java/util/AbstractSequentialList.js
+java/util/AbstractSet.js
+java/util/ArrayList.js
+java/util/Arrays.js
+java/util/Collection.js
+java/util/Collections.js
+java/util/Comparator.js
+java/util/Deque.js
+java/util/Dictionary.js
+java/util/Enumeration.js
+java/util/EventListener.js
+java/util/EventObject.js
+java/util/HashMap.js
+java/util/HashSet.js
+java/util/Hashtable.js
+java/util/IdentityHashMap.js
+java/util/Iterator.js
+java/util/LinkedHashMap.js
+java/util/LinkedList.js
+java/util/List.js
+java/util/ListResourceBundle.js
+java/util/Locale.js
+java/util/Map.js
+java/util/Objects.js
+java/util/Queue.js
+java/util/Random.js
+java/util/RandomAccess.js
+java/util/ResourceBundle.js
+java/util/Set.js
+java/util/TimSort.js
+java/util/Vector.js
+javajs/api/JSFunction.js
+javajs/util/AjaxURLConnection.js
+javajs/util/AjaxURLStreamHandlerFactory.js
+javajs/util/AU.js
+javajs/util/JSThread.js
+javajs/util/Lst.js
+javajs/util/PT.js
+javajs/util/Rdr.js
+javajs/util/SB.js
+javax/swing/AbstractAction.js
+javax/swing/AbstractButton.js
+javax/swing/AbstractListModel.js
+javax/swing/Action.js
+javax/swing/ActionMap.js
+javax/swing/AncestorNotifier.js
+javax/swing/ArrayTable.js
+javax/swing/border/AbstractBorder.js
+javax/swing/border/BevelBorder.js
+javax/swing/border/Border.js
+javax/swing/border/CompoundBorder.js
+javax/swing/border/EmptyBorder.js
+javax/swing/border/EtchedBorder.js
+javax/swing/border/LineBorder.js
+javax/swing/border/TitledBorder.js
+javax/swing/BorderFactory.js
+javax/swing/BoundedRangeModel.js
+javax/swing/BoxLayout.js
+javax/swing/ButtonGroup.js
+javax/swing/ButtonModel.js
+javax/swing/ClientPropertyKey.js
+javax/swing/ComboBoxModel.js
+javax/swing/DefaultBoundedRangeModel.js
+javax/swing/DefaultButtonModel.js
+javax/swing/DefaultComboBoxModel.js
+javax/swing/DefaultSingleSelectionModel.js
+javax/swing/DropMode.js
+javax/swing/event/AncestorEvent.js
+javax/swing/event/AncestorListener.js
+javax/swing/event/CaretEvent.js
+javax/swing/event/CaretListener.js
+javax/swing/event/ChangeEvent.js
+javax/swing/event/ChangeListener.js
+javax/swing/event/DocumentEvent.js
+javax/swing/event/DocumentListener.js
+javax/swing/event/EventListenerList.js
+javax/swing/event/ListDataEvent.js
+javax/swing/event/ListDataListener.js
+javax/swing/event/UndoableEditEvent.js
+javax/swing/event/UndoableEditListener.js
+javax/swing/FocusManager.js
+javax/swing/InternalFrameFocusTraversalPolicy.js
+javax/swing/LayoutComparator.js
+javax/swing/LayoutFocusTraversalPolicy.js
+javax/swing/SortingFocusTraversalPolicy.js
+javax/swing/SwingContainerOrderFocusTraversalPolicy.js
+javax/swing/SwingDefaultFocusTraversalPolicy.js
+javax/swing/Icon.js
+javax/swing/ImageIcon.js
+javax/swing/InputMap.js
+javax/swing/JApplet.js
+javax/swing/JButton.js
+javax/swing/JCheckBox.js
+javax/swing/JCheckBoxMenuItem.js
+javax/swing/JComboBox.js
+javax/swing/JComponent.js
+javax/swing/JFrame.js
+javax/swing/JLabel.js
+javax/swing/JLayeredPane.js
+javax/swing/JMenu.js
+javax/swing/JMenuBar.js
+javax/swing/JMenuItem.js
+javax/swing/JPanel.js
+javax/swing/JPopupMenu.js
+javax/swing/JRadioButtonMenuItem.js
+javax/swing/JRootPane.js
+javax/swing/JScrollBar.js
+javax/swing/JScrollPane.js
+javax/swing/JSeparator.js
+javax/swing/JTextArea.js
+javax/swing/JTextField.js
+javax/swing/JToggleButton.js
+javax/swing/JViewport.js
+javax/swing/KeyboardManager.js
+javax/swing/KeyStroke.js
+javax/swing/ListModel.js
+javax/swing/LookAndFeel.js
+javax/swing/MenuElement.js
+javax/swing/MutableComboBoxModel.js
+javax/swing/plaf/ActionMapUIResource.js
+javax/swing/plaf/basic/BasicBorders.js
+javax/swing/plaf/BorderUIResource.js
+javax/swing/plaf/ColorUIResource.js
+javax/swing/plaf/ComponentUI.js
+javax/swing/plaf/DimensionUIResource.js
+javax/swing/plaf/FontUIResource.js
+javax/swing/plaf/InputMapUIResource.js
+javax/swing/plaf/InsetsUIResource.js
+javax/swing/plaf/UIResource.js
+javax/swing/RepaintManager.js
+javax/swing/RootPaneContainer.js
+javax/swing/Scrollable.js
+javax/swing/ScrollPaneConstants.js
+javax/swing/ScrollPaneLayout.js
+javax/swing/SingleSelectionModel.js
+javax/swing/SizeRequirements.js
+javax/swing/SwingConstants.js
+javax/swing/SwingPaintEventDispatcher.js
+javax/swing/SwingUtilities.js
+javax/swing/text/AbstractDocument.js
+javax/swing/text/AttributeSet.js
+javax/swing/text/Caret.js
+javax/swing/text/DefaultCaret.js
+javax/swing/text/DefaultEditorKit.js
+javax/swing/text/Document.js
+javax/swing/text/EditorKit.js
+javax/swing/text/Element.js
+javax/swing/text/GapContent.js
+javax/swing/text/GapVector.js
+javax/swing/text/JTextComponent.js
+javax/swing/text/MutableAttributeSet.js
+javax/swing/text/PlainDocument.js
+javax/swing/text/PlainView.js
+javax/swing/text/Position.js
+javax/swing/text/Segment.js
+javax/swing/text/SegmentCache.js
+javax/swing/text/SimpleAttributeSet.js
+javax/swing/text/Style.js
+javax/swing/text/StyleConstants.js
+javax/swing/text/StyleContext.js
+javax/swing/text/TabExpander.js
+javax/swing/text/TextAction.js
+javax/swing/text/Utilities.js
+javax/swing/text/View.js
+javax/swing/tree/TreeNode.js
+javax/swing/UIDefaults.js
+javax/swing/UIManager.js
+javax/swing/undo/AbstractUndoableEdit.js
+javax/swing/undo/CompoundEdit.js
+javax/swing/undo/UndoableEdit.js
+javax/swing/ViewportLayout.js
+javax/swing/WindowConstants.js
+sun/awt/AppContext.js
+sun/awt/AWTAutoShutdown.js
+sun/awt/CausedFocusEvent.js
+sun/awt/ComponentFactory.js
+sun/awt/KeyboardFocusManagerPeerProvider.js
+sun/awt/MostRecentKeyValue.js
+sun/awt/MostRecentThreadAppContext.js
+sun/awt/PaintEventDispatcher.js
+sun/awt/PostEventQueue.js
+sun/awt/RequestFocusController.js
+sun/awt/SunToolkit.js
+sun/awt/WindowClosingListener.js
+sun/awt/WindowClosingSupport.js
+sun/awt/image/DataStealer.js
+sun/awt/image/IntegerComponentRaster.js
+sun/awt/image/IntegerInterleavedRaster.js
+sun/awt/image/SunWritableRaster.js
+sun/font/FontDesignMetrics.js
+sun/swing/DefaultLookup.js
+sun/swing/SwingLazyValue.js
+sun/text/resources/FormatData.js
+sun/text/resources/en/FormatData_en.js
+sun/util/resources/LocaleData.js
+sun/util/locale/BaseLocale.js
+sun/util/locale/LocaleUtils.js
+sun/util/locale/provider/LocaleProviderAdapter.js
+sun/util/locale/provider/LocaleDataMetaInfo.js
+swingjs/a2s/A2SContainer.js
+swingjs/a2s/A2SEvent.js
+swingjs/a2s/A2SListener.js
+swingjs/a2s/Applet.js
+swingjs/a2s/Button.js
+swingjs/a2s/Label.js
+swingjs/a2s/Panel.js
+swingjs/a2s/Scrollbar.js
+swingjs/a2s/ScrollPane.js
+swingjs/a2s/TextArea.js
+swingjs/a2s/TextField.js
+swingjs/api/Interface.js
+swingjs/api/js/DOMNode.js
+swingjs/api/js/HTML5CanvasContext2D.js
+swingjs/api/js/JSInterface.js
+swingjs/jquery/JQueryUI.js
+swingjs/JSApp.js
+swingjs/JSAppletThread.js
+swingjs/JSAppletViewer.js
+swingjs/JSFocusPeer.js
+swingjs/JSFontMetrics.js
+swingjs/JSFrameViewer.js
+swingjs/JSGraphics2D.js
+swingjs/JSGraphicsConfiguration.js
+swingjs/JSGraphicsEnvironment.js
+swingjs/JSImage.js
+swingjs/JSImagekit.js
+swingjs/JSMouse.js
+swingjs/JSNullComponentPeer.js
+swingjs/JSScreenDevice.js
+swingjs/JSThreadGroup.js
+swingjs/JSToolkit.js
+swingjs/JSUtil.js
+swingjs/plaf/ButtonListener.js
+swingjs/plaf/DefaultMenuLayout.js
+swingjs/plaf/HTML5LookAndFeel.js
+swingjs/plaf/JSAppletUI.js
+swingjs/plaf/JSButtonUI.js
+swingjs/plaf/JSCheckBoxMenuItemUI.js
+swingjs/plaf/JSCheckBoxUI.js
+swingjs/plaf/JSComboBoxUI.js
+swingjs/plaf/JSComponentUI.js
+swingjs/plaf/JSEventHandler.js
+swingjs/plaf/JSFrameUI.js
+swingjs/plaf/JSGraphicsUtils.js
+swingjs/plaf/JSLabelUI.js
+swingjs/plaf/JSLayeredPaneUI.js
+swingjs/plaf/JSLightweightUI.js
+swingjs/plaf/JSMenuBarUI.js
+swingjs/plaf/JSMenuItemUI.js
+swingjs/plaf/JSMenuUI.js
+swingjs/plaf/JSPanelUI.js
+swingjs/plaf/JSPopupMenuSeparatorUI.js
+swingjs/plaf/JSPopupMenuUI.js
+swingjs/plaf/JSRadioButtonMenuItemUI.js
+swingjs/plaf/JSRadioButtonUI.js
+swingjs/plaf/JSRootPaneUI.js
+swingjs/plaf/JSScrollBarUI.js
+swingjs/plaf/JSScrollPaneUI.js
+swingjs/plaf/JSSeparatorUI.js
+swingjs/plaf/JSSliderUI.js
+swingjs/plaf/JSTextAreaUI.js
+swingjs/plaf/JSTextFieldUI.js
+swingjs/plaf/JSTextUI.js
+swingjs/plaf/JSTextViewUI.js
+swingjs/plaf/JSViewportUI.js
+swingjs/plaf/JSWindowUI.js
+swingjs/plaf/LazyActionMap.js
+swingjs/plaf/Resizer.js
+swingjs/plaf/TextListener.js
+
+
--- /dev/null
+java2script/SwingJS Notes
+=========================
+
+updated 12/31/2020 -- full support for 64-bit long
+updated 12/6/2020 -- note about restrictions on long, including BitSet and Scanner
+updated 3/21/2020 -- adds note about HashMap, Hashtable, and HashSet iterator ordering
+updated 3/20/2020 -- adds note about interning, new String("xxx"), and "xxx"
+updated 2/26/2020 -- adds Graphics.setClip issue
+updated 12/22/19 -- additional issues
+updated 11/03/19 -- adds information about File.exists() and points to src/javajs/async
+updated 10/26/19 -- adds information about File.createTempFile()
+updated 8/16/19 -- minor typos and added summary paragraph
+updated 7/19/19 -- clarification that AWT and Swing classes are supported directly
+updated 5/13/19 -- Mandarin U+79D8 reserved character; Missing Math methods; int and long
+updated 5/10/19 -- adds a section on static issues in multi-(duplicate)-applet pages
+updated 1/4/19 -- nio
+updated 9/15/18 -- adds integer 1/0 == Infinity
+updated 7/24/18 -- most classes replaced with https://github.com/frohoff/jdk8u-jdk
+updated 6/5/17 -- reserved package name "window"
+updated 3/11/17 -- myClass.getField
+updated 3/7/17 -- overloading of JSplitPane.setDividerLocation
+updated 3/2/17 -- more indication of classes not implemented (KeyListener)
+
+---IMPORTANT CHARACTER SET NOTE---
+
+It is critical that all development work in Java2Script be done in UTF-8. This means:
+
+- making sure your Eclipse project is set up for UTF-8 (not the Eclipse default?)
+- making sure your server can serve up UTF-8 by default for any browser-loaded files
+- making sure you don't edit a Java2Script class file or one of the site .js files
+ using a non-UTF-8 editor. It may replace non-Latin characters with "?" or garbage.
+- making sure that your web pages are delivered with proper headings indicating HTML5 and UTF-8
+
+<!DOCTYPE html>
+<html>
+<head>
+<meta charset="utf-8">
+
+Note that the DOCTYPE tag is critical for some browsers to switch into HTML5 mode. (MSIE?)
+
+
+In particular, the Mandarin character 秘 (mi; "secret") is used extensively throughout
+the SwingJS class files to distinguish j2s-specific fields and methods that must not
+ever be shadowed or overridden by subclasses. For example, we see in java.lang.Thread.java:
+
+ public static JSThread 秘thisThread;
+
+----------------------------------
+
+
+
+=============================================================================
+SwingJS and OpenJDK 8+
+=============================================================================
+
+SwingJS implements a wide range of the Java language in JavaScript. The base
+version for this implementation is OpenJDK8. some classes are implemented using
+older source code, and there are some missing methods. For the most part, this is
+no real problem. You can add or modify any java class just be adding it as source
+in your project. Or (preferably) you can contact me, and I can get it into the
+distribution. Or (even more preferably) you can do that via a patch submission.
+
+=================
+DESIGN PHILOSOPHY
+=================
+
+The java2script/SwingJS design goal is to recreate a recognizable, easily debuggable
+equivalent in JavaScript for as much of Java as practical. This means, for example,
+that one can call in JavaScript
+
+ new java.util.Hashtable()
+
+and for all practical purposes it will appear that Java is running.
+
+The goal of java2script/SwingJS is NOT to reproduce Java byte code processing in a
+browser. We leave that task and its own issues to others. Here, instead, we have a
+working JavaScript version of the Java classes along with runtime assistance in the
+j2sClazz.js library. This design has several advantages:
+
+ 1) It leads to much smaller downloads, since the class loader can dynamically load
+ code at the class level.
+
+ 2) It allow the browser to use its own optimizations and features, not to ignore those.
+ This leads to huge performance gains and in many cases much simpler coding.
+
+ 3) It allows for in-browser debugging and analysis.
+
+ 4) It allows for code switching between Java and JavaScript. Working Java code
+ can be annotated (@j2sNative, @j2sAlias, @j2sIgnore) in a fashion that
+ allows the code to run slightly differently in a Java than a JavaScript environment.
+ For example:
+
+ int delayMS = /** @j2sNative 10 ||*/2;
+
+ will read "var delayMS = 10 || 2;" (i.e. 10) in JavaScript but read by the Java
+ compiler as "int delayMS = 2".
+
+ 5) Just generally, it allows for a much more integrated environment. JavaScript on
+ the page can call into any SwingJS program, and, likewise, any SwingJS code can
+ access anything on the page.
+
+
+Method and Field Disambiguation
+-------------------------------
+
+This is no problem. SwingJS has no problem with the overloading of methods, for example:
+
+ public void print(int b);
+ public void print(float b);
+
+JavaScript does not allow overloading of methods, and the common practice in
+Java of naming a field the same as a method -- isAllowed and isAllowed() -- is
+not possible in JavaScript. As a result, SwingJS implements "fully-qualified"
+method names using "$" parameter type separation. Thus, these methods in SwingJS
+will be referred to as print$I and print$F. The rules for this encoding are
+relatively simple:
+
+1. The seven primitive types in Java are encoded $I (int), $L (long), $F (float),
+$D (double), $B (byte) $Z (boolean), and $H (short).
+
+2. String and Object are encoded as $S and $O, respectively.
+
+3. "java_lang_" is dropped for all other classes in the java.lang package (as in Java).
+ For example: $StringBuffer, not $java_lang_StringBuffer
+
+4. All other classes are encoded as
+
+ "$" + Class.getName().replace(".","_")
+
+For example, in Java we see:
+
+ public void equals(Object o) {...}
+
+Whereas in SwingJS we have:
+
+ Clazz.newMeth(C$, 'equals$O', function (o) {...}
+
+And
+
+ this.getContentPane().add(bar, "North");
+
+becomes
+
+ this.getContentPane$().add$java_awt_Component$O(bar, "North");
+
+5. Arrays are indicated with appended "A" for each level. So
+
+ setDataVector(Object[][] dataVector, Object[] columnIdentifiers)
+
+becomes
+
+ setDataVector$OAA$OA(dataVector, columnIdentifiers)
+
+(It is recognized that this design does introduce a bit of ambiguity, in that
+ in principal there could be user class named XA and X in the same package,
+ and methods a(X[]) and a(XA) in the same class that cannot be distinguished.
+ The benefit of this simple system, however, triumphed over the unlikelyhood
+ of that scenario.) The transpiler could be set to flag this possibility.
+
+6. Constructors are prepended with "c$". So
+
+ public JLabel(String text) {...}
+
+becomes:
+
+ Clazz.newMeth(C$, 'c$$S', function (text) {...});
+
+Field disambiguation involves prepending.
+
+In Java, a class and its subclass can both have the same field name, such as
+
+ boolean visible;
+
+When this happens, it is called "shadowing", and though not recommended, Java allows
+it. The Java2Script transpiler will prepend such shadowing fields with "$" so that the
+subclass instance has both "visible" (for use in its methods inherited from its
+superclass) and "$visible" (for its own methods). Thus, we might see in Java:
+
+ this.visible = super.visible;
+
+while in SwingJS we will see:
+
+ this.$visible=this.visible;
+
+since JavaScript does not have the "super" keyword.
+
+Parameterless methods such as toString() are appended with "$" to become toString$().
+The one exception to this rule is private methods, which are saved in (truly) private
+array in the class (and are not accessible by reflection). Private parameterless
+methods retain their simple Java name, since they cannot conflict with field names.
+
+This renaming of methods has a few consequences, which are discussed more fully below.
+See particularly the section on "qualified field and method names", where it is described
+how you can use packages or classes or interfaces with ".api.js" in them to represent JavaScript
+objects for which all method names are to be left unqualified, and how individual methods
+can have more than one name using @j2sAlias.
+
+The swingjs.api.js package in particular contains a number of useful interfaces that
+you can import into your project for JavaScript-specific capabilities.
+
+
+Applet vs. Application
+----------------------
+
+One of the very cool aspects of SwingJS is that it doesn't particularly matter if a browser-based
+Java app is an "applet" or an "application". We don't need JNLP (Java Network Launch Protocol)
+because now we can just start up any Java application in a browser just as easily as any applet.
+The associative array that passes information to the SwingJS applet (information that formerly
+might have been part of the APPLET tag, such as width, height, and codebase, always referred to
+in our writing as "the Info array") allows the option to specify the JApplet/Applet "code"
+class or the application "main" class. Either one will run just fine.
+
+
+Performance
+-----------
+
+Obviously, there are limitations. One is performance, but we have seen reproducible
+performance at 1/6 - 1/3 the speed of Java. Achieving this performance may require
+some refactoring of the Java to make it more efficient in both Java and JavaScript.
+"for" loops need to be more carefully crafted; use of "new" and "instanceof" need to be
+minimized in critical areas. Note that method overloading -- that is, the same method name
+with different parameters, such as read(int) and read(byte) -- is no longer any problem.
+
+Threads
+-------
+
+Although there is only a single thread in JavaScript, meaning Thread.wait(), Thread.sleep(int) and
+Thread.notify() cannot be reproduced, we have found that this is not a serious limitation.
+For example, javax.swing.Timer() works perfectly in JavaScript. All it means is that threads
+that use sleep(int) or notify() must be refactored to allow Timer-like callbacks. That is,
+they must allow full exit and re-entry of Thread.run(), not the typical while/sleep motif.
+
+The key is to create a state-based run() that can be exited and re-entered in JavaScript.
+
+The javajs.async package can be added to any Java program to provide Java+JavaScript asynchronous
+classes, including AsyncColorChooser, AsyncDialog, AsyncFileChooser, and AsyncSwingWorker. All
+of these classes work just as well in Java as in JavaScript. There is no need to run them
+only when in JavaScript.
+
+Static fields
+-------------
+
+Final static primitive "constant" fields (String, boolean, int, etc.) such as
+
+static final int TEST = 3;
+static final String MY_STRING = "my " + "string";
+
+are converted to their primitive form automatically by the Eclipse Java compiler
+and do not appear in the JavaScript by their names.
+
+Other static fields are properties of their class and can be used as expected.
+
+Note, however, that SwingJS runs all "Java" code on a page in a common "jvm"
+(like older versions of Java). So, like the older Java schema, the JavaScript
+equivalents of both applets and applications will share all of their static
+fields and methods. This includes java.lang.System.
+
+Basically, SwingJS implementations of Java run in a browser page-based sandbox
+instead of an applet-specific one.
+
+In general, this is no problem. But if we are to implement pages with
+multiple applets present, we must be sure to only have static references
+that are "final" or specifically meant to be shared in a JavaScript
+environment only (since they will not be shared in Java).
+
+A simple solution, if static non-constant references are needed, is to attach the
+field to Thread.currentThread.threadGroup(), which is an applet-specific reference.
+Be sure, if you do this, that you use explicit setters and getters:
+
+For example,
+
+private static String myvar;
+
+...
+
+public void setMyVar(String x) {
+ ThreadGroup g = Thread.currentThread().threadGroup();
+ /**
+ * @j2sNative g._myvar = x;
+ *
+ */
+ {
+ myvar = x;
+ }
+}
+
+public String getMyVar() {
+ ThreadGroup g = Thread.currentThread().threadGroup();
+ /**
+ * @j2sNative return g._myvar || null;
+ *
+ */
+ {
+ return myvar;
+ }
+}
+
+ in Java will get and set x the same in JavaScript and in Java.
+
+
+A convenient way to do this in general is to supply a singleton class with
+explicitly private-only constructors and then refer to it in Java and in JavaScript
+instead of using static field, referring to myclass.getIntance().xxx instead of
+myclass.xxx in Java (and JavaScript).
+
+This was done extensively in the Jalview project. See jalview.bin.Instance.
+
+
+Helper Packages -- swingjs/ and javajs/
+---------------------------------------
+
+The SwingJS library is the swingjs/ package. There are interfaces that may be of assistance
+in swingjs/api, but other than that, it is not recommended that developers access classes in
+this package. The "public" nature of their methods is really an internal necessity. Most access
+to this package in working Java should be via the swingjs.api.JSUtilI interface.
+
+In addition to swingjs/, though, there are several useful classes in the javajs/ package
+that could be very useful. This package is a stand-alone package that can be
+cloned in any Java project that also would be great to have in any JavaScript project
+-- SwingJS-related or not. Functionality ranges from reading and writing various file
+formats, including PDF, BMP, PNG, GIF, JPG, JSON, ZIP, and CompoundDocument formats.
+
+A variety of highly efficient three- and four-dimensional point, vector, matrix, and
+quaternion classes are included, as they were developed for JSmol and inherited from that
+project.
+
+Of particular interest should be javajs/async/, which includes
+
+javajs.async.Async
+javajs.async.AsyncColorChooser
+javajs.async.AsyncDialog
+javajs.async.AsyncFileChooser
+
+See javajs.async.Async JavaDoc comments for a full description of
+these useful classes.
+
+
+Modal Dialogs
+-------------
+
+Although true modal dialogs are not possible with only one thread, a functional equivalent --
+asynchronous modal dialogs -- is relatively easy to set up. All the JOptionPane dialogs will
+return PropertyChangeEvents to signal that they have been disposed of and containing the results.
+See below and classes in the javajs.async package.
+
+
+Native calls
+------------
+
+Native calls in Java are calls to operating system methods that are not in Java. JavaScript
+has no access to these, of course, and they must all be replaced by JavaScript equivalents.
+Fortunately, they are not common, and those that are present in Java (for example, in calculating
+checksums in ZIP file creation) are at a low enough level that most developers do not utilize them
+or do not even have access to them. All native calls in Java classes have been replaced by
+Java or JavaScript equivalents.
+
+
+Swing GUI Peers and UIClasses
+-----------------------------
+
+One of the biggest adaptations introduced in SwingJS is in the area of the graphical
+user interface. Basically, what we have is a Java Swing "LookAndFeel" customized for HTML.
+
+The issue here is complex but workable. In Java there are two background concepts -- the
+Component "peer" (one per "heavy-weight" component, such as a Frame) and the
+component "uiClass" (one per component, such as BasicButtonUI or BasicTextFieldUI).
+
+Peers are native objects of the operating system. These are the virtual buttons and text areas
+that the user is interacting with at a very base level. They are chunks of low-level code that
+paint the screen to give the illusion that you really are pressing a button or typing text
+ot the screen. Their events are being passed on to Java or the browser by the operating system.
+
+UI classes provide a consistent "look and feel" for these native objects, rendering them onto
+the native window canvas and handling all user-generated events. They paint the borders,
+the backgrounds, the highlights, of every control you see in Java. There is one-to-one
+correspondence of Swing classes and UI classes. Setting the Look and Feel for a project amounts
+to selecting the directory from which to draw these UI classes. Java's UI class interfaces can
+be found in the javax.swing.plaf ("platform look and feel") package. Individual look and feel
+implementations are found in sun.plaf.basic, sun.plaf.metal, and other such specialized packages.
+
+Early on in the development of SwingJS, we decided not to fully reproduce the painfully detailed
+bit-by-bit painting of controls as is done in Java. Instead, we felt it was wiser to utilize the standard
+HTML5 UI capabilities as much as possible, using DIV, and INPUT especially, with extensive use
+of CSS and sometimes jQuery (menus, and sliders, for example). Thus, we have created a new
+set of UIs -- the "HTML5 Look and Feel". These classes can be found in swingjs.plaf. Besides being
+more adaptable, this approach allows far more versatility to SwingJS developers, allowing them
+to modify the GUI to suit their needs if desired.
+
+In SwingJS, since we have no access to native peers except through the browser DOM,
+it seemed logical to merge the peer and UI idea. So instead of having one peer per heavy-weight control and
+one UI class instance for each control type, we just have one UI class instance per control, and
+that UI class instance is what is being referred to when a "peer" is notified.
+
+In some ways this is a throw back to when all of Swing's components were subclasses of
+specific AWT components such as Button and List. These "heavy-weight components" all had their
+own individual native peers and thus automatically took on the look and feel provided by the OS.
+Later Swing versions implemented full look and feel for all peers, leaving only JDialog, JFrame,
+and a few other classes to have native peers. But in SwingJS we have again a 1:1 map of component
+and UI class/peer instance.
+
+The origin of most issues (read "bugs") in relation to the GUI will probably be found in the
+swingjs.plaf JSxxxxUI.java code.
+
+
+Swing-only Components -- no longer an issue
+-------------------------------------------
+
+Swing was introduced into Java well after the Java Abstract Window Toolkit (AWT) was well
+established. As such, its designers chose to allow AWT controls such as Button and List to be used
+alongside their Swing counterparts JButton and JList. Reading the code, it is clear that this
+design choice posed a huge headache for Swing class developers.
+
+For SwingJS, we decided from the beginning NOT to allow this mixed-mode programming and
+instead to require that all components be Swing components. However, this is not really an
+issue. We have reconfigured the class relationships a bit. In SwingJS, all AWT components
+are now subclasses of javax.swing.JComponent. While this might seem error prone, so far we have
+found no problem with this arrangement. It's a little surprising to me that the original developers
+of Swing did not think of this.
+
+
+The a2s Adapter Package
+-----------------------
+
+Originally, we thought that we would restrict ourselves to JApplets only. That is, only
+Swing-based applets. But as we worked, we discovered that there are a lot of great
+applets out there that are pre-Swing pure-AWT java.applet.Applet applets. Our problem was
+that we also wanted it to be possible to quickly adapt these applets to JavaScript as well.
+
+The solution turned out to be simple: Write a package (a2s) that recreates the interface for
+non-Swing components as subclasses of Swing components. Thus, a2s.Button subclasses javax.swing.JButton
+but also accepts all of the methods of java.awt.Button. This works amazingly well, with a few
+special adaptations to the core javax.swing to be "AWT-aware."
+
+Then, to tie it all togeter, all AWT components such as java.awt.Button now subclass their respective
+a2s components, which in turn subclass JComponents. So no changes in code are necessary. We have
+successfully transpiled over 500 applets using this strategy.
+
+Working with Files
+==================
+
+Simple String file names are not optimal for passing information about
+files read by SwingJS applications. That is because just peeking at a file
+in SwingJS will load its entire byte[] data.
+
+Optimally, all work with files should either use Path or File objects exclusively.
+These objects, after a file is read or checked for existence, will already
+contain the file byte[] data. The string name can be used alone, since SwingJS will
+cache the files itself and not reload them -- just as the browser normally does.
+
+SwingJS uses the following criteria to determine if File.exists() returns true:
+
+(1) if this File object has been used directly to read data, or
+(2) if reading data using this File object is successful.
+
+Note that you cannot check to see if a file exists before input or if it
+was actually written or if it already exists prior to writing in SwingJS.
+
+Thus, you should check each use of file.exists() carefully, and if necessary, provide a J2sNative
+block that gives an appropriate "OK" message, for example:
+
+(/** @j2sNative 1 ? false : */ outputfile.exits())
+
+or
+
+(/** @j2sNative 1 ? true : */ inputfile.exits())
+
+Temporary files can be created in SwingJS. SwingJS will maintain a pseudo-filesystem for files
+created with File.createTempFile(). This is useful in that closure of writing to a temporary file
+does not generate a pseudo-download to the user's machine. Temporary files will be placed in the
+"/TEMP/" directory, as seen from the running Java program. Any file written to this directory will
+simply be stored in memory; files written to any other directory, when closed, will appear to the
+user as a download, often involving a "What do you want to do with this file" dialog.
+
+
+See below for details relating to each of the subjects below:
+
+
+UNIMPLEMENTED CLASSES BY DESIGN
+===============================
+
+The SwingJS implementation of the following classes are present
+in a way that gracefully bypasses their functionality:
+
+accessibility
+security
+serialization
+
+
+
+TODO LIST FOR UNIMPLEMENTED CLASSES
+===================================
+
+none as of 2020.12.31. Source code for classes and methods missing
+from Java 8 or from Java 9+ can be inserted by any developer along
+with their running code source, and they should run.
+
+
+MINOR ISSUES--required some rewriting/refactoring by Bob and Udo
+================================================================
+
+Thread.currentThread() == dispatchThread
+
+
+MINOR ISSUES--requiring some rewriting/refactoring outside of SwingJS
+=====================================================================
+
+See below for a full discussion.
+
+primitive type restrictions - int, long, and float
+HashMap, Hashtable, and HashSet iterator ordering
+interning, new String("xxx") vs "xxx"
+Names with "$" and "_"
+ArrayIndexOutOfBounds
+java.awt.Color
+native methods
+javax.swing.JFileDialog
+key focus
+LookAndFeel and UI Classes
+System.exit(0) does not stop all processes
+list cell renderers must be JComponents
+myClass.getField not implemented
+"window" and other reserved JavaScript names
+reserved field and method names
+qualified field and method names
+Component.getGraphics(), Graphics.dispose()
+Graphics.setClip()
+
+MAJOR ISSUES--for Bob and Udo within SwingJS
+============================================
+
+fonts
+OS-dependent classes
+AWT component peers
+some aspects of reflection
+
+MAJOR ISSUES--to be resolved by implementers
+============================================
+
+fonts
+threads
+modal dialogs
+image loading
+no format internationalization
+Graphics2D: missing winding rules
+text-related field implementation
+Formatter/Regex limitations
+
+========================================================================
+
+DISCUSS
+=======
+
+Table row/col sorter needs checking after removal of java.text.Collator references
+
+==========================================================================
+
+//////////////////////////////////////////////////////////////////////////////
+
+UNIMPLEMENTED CLASSES
+=====================
+
+accessibility
+-------------
+
+All Accessibility handling has been commented out to save the download footprint.
+This removes the need for sun.misc.SharedSecrets as well.
+Nothing says we could not implement accessibility. We just didn't.
+
+
+security
+--------
+
+All JavaScript security is handled by the browser natively.
+Thus, Java security checking is no longer necessary, and
+java.security.AccessController has been simplified to work without
+native security checking.
+
+Note that private methods in a class are REALLY private.
+
+
+serialization
+-------------
+
+All serialization has been removed. It was never very useful for Swing anyway,
+because one needs exactly the same Java version to save and restore serialized objects.
+
+
+keyboard accelerators and mnemonics
+-----------------------------------
+
+This work was completed in the spring of 2019. Note that in a browser, some
+key strokes, particularly CTRL-keys, are not available. Bummer.
+
+
+MINOR ISSUES--required some rewriting/refactoring by Bob and Udo
+================================================================
+
+
+Thread.currentThread() == dispatchThread
+----------------------------------------
+
+changed to JSToolkit.isDispatchThread()
+
+
+MINOR ISSUES--requiring some rewriting/refactoring outside of SwingJS
+=====================================================================
+
+primitive restrictions - int, long, and float
+---------------------------------------------
+
+int
+
+For performance reasons, int addition and multiplication do not by default overflow to
+negative values. Instead, they just get bigger. Java code that relies on overflow to
+negative values should be surrounded by ()|0 -- an OR with integer 0:
+
+
+int bigI, bigJ;
+...
+
+bigI = (bigI + bigJ)|0;
+
+bigI = (bigI + 1)|0; //instead of bigI++
+
+
+Thus, in Java, the following is true:
+
+ 2000000000 + 2000000000 == -294967296
+
+But in SwingJS, that will be 4000000000. So, for example, the following
+strategy will fail in SwingJS:
+
+ int newLength = lineBuf.length * 2;
+ if (newLength < 0) {
+ newLength = Integer.MAX_VALUE;
+ }
+
+This is because, generally, "-1" in JavaScript is not 0xFFFFFFFF. The simple ()|0 takes
+caes of this:
+
+ int newLength = (lineBuf.length * 2)|0;
+ if (newLength < 0) {
+ newLength = Integer.MAX_VALUE;
+ }
+
+JavaScript does process bitwise operators & | ^ ~ properly for int values. There is no issue using
+these operations.
+
+Note that int 1/0 in Java throws "java.lang.ArithmeticException: / by zero", but in JavaScript is just Infinity.
+
+Importantly, the JavaScript Int32Array does behave properly. From the Firefox developer console:
+
+>> x = new Int32Array(1)
+<- Int32Array(1) [ 0 ]
+>> x[0] = 4000000000
+<- 4000000000
+>> x[0]
+<- -294967296
+
+Notice that, perhaps unexpectedly, the following two constructs produce
+different results in JavaScript:
+
+x = new Int32Array(1);
+b = x[0] = 4000000000;
+
+(b will be 4000000000)
+
+and
+
+x = new Int32Array(1);
+x[0] = 4000000000;
+b = x[0];
+
+(b will be -294967296)
+
+
+SwingJS leverages array typing to handle all byte and short arithmetic so as
+to ensure that any byte or short operation in JavaScript does give the same
+result in Java.
+
+long
+
+Java's 64-bit long type is fully supported, starting with java2script 3.3.1 (2020.12.31)
+The transpiler handles all conversions to and from long appropriately. See the discussion
+at https://github.com/BobHanson/java2script/issues/202 for how this is done.
+
+float
+
+SwingJS does not distinguish between float and double. Everything is double.
+
+
+HashMap, Hashtable, and HashSet iterator ordering
+-------------------------------------------------
+
+In Java, iterators for HashMap, Hashtable, and HashSet do not guarantee any particular order.
+From the HashMap documentation for Java 8:
+
+ This class makes no guarantees as to the order of the map; in particular, it does not
+ guarantee that the order will remain constant over time.
+
+Likewise, for HashSet (because it is simply a convenience method for HashMap<Object,PRESENT>:
+
+ [HashSet] makes no guarantees as to the iteration order of the set.
+
+JavaScript's Map object is different. It is basically a LinkedHashMap, so it guarantees iteration
+in order of object addition.
+
+Starting with java2script 3.2.9.v1, these classes use the JavaScript Map object rather than hash codes
+whenever all keys are strictly of JavaScript typeof "string". If any key is introduced that is not a string, the
+implementation falls back to using hash codes, the same as Java.
+
+The result is significantly faster performance (3-12 x faster) than originally, and up to 3 x faster
+performance in JavaScript than in Java itself. That is not a misprint. Faster than Java.
+
+The JavaScript Map implementation is implemented UNLESS the constructor used is the one that
+specifies both initial capacity and load factor in their constructor. Thus,
+
+new Hashtable()
+new HashMap()
+new HashMap(16)
+new HashSet()
+
+all use the JavaScript Map. But
+
+new Hashtable(11, 0.75f)
+new HashMap(16, 0.75f)
+new HashSet(16, 0.75f)
+
+do not.
+
+This design allows for opting out of the JavaScript Map use in order to retain the exact behavior of
+iterators in JavaScript as in Java.
+
+
+interning, new String("xxx") vs "xxx"
+-------------------------------------
+
+Note that the following are true in JavaScript:
+
+typeof new String("xxxx") == "object"
+typeof "xxxx" == "string"
+var s = "x";typeof ("xxx" + s) == "string"
+
+There is no equivalence to this behavior in Java, where a String is a String is a String.
+
+Be aware that SwingJS does not always create a JavaScript String object using JavaScript's
+new String(...) constructor. It only does this for Java new String("xxxx") or new String(new String()).
+
+In all other cases, new String(...) (in Java) results in a simple "xxxx" string in JavaScript.
+That is, it will be JavaScript typeof "string", not typeof "object".
+
+The reason for this design is that several classes in the Java core use toString()
+methods that return new String(), and those classes that do that would cause a JavaScript error
+if implicitly stringified if new String() returned a JavaScript String object.
+
+This is fine in JavaScript:
+
+test1 = function() { return { toString:function(){ return "OK" } } }
+"testing" + new test1()
+>> "testingOK"
+
+But for whatever reason in JavaScript:
+
+test2 = function() { return { toString:function(){ return new String("OK") } } }
+"testing" + new test2()
+>> Uncaught TypeError: Cannot convert object to primitive value
+
+The lesson here is never to use
+
+ return new String("...");
+
+in a Java toString() method. In Java it will be fine; in JavaScript it will also be fine as long as
+that method is never called in JavaScript implicitly in the context of string concatenation.
+
+A note about interning. Consider the following six Java constructions, where we have a == "x";
+
+"xxx"
+"xx" + "x"
+new String("xxx").intern()
+
+new String("xxx")
+"xx" + a.toString()
+"xx" + a
+
+All six of these will return java.lang.String for .getClass().getName().
+However, the first three are String literals, while the last three are String objects.
+Thus:
+ "xxx" == "xxx"
+ "xxx" == "xx" + "x"
+ "xxx" == new String("xxx").intern()
+
+but none of the other three are equivalent to "xxx" or each other:
+
+ "xxx" != new String("xxx")
+ "xxx" != "xx" + a.toString()
+ "xxx" != "xx" + a
+ new String("xxx") != new String("xxx")
+ "xx" + a != new String("xxx")
+
+etc.
+
+As in Java, in SwingJS, all of the following Java assertions pass as true:
+
+ assert("xxx" == "xx" + "x");
+ assert("xxx" == ("xx" + a).intern());
+ assert("xxx" === new String("xxx").intern());
+
+and both of these do as well:
+
+ assert(new String("xxx") != "xxx");
+ assert(new String("xxx") != new String("xxx"));
+
+But the following two fail to assert true in SwingJS:
+
+ assert("xxx" != "xx" + a);
+ assert("xxx" != "xx" + a.toString());
+
+because, in JavaScript, both of these right-side expressions evaluate to a simple "interned" string.
+
+In Java, however, these assertions are true because Java implicitly "boxes" String
+concatentaion as a String object, not a literal.
+
+Most of us know not to generally use == with Strings unless they are explicitly interned.
+Where this problem may arise, though, is in IdentityHashMap, which compares objects using
+System.identityHashCode(), which is not the same for different objects or their string literal equivalents.
+
+My recommendation, if you need to use IdentityHashMap with strings is to always use an explicit String.intern()
+for any keys -- unless you really want to keep every string as separate keys even if they are the same sequence,
+in which case, use new String(). This will work in Java and in JavaScript.
+
+Be aware when working with strings that come from SwingJS and are being used by other JavaScript modules
+that those that are String objects will return "object" for the JavaScript typeof operator, not "string".
+
+The easy way to ensure this is no problem is to concatenate strings with "" to force immediate interning:
+
+ var x = aJavaObject.getString() + "";
+
+unless you are certain that the string is being returned is a raw JavaScript string.
+
+
+Names with "$" and "_"
+----------------------
+
+For the most part, this should be no problem.
+
+Note that the use of $ and _ in Java field names has always been discouraged:
+[https://docs.oracle.com/javase/tutorial/java/nutsandbolts/variables.html]
+
+ You may find some situations where auto-generated names will contain the dollar sign,
+ but your variable names should always avoid using it. A similar convention
+ exists for the underscore character; while it's technically legal to begin your
+ variable's name with "_", this practice is discouraged.
+
+Some impacts of transpiling method names with full qualification:
+
+1) SwingJS will introduce fields that start with $ or _. These will not conflict
+ if the above convention is followed.
+
+2) Fields that have the same Java name as a method are not an issue.
+
+3) Fields that have a Java name with $ that matches a transpiled method name,
+ such as toString$, will need to be refactored in Java to not have that name collision.
+
+4) Fields in a subclass that have the same name as private fields in a superclass
+ represent a name collision, because the superclass method needs to call its private
+ field even if invoked from a subclass. The solution was to modify the subclass field
+ name using one or more prepended $.
+
+5) Use of Class.getDeclaredMethods() reflection will return Method objects having the transpiled
+ name, not the Java name. This could require some j2sNative adjustment
+ to strip the $... parameters from the name if that is needed.
+
+6) Use of Method.getParameterTypes() should work fine, provided class names
+ do not contain "_". This is because the transpiler converts "." to "_" when
+ creating the fully qualified JavaScript name.
+
+
+ArrayIndexOutOfBounds
+---------------------
+
+You cannot implicitly throw an ArrayIndexOutOfBoundsException in JavaScript.
+JavaScript will simply return "undefined", not throw an Exception. So:
+
+boolean notAGoodIdeaIsOutOfBounds(String[] sa, int i) {
+ try {
+ return (sa[i] == sa[i]);
+ } catch (ArrayIndexOutOfBoundsException e) {
+ return false;
+ }
+}
+
+will work in Java but not in JavaScript. Code should not depend upon this sort
+of trap anyway, if you ask me.
+
+
+Throwable vs Error vs Exception
+-------------------------------
+
+True JavaScript errors are trapped as Throwable, whereas you can still trap
+Error and Exception as well. So if you want to be sure to catch any JavaScript
+error, use try{}catch (Throwable t){}, not try{}catch (Exception e){}.
+
+java.awt.Color
+--------------
+
+ColorSpace: only "support" CS_sRGB.
+
+ TODO -- any volunteers??
+
+
+javax.swing.JFileDialog
+-----------------------
+
+HTML5 cannot expose a file reading directory structure. But you certainly
+can still do file reading and writing. It just works a little differently.
+It's a simple modification:
+
+ b = new JButton("FileOpenDialog");
+ b.addActionListener(new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ JFileChooser fc = new JFileChooser();
+ Test_Dialog.this.onDialogReturn(fc.showOpenDialog(Test_Dialog.this));
+ // Java will wait until the dialog is closed, then enter the onDialogReturn method.
+ // JavaScript will exit with NaN immediately, and then call back with its actual value
+ // asynchronously.
+ }
+
+ });
+
+ public void onDialogReturn(int value) {
+ if (value != Math.floor(value))
+ return; // in JavaScript, this will be NaN, indicating the dialog has been opened
+ // If we are here, the dialog has closed, in both Java and JavaScript.
+ System.out.println("int value is " + value);
+ }
+
+
+ @Override
+ public void propertyChange(PropertyChangeEvent event) {
+ Object val = event.getNewValue();
+ String name = event.getPropertyName();
+ System.out.println(name);
+ switch (event.getSource().getClass().getName()) {
+ case "javax.swing.JOptionPane":
+ switch (name) {
+ case "inputValue":
+ onDialogReturn(val);
+ return;
+ case "value":
+ if (val instanceof Integer)
+ onDialogReturn(((Integer) val).intValue());
+ else
+ onDialogReturn(val);
+ return;
+ }
+ break;
+ case "javax.swing.ColorChooserDialog":
+ switch (name) {
+ case "SelectedColor":
+ onDialogReturn(val);
+ return;
+ }
+ break;
+ case "javax.swing.JFileChooser":
+ switch (name) {
+ case "SelectedFile":
+ File file = (File) val;
+ byte[] array = (val == null ? null : /** @j2sNative file.秘bytes || */
+ null);
+ onDialogReturn("fileName is '" + file.getName() + "'\n\n" + new String(array));
+ return;
+ }
+ break;
+ }
+ System.out.println(
+ event.getSource().getClass().getName() + " " + event.getPropertyName() + ": " + event.getNewValue());
+ }
+
+
+Developers are encouraged to create a separate class that handles general calls to JFileDialog.
+An example class can be found in the SwingJS distribution as
+
+/sources/net.sf.j2s.java.core/src/javajs/async/AsyncFileChooser.java.
+
+
+javax.swing.JOptionPane dialogs
+-------------------------------
+
+For a full discussion of modal dialogs, see the javajs.asyc.AsyncDialog.java discussion.
+
+For this action to work, the parent component must implement
+propertyChangeListener, and any call to JOptionPanel should allow for
+an asynchronous response, meaning that there is no actionable code following the
+call to the dialog opening.
+
+In addition, for compatibility with the Java version, implementation should
+wrap the call to getConfirmDialog or getOptionDialog in a method call to
+handle the Java:
+
+onDialogReturn(JOptionPane.showConfirmDialog(parentFrame,
+messageOrMessagePanel, "title", JOptionPane.OK_CANCEL_OPTION));
+
+Then parentFrame.propertyChange(event) should also call onDialogReturn.
+
+This will then work in both Java and JavaScript.
+
+Note that there is an int and an Object version of onDialogReturn().
+
+
+In JavaScript:
+
+The initial return from JOptionPane.showConfirmDialog and showMessageDialog
+will be (SwingJS) JDialog.ASYNCHRONOUS_INTEGER (NaN), testable as an impossible
+Java int value using ret != -(-ret) if the parent implements PropertyChangeListener, or -1
+(CLOSE_OPTION) if not.
+
+For showOptionDialog (which returns Object) or showInputDialog (which returns
+String), the initial return will be (SwingJS) JDialog.ASYNCHRONOUS_OBJECT, testable as
+((Object) ret) instanceof javax.swing.plaf.UIResource if the parent implements
+PropertyChangeListeneer, or null if not.
+
+The second return will be the desired return.
+
+In Java:
+
+The initial return will be the one and only modal final return.
+
+
+
+For full compatibility, The calling method must not continue beyond this call.
+
+All of the standard Java events associated with Components are also available.
+
+Certain fall back mechanisms are possible, where onReturn does not exist, but
+only for the following cases:
+
+
+For showMessageDialog, for WARNING_MESSAGE and ERROR_MESSAGE, a simple
+JavaScript alert() is used, returning 0 (OK_OPTION) or -1 (CLOSED_OPTION).
+
+For showInputDialog, if the message is a string, a simple JavaScript prompt()
+with input box is used, returning the entered string or null.
+
+For showConfirmDialog, a simple JavaScript confirm() is used, in which case:
+
+for YES_NO_OPTION: YES_OPTION or NO_OPTION
+
+for YES_NO_CANCEL_OPTION: YES_OPTION or CANCEL_OPTION
+
+for OK_CANCEL_OPTION or any other: OK_OPTION or CANCEL_OPTION
+
+Note that you should implement a response for CLOSED_OPTION for
+showConfirmDialog. For other dialogs, a null return indicates the dialog was
+closed, just as for Java.
+
+Developers are encouraged to create a separate class that handles general calls.
+An example class can be found in the SwingJS distribution as src/javajs/async/AsyncDialog.java.
+Very simple modifications to the Java allows asynchronous operation using AsyncDialog. Here
+is a simple "do you want to close this frame" example, where you can see that what we have
+done is to set the reply into an ActionListener that is defined in the constructor of
+the AsyncDisplay object:
+
+// Original:
+//
+// private void promptQuit() {
+// int sel = JOptionPane.showConfirmDialog(null, PROMPT_EXIT, NAME, JOptionPane.YES_NO_OPTION);
+// switch (sel) {
+// case JOptionPane.YES_OPTION:
+// resultsTab.clean();
+// seqs.dispose();
+// if (fromMain) {
+// System.exit(0);
+// }
+// break;
+// }
+// }
+
+ private void promptQuitAsync() {
+ new AsyncDialog(new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ int sel = ((AsyncDialog)e.getSource()).getOption();
+ switch (sel) {
+ case JOptionPane.YES_OPTION:
+ resultsTab.clean();
+ seqs.dispose();
+ if (fromMain) {
+ System.exit(0);
+ }
+ break;
+ }
+ }}).showConfirmDialog(null, PROMPT_EXIT, NAME, JOptionPane.YES_NO_OPTION);
+ }
+
+Very simple!
+
+
+native methods
+--------------
+
+The J2S compiler ignores all static native method declarations.
+Anything of this nature needs to be implemented in JavaScript if it is needed,
+using j2sNative blocks:
+
+/**
+ * @j2sNative
+ *
+ * var putYourJavaScriptCodeHere
+ *
+ */
+
+ Note that if you follow that directly with a {...} block, then
+ only the javadoc code will run in JavaScript, and only the {...} code will run in Java.
+
+
+key Focus
+---------
+
+As of June, 2019, the keyboard focus manager is fully implemented.
+The one catch is that JTextPane and JTextArea, which already consume
+VK_TAB in Java, cannot use CTRL-TAB to continue a tabbing cycle around
+the components in a window. Instead, CTRL-TAB is absorbed by the browser.
+
+
+LookAndFeel and UI Classes
+--------------------------
+
+SwingJS implements the native browser look and feel as swingjs.plaf.HTML5LookAndFeel.
+There are small differences between all look and feels -- MacOS, Windows, SwingJS.
+
+Expert developers know how to coerce changes in the UI by subclassing the UI for a
+component. This probably will not work in SwingJS.
+
+Note that LookAndFeel in Java usually determines canvas size in a Frame because
+different operating systems (Mac OS vs Windows vs HTML5) will have
+different edge sizes on their frames. If you want to ensure a component size,
+use getContentPane().setPreferredSize().
+
+
+System.exit(0) does not stop all processes
+------------------------------------------
+
+Although System.ext(int) has been implemented in JavaScript, it just closes the
+frames, stops all pending javax.swing.Timer objects in the queue, and runs any
+threads added using Runtime.getRuntime().addShutdownHook(Thread).
+It may not stop all "threads." So don't rely on that.
+Applications are responsible for shutting down prior to executing System.exit(0).
+
+
+myClass.getField not implemented
+--------------------------------
+
+java.lang.reflect.Field is implemented minimally. It is not
+certain that Field.getDeclaringClass() will work. If you just want a
+value of a field, you can do this:
+
+/**
+ *@j2sNative
+ *
+ * return myClass[name]
+ */
+
+But that is not a java.lang.reflection.Field object.
+
+
+"window" and other reserved JavaScript names
+--------------------------------------------
+
+No reserved top-level JavaScript name is allowed for a package name. So, for example,
+one must rename packages such as "window" or "document" to names such as "win" or "doc".
+
+
+reserved field and method names
+-------------------------------
+
+In order to minimize the chance of added SwingJS field and method names colliding with ones
+developers might use in subclassing Java classes, we have added U+79D8 (first character of Mandarin
+"secret") to the characters already disrecommended by Java documentation ("$" and "_"). The only problem
+would be if you use that character followed by certain English words in certain classes. For example
+\u79D8canvas for JComponents (in java.awt.JSComponent) and \u79D8byte (in java.io.File).
+
+
+qualified field and method names
+--------------------------------
+
+Method names in SwingJS are fully qualified, meaning two methods with the same Java name but different
+parameters, such as write(int) and write(double), must not have the same name in JavaScript. (In this
+case, we will have write$I and write$D.) However, in certain cases it may be desirable to leave the
+method names unqualified. In particular, when an interface actually represents a JavaScript object,
+the transpiler can leave a method name unqualified.
+
+You can implement a simple name for a method using the @j2sAlias annoation in the javadoc for the
+method involved. For example:
+
+
+/**
+ * @j2sAlias read
+ *
+ */
+public void read(byte[] buf, int pos, int len) {...}
+
+will allow the method to be accesible either as "read" or "read$BA$I$I" in JavaScript.
+
+
+The default situation for this is a class name includes ".api.js" (case-sensitive).
+This means that any method in any class in a package js within a package api, or any private interface js
+that has an outer interface api, will have all-unqualified methods. An example of this is
+swingjs.plaf.JSComboPopupList, which needs to communicate with a jQuery
+object directly using the following interface:
+
+ private interface api {
+
+ interface js extends JQueryObject {
+
+ abstract js j2sCB(Object options);
+
+ abstract Object[] j2sCB(String method);
+
+ abstract Object[] j2sCB(String method, Object o);
+
+ abstract Object[] j2sCB(String method, int i);
+
+ abstract int j2sCB(String OPTION, String name);
+
+ }
+ }
+
+Notice that all these variants of j2sCB() will call the same method in JavaScript by design.
+
+
+Component.getGraphics(), Graphics.dispose()
+-------------------------------------------
+
+Use of component.getGraphics() is discouraged in Java and in SwingJS.
+Specifically in SwingJS, any call to component.getGraphics() or
+BufferedImage.createGraphics() or Graphics.create(...) should be matched with graphics.dispose(),
+particularly when it is called outside the context of a paint(Graphics) call from the system.
+
+If you see your graphics scrolling down the page with each repaint,
+look for where you have used Component.getGraphics() and not Graphics.dispose().
+For example, this will definitely NOT work in SwingJS:
+
+ this.paint(getGraphics())
+
+and really should not work in Java, either, as it is technically a resource memory leak.
+
+Instead, if you really do not want to use repaint(), use this:
+
+ Graphics g = getGraphics();
+ paint(g);
+ g.dispose();
+
+
+
+Graphics.setClip()
+------------------
+
+The HTML5 canvas.clip() method is permanent. You can only reset the clip using
+save/restore. This is different from Java, where you can temporarily change it using
+
+ Shape oldClip = Graphics.getClip();
+ Graphics.setClip(newClip);
+ ...
+ Graphics.setClip(oldClip);
+
+If you need to do something like this, you must schedule the paints to not have overlapping clip needs.
+
+
+MAJOR ISSUES--for Bob and Udo within SwingJS
+============================================
+
+fonts
+-----
+
+Fonts and FontMetrics will all be handled in JavaScript. Font matching will
+not be exact, and composite (drawn) fonts will not be supported.
+
+SwingJS handles calls such as font.getFontMetrics(g).stringWidth("xxx") by
+creating a <div> containing that text, placing it in an obscure location on
+the page, and reading div.getBoundingClientRect(). This is a VERY precise
+value, but can be a pixel or two off from what Java reports for the same font.
+
+
+OS-dependent classes
+--------------------
+
+Static classes such as:
+
+ java.awt.Toolkit
+ java.awt.GraphicsEnvironment
+
+which are created using Class.forName are implemented using classes in the swingjs package.
+
+sun.awt.AWTAccessor is not implemented.
+
+
+AWT component peers and component "ui" user interfaces
+------------------------------------------------------
+
+ComponentPeer is a class that represents a native AWT component.
+Components with such peers are called "heavy-weight" components.
+They are expected to do the dirty work of graphics drawing.
+
+Java Swing implements peers only for JApplet, JDialog, JFrame, and JWindow.
+References to such objects have been removed, but clearly there must be
+some connection to similar DOM objects, even for "light-weight" components.
+
+
+MAJOR ISSUES--to be resolved by implementers
+============================================
+
+fonts
+-----
+
+Glyph/composite/outline fonts are not supported.
+
+
+
+threads
+-------
+
+Thread locking and synchronization are not relevant to JavaScript.
+Thus, anything requiring "notify.." or "waitFor.." could be a serious issue.
+
+All threading must be "faked" in JavaScript. Specifically not available is:
+
+ Thread.sleep()
+
+javax.swing.AbstractButton#doClick(pressTime) will not work, as it requires Thread.sleep();
+
+However, java.lang.Thread itself is implemented and used extensively.
+
+Methods thread.start() and thread.run() both work fine.
+
+For simple applications that use Thread.sleep() just to have a delay, as in a frame rate, for
+example, one can use javax.swing.Timer instead. That is fully implemented.
+
+Likewise, java.util.Timer can be replaced with no loss of performance with javax.Swing.Timer.
+Note that java.util.TimerTask is implemented, but it can also be replaced by an implementation of Runnable.
+
+task = new TimerTask(){....};
+t = new java.util.Timer();
+t.schedule(task, 0, 1);
+
+becomes
+
+task = new TimerTask(){....}; // or task = new Runnable() {...}
+t = new javax.swing.Timer(1, new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ task.run();
+ }
+};
+t.setInitialDelay(0); // not particularly necessary
+t.start();
+
+In addition, SwingJS provides swingjs.JSThread, which can be subclassed
+if desired. This class allows simple
+
+ while(!interrupted()){
+ wait()
+ ...
+ }
+
+action through an asynchronous function run1(mode). For example:
+
+ protected void run1(int mode) {
+ try {
+ while (true)
+ switch (mode) {
+ case INIT:
+ // once-through stuff here
+ mode = LOOP;
+ break;
+ case LOOP:
+ if (!doDispatch || isInterrupted()) {
+ mode = DONE;
+ } else {
+ Runnable r = new Runnable() {
+ public void run() {
+ // put the loop code here
+ }
+ };
+ dispatchAndReturn(r);
+ if (isJS)
+ return;
+ }
+ break;
+ // add more cases as needed
+ case DONE:
+ // finish up here
+ if (isInterrupted())
+ return;
+ // or here
+ break;
+ }
+ } finally {
+ // stuff here to be executed after each loop in JS or at the end in Java
+ }
+ }
+
+
+image loading
+-------------
+- All image loading in SwingJS is synchronous. A MediaTracker call will immediately return "complete".
+ However, it still may take one system clock tick to fully load images. Thus, it is recommended that
+ images be preloaded in the static block of the applet if it is necessary that they be available in init().
+ This is only an issue if you are trying to access the pixel buffer of the image in JavaScript.
+
+- Applet.getImage(path, name) will return null if the image does not exist.
+
+- BufferedImage: only "support" imageType RGB and ARGB
+
+ -BH: This is a temporary edit, just to get us started. Certainly GRAY will be needed
+
+
+BigInteger and BigDecimal
+-------------------------
+
+java.math.BigInteger and java.math.BigDecimal are fully supported.
+
+
+no format internationalization
+------------------------------
+
+For now, just "en" for number and date formatters
+
+
+missing winding rules
+---------------------
+
+When filling a graphic, only nonzero winding rule is implemented in HTML5 Canvas2D.
+
+
+
+text-related field implementation
+---------------------------------
+
+Text fields are:
+
+JTextField (JavaScript <input type="text">)
+JTextArea (JavaScript <textarea>)
+JTextPane (JavaScript <div>)
+JEditorPane (JavaScript <div>)
+
+For the initial implementation, we don't implement infinite undo/redo, and the abstract
+document model is much less elaborate. Only PlainDocument (in the form of JSPlainDocument)
+is implemented. The Document returned by JTextField.getDocument() is a javax.swing.text.Document.
+
+All scrolling is handled by HTML5. javax.swing.AutoScroller is not implemented.
+public static methods .stop, .isRunning, .processMouseDragged require true Java threading
+and so are not implmented. javax.swing.text.View and its subclasses are not implemented.
+
+The JS document model does not allow two text fields to address the same underlying document.
+
+JavaScript is slightly different from Java in that the field value is changed asynchronously after
+the keypressed event, so Java actions that are keyed to KEY_PRESSED may not pick up the new
+key value even after SwingUtilities.invokeLater() is called. Thus, key pressed actions may need
+to be recorded after a key released event instead.
+
+
+Formatter/Regex limitations
+---------------------------
+
+Some browsers cannot process Regex "look-behind" process such as (?<=\W)
+java.util.regex.Matcher and Pattern use JavaScript's RegExp object rather than
+the native Java object. These are not identical. Only flags /igm are supported.
+Matcher.start(groupID) is not supported.
+
+java.util.Formatter will function correctly for all standard %... patterns.
+
+In addition, JavaScript does not implement some of the more arcane POSIX {...} formats.
+From java.util.regex.Pattern.java, we find the listing of conversions SwingJS does use:
+
+ "\\p{javaWhitespace}","\\s",
+ "\\p{javaDigit}","\\d",
+ "\\p{Lower}", "[a-z]",
+ "\\p{Upper}", "[A-Z]",
+ "\\p{ASCII}", "[\u0000-\u007F]",
+ "\\p{Alpha}", "[A-Za-z]",
+ "\\p{Digit}", "[0-9]",
+ "\\p{Alnum}", "[A-Za-z0-9]",
+ "\\p{Punct}", "[!\"#$%&'\\(\\)\\*\\+,-./:;<=>?@\\[\\\\\\]^_`{\\|}~]",
+ "\\p{Graph}", "[A-Za-z0-9]!\"#$%&'\\(\\)\\*\\+,-./:;<=>?@\\[\\\\\\]^_`{\\|}~]",
+ "\\p{Print}", "[A-Za-z0-9]!\"#$%&'\\(\\)\\*\\+,-./:;<=>?@\\[\\\\\\]^_`{\\|}~]",
+ "\\p{Blank}", "[ \t]",
+ "\\p{Cntrl}", "[\u0000-\u001F\u007F]",
+ "\\p{XDigit}", "[0-9a-fA-F]",
+ "\\p{Space}", "[ \t\n\u000B\f\r]",
+ "\\p{javaLowerCase}", "[a-z]",
+ "\\p{javaUpperCase}", "[A-Z]",
+ "\\p{Sc}", "[\u0024\u00A2\u00A3\u00A4\u00A5\u058F\u060B\u07FE\u07FF\u09F2\u09F3\u09FB\u0AF1\u0BF9\u0E3F\u20A0\u20A1\u20A2\u20A3\u20A4\u20A5\u20A6\u20A7\u20A8\u20A9\u20AA\u20AB\u20AC\u20AD\u20AE\u20AF\u20B0\u20B1\u20B2\u20B3\u20B4\u20B5\u20B6\u20B7\u20B8\u20B9\u20BA\u20BB\u20BC\u20BD\u20BE\u20BF\uA838\uFDFC\uFE69\uFF04\uFFE0\uFFE1\uFFE5\uFFE6]"
+
+Java's \Q \E quoting is handled appropriately.
+
+Additional Issues
+-----------------
+
+Method reflection is limited. Fields and methods do not retain public or default characteristics.
+(This could be easily adapted, though.) Interfaces do not expose their methods, as the transpiler does not
+actually transpile the interfaces themselves unless they contain default methods.
+And method reflection only includes annotated methods.
+
+java.util.concurrent is not fully elaborated. This package is rewritten to not actually use the
+memory handling capabilities of concurrency, which JavaScript does not have access to.
+
+System.getProperties() just returns a minimal set of properties.
+
+
+Summary
+-------
+
+These are all the known limitations of SwingJS. We have not found any of these limitations
+to be show-stoppers. The primary issue for newcomers to SwingJS is having the source code.
+You must check that source code for all your library jar files is available or, if you
+choose, you will need to decompile those classes. We have used decompilation on some projects,
+and it works just fine. So, technically, all we really need are JAR/class files. But the
+source is by far superior. It's generally prettier, and it has the license information that
+may or may not be present with the JAR or class files. Use class files at your own risk.
+
+Bob Hanson
+
+
--- /dev/null
+20210728172208
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
ps = new PrintStream(new File(args[6]));
}
- boolean nucleotide = args[0].toLowerCase().startsWith("n");
+ boolean nucleotide = args[0].toLowerCase(Locale.ROOT).startsWith("n");
int width = Integer.parseInt(args[1]);
int height = Integer.parseInt(args[2]);
long randomSeed = Long.valueOf(args[3]);
@Test(groups = { "Functional_Failing" })
public void testFindXrefSequences_withFetch()
{
+ // JBPNote: this fails because pep1 and pep2 do not have DbRefEntrys with mappings
+ // Fix#1 would be to revise the test data so it fits with 2.11.2+ Jalview assumptions
+ // that ENA retrievals yield dbrefs with Mappings
+
SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "Q9ZTS2"));
dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P30419"));
dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P00314"));
final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW");
- pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+ pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2",null,true));
final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG");
- pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
+ pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314",null,true));
/*
* argument false suppresses adding DAS sources
*/
package jalview.analysis;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
char second = bases.charAt(j);
boolean result = Rna.isCanonicalOrWobblePair(first, second);
String pair = new String(new char[] { first, second })
- .toUpperCase();
+ .toUpperCase(Locale.ROOT);
if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
|| pair.equals("UA") || pair.equals("GC")
|| pair.equals("CG") || pair.equals("GT")
char second = bases.charAt(j);
boolean result = Rna.isCanonicalPair(first, second);
String pair = new String(new char[] { first, second })
- .toUpperCase();
+ .toUpperCase(Locale.ROOT);
if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
|| pair.equals("UA") || pair.equals("GC")
|| pair.equals("CG"))
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed
+ private static final int TEST_TIMEOUT = 12500; // Note longer timeout needed
// on
// full test run than on
// individual tests
public void setUpForHeadlessCommandLineInputOperations()
throws IOException
{
- String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo "
+ String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/bin/testProps.jvprops -colour zappo "
+ "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
+ "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
public void setUpForCommandLineInputOperations() throws IOException
{
String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
- Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
- String ln = null;
- int count = 0;
- while ((ln = worker.getErrorReader().readLine()) != null)
+ final Worker worker = getJalviewDesktopRunner(false, cmds,
+ SETUP_TIMEOUT);
+
+
+ // number of lines expected on STDERR when Jalview starts up normally
+ // may need to adjust this if Jalview is excessively noisy ?
+ final int STDERR_SETUPLINES=30;
+
+ // thread monitors stderr - bails after SETUP_TIMEOUT or when
+ // STDERR_SETUPLINES have been read
+ Thread runner = new Thread(new Runnable()
{
- System.out.println(ln);
- successfulCMDs.add(ln);
- if (++count > 25)
+ public void run()
+ {
+ String ln = null;
+ int count = 0;
+ try
+ {
+ while ((ln = worker.getErrorReader().readLine()) != null)
+ {
+ System.out.println(ln);
+ successfulCMDs.add(ln);
+ if (++count > STDERR_SETUPLINES)
+ {
+ break;
+ }
+ }
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Unexpected Exception reading stderr from the Jalview process");
+ e.printStackTrace();
+ }
+ }
+ });
+ long t = System.currentTimeMillis() + SETUP_TIMEOUT;
+ runner.start();
+ while (!runner.isInterrupted() && System.currentTimeMillis() < t)
+ {
+ try
+ {
+ Thread.sleep(500);
+ } catch (InterruptedException e)
{
- break;
}
}
+ runner.interrupt();
if (worker != null && worker.exit == null)
{
worker.interrupt();
@Test(
groups =
- { "Functional", "testben" },
+ { "Functional" },
dataProvider = "headlessModeOutputOperationsData")
public void testHeadlessModeOutputOperations(String harg, String type,
String fileName, boolean withAWT, int expectedMinFileSize,
// headless mode input operations
{ "CMD [-color zappo] executed successfully!",
"Failed command : -color zappo" },
- { "CMD [-props test/jalview/io/testProps.jvprops] executed successfully!",
+ { "CMD [-props test/jalview/bin/testProps.jvprops] executed successfully!",
"Failed command : -props File" },
{ "CMD [-sortbytree] executed successfully!",
"Failed command : -sortbytree" },
@Test(groups = { "Functional" }, dataProvider = "hidpiScaleArguments")
public void testHiDPISettings(int scale)
{
- if (Platform.isLinux())
+ if (!Platform.isLinux())
{
throw new SkipException(
"Not linux platform, not testing actual scaling with "
VERSION_CHECK=true
LATEST_VERSION=test
+logs.Jalview.level=INFO
*/
package jalview.commands;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
assertEquals("fghjZ-xYopq", seqs[1].getSequenceAsString());
// Dataset Sequence should always be uppercase
- assertEquals("fghjZxYopq".toUpperCase(),
+ assertEquals("fghjZxYopq".toUpperCase(Locale.ROOT),
seqs[1].getDatasetSequence().getSequenceAsString());
assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString());
assertEquals("1234567890", seqs[3].getSequenceAsString());
assertEquals(1, seq.getStart());
assertEquals(8, seq.getEnd());
// Dataset sequence always uppercase
- assertEquals("ABxyZDEF".toUpperCase(),
+ assertEquals("ABxyZDEF".toUpperCase(Locale.ROOT),
seq.getDatasetSequence().getSequenceAsString());
assertEquals(8, seq.getDatasetSequence().getEnd());
assertEquals(1, seq.getStart());
assertEquals(8, seq.getEnd());
// dataset sequence should be Uppercase
- assertEquals("ABxyZDEF".toUpperCase(),
+ assertEquals("ABxyZDEF".toUpperCase(Locale.ROOT),
seq.getDatasetSequence().getSequenceAsString());
assertEquals(8, seq.getDatasetSequence().getEnd());
// and ds is preserved
assertTrue(dsseq == seqs[1].getDatasetSequence());
// and it is unchanged and UPPERCASE !
- assertEquals("fghjklmnopq".toUpperCase(), dsseq.getSequenceAsString());
+ assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT), dsseq.getSequenceAsString());
// and that alignment sequence start has been adjusted
assertEquals(5, seqs[1].getStart());
assertEquals(11, seqs[1].getEnd());
// and ds is preserved
assertTrue(dsseq == seqs[1].getDatasetSequence());
// and it is unchanged AND UPPERCASE !
- assertEquals("fghjklmnopq".toUpperCase(), dsseq.getSequenceAsString());
+ assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT), dsseq.getSequenceAsString());
// and that alignment sequence start has been adjusted
assertEquals(5, seqs[1].getStart());
assertEquals(11, seqs[1].getEnd());
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
-import jalview.gui.JvOptionPane;
-import jalview.util.MapList;
-
import java.util.Arrays;
import java.util.List;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
+import jalview.gui.JvOptionPane;
+import jalview.util.MapList;
+
public class AlignedCodonFrameTest
{
public void testGetMappedRegion()
{
// introns lower case, exons upper case
- final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
- seq1.createDatasetSequence();
- final Sequence seq2 = new Sequence("Seq2", "-TA-gG-Gg-CG-a");
- seq2.createDatasetSequence();
+ final Sequence dna1 = new Sequence("Seq1/10-18", "c-G-TA-gC-gT-T");
+ dna1.createDatasetSequence();
+ final Sequence dna2 = new Sequence("Seq2/20-28", "-TA-gG-Gg-CG-a");
+ dna2.createDatasetSequence();
- final Sequence aseq1 = new Sequence("Seq1", "-P-R");
- aseq1.createDatasetSequence();
- final Sequence aseq2 = new Sequence("Seq2", "-LY-Q");
- aseq2.createDatasetSequence();
+ final Sequence pep1 = new Sequence("Seq1/3-4", "-P-R");
+ pep1.createDatasetSequence();
+ final Sequence pep2 = new Sequence("Seq2/7-9", "-LY-Q");
+ pep2.createDatasetSequence();
/*
* First with no mappings
*/
AlignedCodonFrame acf = new AlignedCodonFrame();
- assertNull(acf.getMappedRegion(seq1, aseq1, 1));
+ assertNull(acf.getMappedRegion(dna1, pep1, 3));
/*
* Set up the mappings for the exons (upper-case bases)
* Note residue Q is unmapped
*/
- MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
- 1, 2 }, 3, 1);
- acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- map = new MapList(new int[] { 1, 2, 4, 5, 7, 8 }, new int[] { 1, 2 },
+ MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 }, new int[] {
+ 3, 4 }, 3, 1);
+ acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map1);
+ MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 }, new int[] { 7, 9 },
3, 1);
- acf.addMap(seq2.getDatasetSequence(), aseq2.getDatasetSequence(), map);
+ acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map2);
- assertArrayEquals(new int[] { 2, 4 },
- acf.getMappedRegion(seq1, aseq1, 1));
- assertArrayEquals(new int[] { 6, 6, 8, 9 },
- acf.getMappedRegion(seq1, aseq1, 2));
- assertArrayEquals(new int[] { 1, 2, 4, 4 },
- acf.getMappedRegion(seq2, aseq2, 1));
- assertArrayEquals(new int[] { 5, 5, 7, 8 },
- acf.getMappedRegion(seq2, aseq2, 2));
+ /*
+ * get codon positions for peptide position
+ */
+ assertArrayEquals(new int[] { 11, 13 },
+ acf.getMappedRegion(dna1, pep1, 3));
+ assertArrayEquals(new int[] { 15, 15, 17, 18 },
+ acf.getMappedRegion(dna1, pep1, 4));
+ assertArrayEquals(new int[] { 20, 21, 23, 23 },
+ acf.getMappedRegion(dna2, pep2, 7));
+ assertArrayEquals(new int[] { 24, 24, 26, 27 },
+ acf.getMappedRegion(dna2, pep2, 8));
/*
- * No mapping from seq2 to Q
+ * No mapping from dna2 to Q
*/
- assertNull(acf.getMappedRegion(seq2, aseq2, 3));
+ assertNull(acf.getMappedRegion(dna2, pep2, 9));
/*
- * No mapping from sequence 1 to sequence 2
+ * No mapping from dna1 to pep2
*/
- assertNull(acf.getMappedRegion(seq1, aseq2, 1));
+ assertNull(acf.getMappedRegion(dna1, pep2, 7));
+
+ /*
+ * get peptide position for codon position
+ */
+ assertArrayEquals(new int[] { 3, 3 },
+ acf.getMappedRegion(pep1, dna1, 11));
+ assertArrayEquals(new int[] { 3, 3 },
+ acf.getMappedRegion(pep1, dna1, 12));
+ assertArrayEquals(new int[] { 3, 3 },
+ acf.getMappedRegion(pep1, dna1, 13));
+ assertNull(acf.getMappedRegion(pep1, dna1, 14)); // intron base, not mapped
+
}
@Test(groups = { "Functional" })
assertEquals(1, acf.getMappingsFromSequence(seq1).size());
assertSame(before, acf.getMappingsFromSequence(seq1).get(0));
}
+
+ @Test(groups = { "Functional" })
+ public void testGetCoveringMapping()
+ {
+ SequenceI dna = new Sequence("dna", "acttcaATGGCGGACtaattt");
+ SequenceI cds = new Sequence("cds/7-15", "ATGGCGGAC");
+ cds.setDatasetSequence(dna);
+ SequenceI pep = new Sequence("pep", "MAD");
+
+ /*
+ * with null argument or no mappings
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ assertNull(acf.getCoveringMapping(null, null));
+ assertNull(acf.getCoveringMapping(dna, null));
+ assertNull(acf.getCoveringMapping(null, pep));
+ assertNull(acf.getCoveringMapping(dna, pep));
+
+ /*
+ * with a non-covering mapping e.g. overlapping exon
+ */
+ MapList map = new MapList(new int[] { 7, 9 }, new int[] {
+ 1, 1 }, 3, 1);
+ acf.addMap(dna, pep, map);
+ assertNull(acf.getCoveringMapping(dna, pep));
+
+ acf = new AlignedCodonFrame();
+ MapList map2 = new MapList(new int[] { 13, 18 }, new int[] {
+ 2, 2 }, 3, 1);
+ acf.addMap(dna, pep, map2);
+ assertNull(acf.getCoveringMapping(dna, pep));
+
+ /*
+ * with a covering mapping from CDS (dataset) to protein
+ */
+ acf = new AlignedCodonFrame();
+ MapList map3 = new MapList(new int[] { 7, 15 }, new int[] {
+ 1, 3 }, 3, 1);
+ acf.addMap(dna, pep, map3);
+ assertNull(acf.getCoveringMapping(dna, pep));
+ SequenceToSequenceMapping mapping = acf.getCoveringMapping(cds, pep);
+ assertNotNull(mapping);
+
+ /*
+ * with a mapping that extends to stop codon
+ */
+ acf = new AlignedCodonFrame();
+ MapList map4 = new MapList(new int[] { 7, 18 }, new int[] {
+ 1, 3 }, 3, 1);
+ acf.addMap(dna, pep, map4);
+ assertNull(acf.getCoveringMapping(dna, pep));
+ assertNull(acf.getCoveringMapping(cds, pep));
+ SequenceI cds2 = new Sequence("cds/7-18", "ATGGCGGACtaa");
+ cds2.setDatasetSequence(dna);
+ mapping = acf.getCoveringMapping(cds2, pep);
+ assertNotNull(mapping);
+ }
+
+ /**
+ * Test the method that adds mapped positions to SearchResults
+ */
+ @Test(groups = { "Functional" })
+ public void testMarkMappedRegion()
+ {
+ // introns lower case, exons upper case
+ final Sequence dna1 = new Sequence("Seq1/10-18", "c-G-TA-gC-gT-T");
+ dna1.createDatasetSequence();
+ final Sequence dna2 = new Sequence("Seq2/20-28", "-TA-gG-Gg-CG-a");
+ dna2.createDatasetSequence();
+
+ final Sequence pep1 = new Sequence("Seq1/3-4", "-P-R");
+ pep1.createDatasetSequence();
+ final Sequence pep2 = new Sequence("Seq2/7-9", "-LY-Q");
+ pep2.createDatasetSequence();
+
+ /*
+ * First with no mappings
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ SearchResults sr = new SearchResults();
+ acf.markMappedRegion(dna1, 12, sr);
+ assertTrue(sr.isEmpty());
+
+ /*
+ * Set up the mappings for the exons (upper-case bases)
+ * Note residue Q is unmapped
+ */
+ MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 }, new int[] {
+ 3, 4 }, 3, 1);
+ acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map1);
+ MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 }, new int[] { 7, 8 },
+ 3, 1);
+ acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map2);
+
+ /*
+ * intron bases are not mapped
+ */
+ acf.markMappedRegion(dna1, 10, sr);
+ assertTrue(sr.isEmpty());
+
+ /*
+ * Q is not mapped
+ */
+ acf.markMappedRegion(pep2, 9, sr);
+ assertTrue(sr.isEmpty());
+
+ /*
+ * mark peptide position for exon position (of aligned sequence)
+ */
+ acf.markMappedRegion(dna1, 11, sr);
+ SearchResults expected = new SearchResults();
+ expected.addResult(pep1.getDatasetSequence(), 3, 3);
+ assertEquals(sr, expected);
+
+ /*
+ * mark peptide position for exon position of dataset sequence - same result
+ */
+ sr = new SearchResults();
+ acf.markMappedRegion(dna1.getDatasetSequence(), 11, sr);
+ assertEquals(sr, expected);
+
+ /*
+ * marking the same position a second time should not create a duplicate match
+ */
+ acf.markMappedRegion(dna1.getDatasetSequence(), 12, sr);
+ assertEquals(sr, expected);
+
+ /*
+ * mark exon positions for peptide position (of aligned sequence)
+ */
+ sr = new SearchResults();
+ acf.markMappedRegion(pep2, 7, sr); // codon positions 20, 21, 23
+ expected = new SearchResults();
+ expected.addResult(dna2.getDatasetSequence(), 20, 21);
+ expected.addResult(dna2.getDatasetSequence(), 23, 23);
+ assertEquals(sr, expected);
+
+ /*
+ * add another codon to the same SearchResults
+ */
+ acf.markMappedRegion(pep1.getDatasetSequence(), 4, sr); // codon positions 15, 17, 18
+ expected.addResult(dna1.getDatasetSequence(), 15, 15);
+ expected.addResult(dna1.getDatasetSequence(), 17, 18);
+ assertEquals(sr, expected);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetCoveringCodonMapping()
+ {
+ SequenceI dna = new Sequence("dna/10-30", "acttcaATGGCGGACtaattt");
+ // CDS sequence with its own dataset sequence (JAL-3763)
+ SequenceI cds = new Sequence("cds/1-9", "-A--TGGC-GGAC");
+ cds.createDatasetSequence();
+ SequenceI pep = new Sequence("pep/1-3", "MAD");
+
+ /*
+ * with null argument or no mappings
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ assertNull(acf.getCoveringCodonMapping(null));
+ assertNull(acf.getCoveringCodonMapping(dna));
+ assertNull(acf.getCoveringCodonMapping(pep));
+
+ /*
+ * with a non-covering mapping e.g. overlapping exon
+ */
+ MapList map = new MapList(new int[] { 16, 18 }, new int[] {
+ 1, 1 }, 3, 1);
+ acf.addMap(dna, pep, map);
+ assertNull(acf.getCoveringCodonMapping(dna));
+ assertNull(acf.getCoveringCodonMapping(pep));
+
+ acf = new AlignedCodonFrame();
+ MapList map2 = new MapList(new int[] { 13, 18 }, new int[] {
+ 2, 2 }, 3, 1);
+ acf.addMap(dna, pep, map2);
+ assertNull(acf.getCoveringCodonMapping(dna));
+ assertNull(acf.getCoveringCodonMapping(pep));
+
+ /*
+ * with a covering mapping from CDS (dataset) to protein
+ */
+ acf = new AlignedCodonFrame();
+ MapList map3 = new MapList(new int[] { 1, 9 }, new int[] {
+ 1, 3 }, 3, 1);
+ acf.addMap(cds.getDatasetSequence(), pep, map3);
+ assertNull(acf.getCoveringCodonMapping(dna));
+ SequenceToSequenceMapping mapping = acf.getCoveringCodonMapping(pep);
+ assertNotNull(mapping);
+ SequenceToSequenceMapping mapping2 = acf.getCoveringCodonMapping(cds.getDatasetSequence());
+ assertSame(mapping, mapping2);
+
+ /*
+ * with a mapping that extends to stop codon
+ * (EMBL CDS location often includes the stop codon)
+ * - getCoveringCodonMapping is lenient (doesn't require exact length match)
+ */
+ SequenceI cds2 = new Sequence("cds/1-12", "-A--TGGC-GGACTAA");
+ cds2.createDatasetSequence();
+ acf = new AlignedCodonFrame();
+ MapList map4 = new MapList(new int[] { 1, 12 }, new int[] {
+ 1, 3 }, 3, 1);
+ acf.addMap(cds2, pep, map4);
+ mapping = acf.getCoveringCodonMapping(cds2.getDatasetSequence());
+ assertNotNull(mapping);
+ mapping2 = acf.getCoveringCodonMapping(pep);
+ assertSame(mapping, mapping2);
+ }
}
assertEquals("3", ref1.getVersion());
/*
+ * canonical == false superseded by canonical == true
+ */
+ ref1.setCanonical(false);
+ ref2.setCanonical(true);
+ assertTrue(ref1.updateFrom(ref2));
+ assertTrue(ref1.isCanonical());
+
+ /*
+ * canonical == true NOT superseded by canonical == false
+ */
+ ref1.setCanonical(true);
+ ref2.setCanonical(false);
+ assertFalse(ref1.updateFrom(ref2));
+
+ /*
* version "source:n" with n>0 is not superseded
*/
ref1.setVersion("UNIPROT:1");
PDBEntry case9 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
// different file only
PDBEntry case10 = new PDBEntry("1xyz", "A", null, "a/b/c/File");
-
+
/*
* assertEquals will invoke PDBEntry.equals()
*/
assertTrue(pdb1.updateFrom(pdb2));
assertEquals(pdb1.getFile(), "filePath");
assertEquals(pdb1.getType(), Type.FILE.toString());
-
+ assertEquals(pdb1.getChainCode(),"B");
/*
* change of file is not allowed
*/
pdb2.setProperty("hello", "moon");
assertTrue(pdb1.updateFrom(pdb2));
assertEquals(pdb1.getProperty("hello"), "moon");
+
+ /*
+ * different id but authoritative
+ */
+ pdb1 = new PDBEntry("af:1xyz", "A", null, "a/b/c/File");
+ pdb2 = new PDBEntry("af-1xyz", "A", null, "a/b/c/File");
+ pdb1.setAuthoritative(true);
+
+ assertTrue(pdb1.isAuthoritative());
+ assertFalse(pdb2.isAuthoritative());
+ // can update pdb1 (authoritative) from pdb2 (non-authoritative)
+ assertTrue(pdb1.updateFrom(pdb2));
+ // but the ID must remain the same
+ assertEquals(pdb1.getId(),"af:1xyz");
+
}
@Test(groups = { "Functional" })
*/
package jalview.datamodel;
+import java.util.Locale;
+
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertTrue;
ResidueCount rc = new ResidueCount(false);
// expected characters (upper or lower case):
String aas = "ACDEFGHIKLMNPQRSTVWXY";
- String lower = aas.toLowerCase();
+ String lower = aas.toLowerCase(Locale.ROOT);
for (int i = 0; i < aas.length(); i++)
{
rc.put(aas.charAt(i), i);
ResidueCount rc = new ResidueCount(true);
// expected characters (upper or lower case):
String nucs = "ACGTUN";
- String lower = nucs.toLowerCase();
+ String lower = nucs.toLowerCase(Locale.ROOT);
for (int i = 0; i < nucs.length(); i++)
{
rc.put(nucs.charAt(i), i);
@Test(groups = { "Functional" })
public void testCopyConstructors()
{
- SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
- 12.5f, "group");
+ SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+ "group");
sf1.setValue("STRAND", "+");
sf1.setValue("Note", "Testing");
Integer count = Integer.valueOf(7);
/*
* copy constructor modifying type/begin/end/group/score
*/
- SequenceFeature sf4 = new SequenceFeature(sf1, "Disulfide bond", 12,
- 15, "group3", -9.1f);
+ SequenceFeature sf4 = new SequenceFeature(sf1, "Disulfide bond", 12, 15,
+ "group3", -9.1f);
assertEquals("Disulfide bond", sf4.getType());
assertTrue(sf4.isContactFeature());
assertEquals("desc", sf4.getDescription());
@Test(groups = { "Functional" })
public void testGetValue()
{
- SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
- 12.5f, "group");
+ SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+ "group");
sf1.setValue("STRAND", "+");
assertEquals("+", sf1.getValue("STRAND"));
assertNull(sf1.getValue("strand")); // case-sensitive
@Test(groups = { "Functional" })
public void testEqualsAndHashCode()
{
- SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
- 12.5f, "group");
+ SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+ "group");
sf1.setValue("ID", "id");
sf1.setValue("Name", "name");
sf1.setValue("Parent", "parent");
sf1.setStrand("+");
sf1.setPhase("1");
- SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33,
- 12.5f, "group");
+ SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+ "group");
sf2.setValue("ID", "id");
sf2.setValue("Name", "name");
sf2.setValue("Parent", "parent");
assertEquals(sf1.hashCode(), sf2.hashCode());
// changing type breaks equals:
- SequenceFeature sf3 = new SequenceFeature("type", "desc", 22, 33,
- 12.5f, "group");
- SequenceFeature sf4 = new SequenceFeature("Type", "desc", 22, 33,
- 12.5f, "group");
+ SequenceFeature sf3 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+ "group");
+ SequenceFeature sf4 = new SequenceFeature("Type", "desc", 22, 33, 12.5f,
+ "group");
assertFalse(sf3.equals(sf4));
// changing description breaks equals:
// changing start position breaks equals:
int restorei = sf2.getBegin();
- sf2 = new SequenceFeature(sf2, 21, sf2.getEnd(), sf2.getFeatureGroup(), sf2.getScore());
+ sf2 = new SequenceFeature(sf2, 21, sf2.getEnd(), sf2.getFeatureGroup(),
+ sf2.getScore());
assertFalse(sf1.equals(sf2));
sf2 = new SequenceFeature(sf2, restorei, sf2.getEnd(),
sf2.getFeatureGroup(), sf2.getScore());
// changing feature group breaks equals:
restores = sf2.getFeatureGroup();
- sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), "Group", sf2.getScore());
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), "Group",
+ sf2.getScore());
assertFalse(sf1.equals(sf2));
- sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), restores, sf2.getScore());
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), restores,
+ sf2.getScore());
// changing ID breaks equals:
restores = (String) sf2.getValue("ID");
String seqName = seq.getName();
// single locus, no group, no score
- SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22, null);
+ SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22,
+ null);
String expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22</td></tr>"
+ "<tr><td>Type</td><td>variant</td><td></td></tr>"
+ "<tr><td>Description</td><td>G,C</td><td></td></tr></table>";
+ "<tr><td>Description</td><td>a description</td><td></td></tr></table>";
assertEquals(expected, sf.getDetailsReport(seqName, null));
- sf = new SequenceFeature("variant", "G,C", 22, 33,
- 12.5f, "group");
+ sf = new SequenceFeature("variant", "G,C", 22, 33, 12.5f, "group");
sf.setValue("Parent", "ENSG001");
sf.setValue("Child", "ENSP002");
expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22-33</td></tr>"
+ "<tr><td>Type</td><td>variant</td><td></td></tr>"
+ "<tr><td>Description</td><td>G,C</td><td></td></tr>"
+ "<tr><td>Consequence</td><td><i>Translated by Jalview</i></td><td>p.Leu9Phe</td></tr>"
- + "<tr><td>alleles</td><td></td><td>G,C</td></tr>"
+ + "<tr><td>alleles</td><td></td><td>G,C</td></tr>"
+ "</table>";
assertEquals(expected, sf.getDetailsReport(seq.getName(), mf));
+
+
+ /*
+ * exon feature extending beyond mapped range; mapped location should be
+ * restricted to peptide mapped range limit i.e. 10-13
+ */
+ SequenceFeature sf2 = new SequenceFeature("exon", "exon 1", 109, 230, null);
+ features.add(sf2);
+ expected = "<br><table><tr><td>Location</td><td>Cds</td><td>109-230</td></tr>"
+ + "<tr><td>Peptide Location</td><td>TestSeq</td><td>10-13</td></tr>"
+ + "<tr><td>Type</td><td>exon</td><td></td></tr>"
+ + "<tr><td>Description</td><td>exon 1</td><td></td></tr>"
+ + "</table>";
+ assertEquals(expected, sf2.getDetailsReport(seq.getName(), mf));
}
}
*/
package jalview.datamodel;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
assertTrue(sq.isProtein());
}
+ @Test(groups = ("Functional"))
+ public void testIsProteinWithXorNAmbiguityCodes()
+ {
+ // test Protein with N - poly asparagine
+ assertTrue(new Sequence("prot", "ASDFASDFASDFNNNNNNNNN").isProtein());
+ assertTrue(new Sequence("prot", "NNNNNNNNNNNNNNNNNNNNN").isProtein());
+ // test Protein with X
+ assertTrue(new Sequence("prot", "ASDFASDFASDFXXXXXXXXX").isProtein());
+ // test DNA with X
+ assertFalse(new Sequence("prot", "ACGTACGTACGTXXXXXXXX").isProtein());
+ // test DNA with N
+ assertFalse(new Sequence("prot", "ACGTACGTACGTNNNNNNNN").isProtein());
+ // test RNA with X
+ assertFalse(new Sequence("prot", "ACGUACGUACGUXXXXXXXXX").isProtein());
+ assertFalse(new Sequence("prot", "ACGUACGUACGUNNNNNNNNN").isProtein());
+ }
+
@Test(groups = { "Functional" })
public void testGetAnnotation()
{
assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty());
}
+
+ @Test(groups = { "Functional" })
+ public void testGetAlignmentAnnotations_forCalcIdLabelAndDescription()
+ {
+ addAnnotation("label1", "desc1", "calcId1", 1f);
+ AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
+ 1f);
+ addAnnotation("label2", "desc3", "calcId3", 1f);
+ AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
+ 1f);
+ addAnnotation("label5", "desc3", null, 1f);
+ addAnnotation(null, "desc3", "calcId3", 1f);
+
+ List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
+ "label2", "desc3");
+ assertEquals(1, anns.size());
+ assertSame(ann4, anns.get(0));
+ /**
+ * null matching should fail
+ */
+ assertTrue(seq.getAlignmentAnnotations("calcId3", "label2",null).isEmpty());
+
+ assertTrue(seq.getAlignmentAnnotations("calcId2", "label3",null).isEmpty());
+ assertTrue(seq.getAlignmentAnnotations("calcId3", "label5",null).isEmpty());
+ assertTrue(seq.getAlignmentAnnotations("calcId2", null,null).isEmpty());
+ assertTrue(seq.getAlignmentAnnotations(null, "label3",null).isEmpty());
+ assertTrue(seq.getAlignmentAnnotations(null, null,null).isEmpty());
+ }
+
/**
* Tests for addAlignmentAnnotation. Note this method has the side-effect of
* setting the sequenceRef on the annotation. Adding the same annotation twice
} catch (IllegalArgumentException e)
{
// TODO Jalview error/exception class for raising implementation errors
- assertTrue(e.getMessage().toLowerCase()
+ assertTrue(e.getMessage().toLowerCase(Locale.ROOT)
.contains("implementation error"));
}
assertTrue(sq.getSequenceFeatures().isEmpty());
seq.addPDBId(pdbe5);
assertEquals(4, seq.getAllPDBEntries().size());
assertSame(pdbe5, seq.getAllPDBEntries().get(3));
+
+ // add with a fake pdbid
+ // (models don't have an embedded ID)
+ String realId = "RealIDQ";
+ PDBEntry pdbe6 = new PDBEntry(realId,null,Type.PDB,"real/localpath");
+ PDBEntry pdbe7 = new PDBEntry("RealID/real/localpath","C",Type.MMCIF,"real/localpath");
+ pdbe7.setFakedPDBId(true);
+ seq.addPDBId(pdbe6);
+ assertEquals(5,seq.getAllPDBEntries().size());
+ seq.addPDBId(pdbe7);
+ assertEquals(5,seq.getAllPDBEntries().size());
+ assertFalse(pdbe6.fakedPDBId());
+ assertSame(pdbe6,seq.getAllPDBEntries().get(4));
+ assertEquals("C",pdbe6.getChainCode());
+ assertEquals(realId, pdbe6.getId());
}
@Test(
assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
}
+ @Test(groups= {"Functional"})
+ public void testTransferAnnotation() {
+ Sequence origSeq = new Sequence("MYSEQ","THISISASEQ");
+ Sequence toSeq = new Sequence("MYSEQ","THISISASEQ");
+ origSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, true));
+ toSeq.transferAnnotation(origSeq, null);
+ assertTrue(toSeq.getDBRefs().size()==1);
+
+ assertTrue(toSeq.getDBRefs().get(0).isCanonical());
+
+ // check for promotion of non-canonical
+ // to canonical (e.g. fetch-db-refs on a jalview project pre 2.11.2)
+ toSeq.setDBRefs(null);
+ toSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, false));
+ toSeq.transferAnnotation(origSeq, null);
+ assertTrue(toSeq.getDBRefs().size()==1);
+
+ assertTrue("Promotion of non-canonical DBRefEntry failed",toSeq.getDBRefs().get(0).isCanonical());
+
+
+ }
}
*/
package jalview.ext.ensembl;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
assertTrue(testee.retainFeature(sf, accId));
// test is not case-sensitive
- assertTrue(testee.retainFeature(sf, accId.toLowerCase()));
+ assertTrue(testee.retainFeature(sf, accId.toLowerCase(Locale.ROOT)));
// feature with wrong parent is not retained
sf.setValue("Parent", "XYZ");
*/
package jalview.ext.ensembl;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
22000, 22500, 0f, null);
// id matching should not be case-sensitive
- sf3.setValue("Parent", geneId.toLowerCase());
+ sf3.setValue("Parent", geneId.toLowerCase(Locale.ROOT));
sf3.setValue("id", "transcript3");
genomic.addSequenceFeature(sf3);
/**
* Check behaviour of feature colour scheme for EnsemblGene sequences.
- * Currently coded to display exon and sequence_variant (or sub-types) only,
- * with sequence_variant in red above exon coloured by label.
+ * Currently coded to hide all except exon and sequence_variant (or sub-types)
+ * only, with sequence_variant in red above exon coloured by label.
*/
@Test(groups = "Functional")
public void testGetFeatureColourScheme()
{
FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme();
- assertTrue(fc.isFeatureDisplayed("exon"));
- assertTrue(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
- assertTrue(fc.isFeatureDisplayed("sequence_variant"));
- assertTrue(fc.isFeatureDisplayed("feature_variant")); // subtype
- assertFalse(fc.isFeatureDisplayed("transcript"));
+ assertFalse(fc.isFeatureDisplayed("exon"));
+ assertFalse(fc.isFeatureHidden("exon"));
+ assertFalse(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
+ assertFalse(fc.isFeatureHidden("coding_exon")); // subtype of exon
+ assertFalse(fc.isFeatureDisplayed("sequence_variant"));
+ assertFalse(fc.isFeatureHidden("sequence_variant"));
+ assertFalse(fc.isFeatureDisplayed("feature_variant")); // subtype
+ assertFalse(fc.isFeatureHidden("feature_variant")); // subtype
+ assertTrue(fc.isFeatureHidden("transcript"));
+ assertTrue(fc.isFeatureHidden("CDS"));
+
assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
.getColour());
assertEquals(Color.RED, fc.getFeatureColour("feature_variant")
import jalview.schemes.JalviewColourScheme;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
public void testGetAtomSpec()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, false), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "2-4:A/1.1");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1|8:A/1.1");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "2-4:A/1.1|8:A/1.1");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-4:A/1.1|8:A/1.1|5-7:B/1.1");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-7:B/1.1");
model.addRange("2", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1");
model.addRange("2", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1|5-9:C/2.1");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
model.addRange("2", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1|25-35:/5.1");
}
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign);
+ toAlign, AtomSpecType.ALPHA); // doesn't matter for Jmol whether nuc or protein
assertEquals(command.size(), 1);
String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1";
String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1";
assertEquals(structureData.getId(), "localstruct");
assertNotNull(structureData.getSeqs());
/*
+ * local structures have a fake ID
+ */
+ assertTrue(structureData.getSeqs().get(0).getAllPDBEntries().get(0).fakedPDBId());
+ /*
* the ID is also the group for features derived from structure data
*/
String featureGroup = structureData.getSeqs().get(0)
*/
package jalview.ext.paradise;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.AlignmentI;
{
{
SequenceI struseq = null;
- String sq_ = sq.getSequenceAsString().toLowerCase();
+ String sq_ = sq.getSequenceAsString().toLowerCase(Locale.ROOT);
for (SequenceI _struseq : pdbf.getSeqsAsArray())
{
final String lowerCase = _struseq.getSequenceAsString()
- .toLowerCase();
+ .toLowerCase(Locale.ROOT);
if (lowerCase.equals(sq_))
{
struseq = _struseq;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
public class PymolCommandsTest
{
public void testGetAtomSpec()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, false), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, false), "1//A/2-4/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4/");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, false), "1//A/2-4+8/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4+8/");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, false), "1//A/2-4+8/ 1//B/5-7/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4+8/ 1//B/5-7/");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, false), "1//A/2-5+8/ 1//B/5-7/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-5+8/ 1//B/5-7/");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 1//A/2-5+8/ 1//B/5-7/");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-7/");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/ 5///25-35/");
}
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> commands = testee.superposeStructures(ref,
- toAlign);
+ toAlign, AtomSpecType.ALPHA);
assertEquals(commands.size(), 2);
- String refSpecCA = "1//A/12-14/CA 1//B/18+22-23/CA";
- String toAlignSpecCA = "2//B/15-17+20-21/CA 2//C/22/CA";
+ String refSpecCA = "(1//A/12-14/CA 1//B/18+22-23/CA";
+ String toAlignSpecCA = "(2//B/15-17+20-21/CA 2//C/22/CA";
String refSpec = "1//A/12-14/ 1//B/18+22-23/";
String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
-
+ String altLoc = " and (altloc '' or altloc 'a'))";
// super command: separate arguments for regions to align
assertEquals(commands.get(0),
- new StructureCommand("super", refSpecCA, toAlignSpecCA));
+ new StructureCommand("pair_fit", toAlignSpecCA+altLoc, refSpecCA+altLoc));
// show aligned regions: one argument for combined atom specs
assertEquals(commands.get(1), new StructureCommand("show", "cartoon",
refSpec + " " + toAlignSpec));
public void testGetAtomSpec_alphaOnly()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, true), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, true), "1//A/2-4/CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "1//A/2-4/CA");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, true), "1//A/2-4+8/CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "1//A/2-4+8/CA");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"1//A/2-4+8/CA 1//B/5-7/CA");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"1//A/2-5+8/CA 1//B/5-7/CA");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 1//A/2-5+8/CA 1//B/5-7/CA");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-7/CA");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA 5///25-35/CA");
}
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
public class ChimeraCommandsTest
{
public void testGetAtomSpec()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, false), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A,8.A");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A,5-7.B");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A,8.A,5-7.B");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1:2-5.A,8.A,5-7.B");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-5.A,8.A,5-7.B");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B|#1:2-5.A,8.A,5-7.B");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35.");
}
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign);
+ toAlign, AtomSpecType.ALPHA);
// qualifier to restrict match to CA and no altlocs
String carbonAlphas = "@CA&~@.B-Z&~@.2-9";
String refSpec = "#1:12-14.A,18.B,22-23.B";
public void testGetAtomSpec_alphaOnly()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, true), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-4.A@CA&~@.B-Z&~@.2-9");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-4.A,8.A@CA&~@.B-Z&~@.2-9");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-4.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
model.addRange("5", 25, 35, " "); // empty chain code
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9|#5:25-35.@CA&~@.B-Z&~@.2-9");
}
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
public class ChimeraXCommandsTest
{
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign);
+ toAlign,AtomSpecType.ALPHA);
assertEquals(command.size(), 1);
String cmd = command.get(0).getCommand();
String refSpec = "#1/A:12-14/B:18,22-23";
public void testGetAtomSpec()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, false), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY
+ ), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-4");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-4,8");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8/B:5-7");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-4,8/B:5-7");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1/A:2-5,8/B:5-7");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-5,8/B:5-7");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4|#1/A:2-5,8/B:5-7");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-7");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10|#5/:25-35");
}
public void testGetAtomSpec_alphaOnly()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, true), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-4@CA");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-4,8@CA");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8/B:5-7@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-4,8/B:5-7@CA");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, true), "#1/A:2-5,8/B:5-7@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-5,8/B:5-7@CA");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4@CA|#1/A:2-5,8/B:5-7@CA");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-7@CA");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA");
model.addRange("5", 25, 35, " "); // empty chain code
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA|#5/:25-35@CA");
}
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
@Test(groups = { "External" })
public void testSingleSeqViewChimera()
{
+
String inFile = "examples/1gaq.txt";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
DataSourceType.FILE);
/*
* Wait for viewer load thread to complete
*/
- while (!binding.isFinishedInit())
+ do
{
try
{
} catch (InterruptedException e)
{
}
- }
+ } while (!binding.isFinishedInit() || !chimeraViewer.isVisible());
assertTrue(binding.isViewerRunning(), "Failed to start Chimera");
assertEquals(chimeraViewer.getBinding().getPdbCount(), 1);
+ assertTrue(chimeraViewer.hasViewerActionsMenu());
+
+ // now add another sequence and bind to view
+ //
+ AlignmentI al = af.getViewport().getAlignment();
+ PDBEntry xpdb = al.getSequenceAt(0).getPDBEntry("1GAQ");
+ sq = new Sequence("1GAQ", al.getSequenceAt(0).getSequence(25, 95).toString());
+ al.addSequence(sq);
+ structureViewer.viewStructures(new PDBEntry[] { xpdb }, new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
+
+ /*
+ * Wait for viewer load thread to complete
+ */
+ do
+ {
+ try {
+ Thread.sleep(1500);
+ } catch (InterruptedException q) {};
+ } while (!binding.isLoadingFinished());
+
+ // still just one PDB structure shown
+ assertEquals(chimeraViewer.getBinding().getPdbCount(), 1);
+ // and the viewer action menu should still be visible
+ assertTrue(chimeraViewer.hasViewerActionsMenu());
+
chimeraViewer.closeViewer(true);
chimeraViewer = null;
return;
String expectedString = "1xyz OR text:2xyz OR text:3xyz";
String outcome = PDBFTSPanel.decodeSearchTerm("1xyz:A;2xyz;3xyz",
"text");
- // System.out.println("1 >>>>>>>>>>> " + outcome);
+ System.out.println("1 >>>>>>>>>>> " + outcome);
assertEquals(expectedString, outcome);
expectedString = "1xyz";
assertTrue(!mainFrame.getTitle().equalsIgnoreCase(
"PDB Sequence Fetcher"));
}
+
+ @Test
+ public void getFTSframeTitleTest() {
+ PDBFTSPanel searchPanel = new PDBFTSPanel(null);
+ String outcome = searchPanel.getFTSFrameTitle();
+ //System.out.println("FTS Frame title :" + outcome);
+ assertEquals(outcome, "PDB Sequence Fetcher");
+ }
}
import static org.testng.AssertJUnit.assertTrue;
import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.core.FTSRestClient;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.gui.JvOptionPane;
{
e1.printStackTrace();
}
+ System.out.println("wantedFields >>" + wantedFields);
+
FTSRestRequest request = new FTSRestRequest();
request.setAllowEmptySeq(false);
assertEquals(expectedErrorMsg, parsedErrorResponse);
}
- @Test(groups = { "External" }, expectedExceptions = Exception.class)
+ @Test(groups = { "External" }, enabled = false, expectedExceptions = Exception.class)
public void testForExpectedRuntimeException() throws Exception
{
+ // FIXME JBPNote: looks like this test fails for no good reason - what exception was supposed to be raised ?
List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
wantedFields.add(PDBFTSRestClient.getInstance()
.getDataColumnByNameOrCode("pdb_id"));
}
// JBP: Is this actually external ? Looks like it is mocked
+ // JBP looks like the mock is not up to date for this test
@Test(groups = { "External" })
public void parsePDBJsonResponseTest()
{
assertTrue(response.getSearchSummary() != null);
assertTrue(response.getNumberOfItemsFound() == 931);
assertTrue(response.getSearchSummary().size() == 14);
+ System.out.println("Search summary : " + response.getSearchSummary());
}
@Test(groups = { "Functional" })
}
}
- public String readJsonStringFromFile(String filePath) throws IOException
+ /**
+ * reads any string from filePath
+ * @param filePath
+ * @return
+ * @throws IOException
+ */
+ public static String readJsonStringFromFile(String filePath) throws IOException
{
String fileContent;
BufferedReader br = new BufferedReader(new FileReader(filePath));
return fileContent;
}
+ public static void setMock()
+ {
+ String[][] mocks = new String[2][];
+ mocks[0] = new String[] {"https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(4igk+OR+7lyb+OR+3k0h+OR+3k0k+OR+1t15+OR+3pxc+OR+3pxd+OR+3pxe+OR+1jm7+OR+7jzv+OR+3pxa+OR+3pxb+OR+1y98+OR+1n5o+OR+4ifi+OR+4y2g+OR+3k15+OR+3k16+OR+4jlu+OR+2ing+OR+4ofb+OR+6g2i+OR+3coj+OR+1jnx+OR+4y18+OR+4u4a+OR+1oqa+OR+1t29+OR+1t2u+OR+1t2v)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort=",
+ "{\n"
+ + " \"responseHeader\":{\n"
+ + " \"status\":0,\n"
+ + " \"QTime\":0,\n"
+ + " \"params\":{\n"
+ + " \"q\":\"(4igk OR 7lyb OR 3k0h OR 3k0k OR 1t15 OR 3pxc OR 3pxd OR 3pxe OR 1jm7 OR 7jzv OR 3pxa OR 3pxb OR 1y98 OR 1n5o OR 4ifi OR 4y2g OR 3k15 OR 3k16 OR 4jlu OR 2ing OR 4ofb OR 6g2i OR 3coj OR 1jnx OR 4y18 OR 4u4a OR 1oqa OR 1t29 OR 1t2u OR 1t2v) AND molecule_sequence:['' TO *] AND status:REL\",\n"
+ + " \"fl\":\"pdb_id,title,experimental_method,resolution\",\n"
+ + " \"start\":\"0\",\n"
+ + " \"sort\":\"\",\n"
+ + " \"rows\":\"500\",\n"
+ + " \"wt\":\"json\"}},\n"
+ + " \"response\":{\"numFound\":64,\"start\":0,\"docs\":[\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4ofb\",\n"
+ + " \"resolution\":3.05,\n"
+ + " \"title\":\"Crystal structure of human BRCA1 BRCT in complex with nonphosphopeptide inhibitor\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxe\",\n"
+ + " \"resolution\":2.85,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: E1836K\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4jlu\",\n"
+ + " \"resolution\":3.5,\n"
+ + " \"title\":\"Crystal structure of BRCA1 BRCT with doubly phosphorylated Abraxas\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4y2g\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Solution NMR\"],\n"
+ + " \"pdb_id\":\"1oqa\",\n"
+ + " \"title\":\"Solution structure of the BRCT-c domain from human BRCA1\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4u4a\",\n"
+ + " \"resolution\":3.51,\n"
+ + " \"title\":\"Complex Structure of BRCA1 BRCT with singly phospho Abraxas\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k16\",\n"
+ + " \"resolution\":3.0,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t15\",\n"
+ + " \"resolution\":1.85,\n"
+ + " \"title\":\"Crystal Structure of the Brca1 BRCT Domains in Complex with the Phosphorylated Interacting Region from Bach1 Helicase\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k15\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t2v\",\n"
+ + " \"resolution\":3.3,\n"
+ + " \"title\":\"Structural basis of phospho-peptide recognition by the BRCT domain of BRCA1, structure with phosphopeptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1y98\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Structure of the BRCT repeats of BRCA1 bound to a CtIP phosphopeptide.\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t29\",\n"
+ + " \"resolution\":2.3,\n"
+ + " \"title\":\"Crystal structure of the BRCA1 BRCT repeats bound to a phosphorylated BACH1 peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k0k\",\n"
+ + " \"resolution\":2.7,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus.\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k0h\",\n"
+ + " \"resolution\":2.7,\n"
+ + " \"title\":\"The crystal structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4ifi\",\n"
+ + " \"resolution\":2.2,\n"
+ + " \"title\":\"Structure of human BRCA1 BRCT in complex with BAAT peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxd\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: R1835P\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxc\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: R1699Q\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1jnx\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Crystal structure of the BRCT repeat region from the breast cancer associated protein, BRCA1\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxa\",\n"
+ + " \"resolution\":2.55,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: G1656D\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Solution NMR\"],\n"
+ + " \"pdb_id\":\"1jm7\",\n"
+ + " \"title\":\"Solution structure of the BRCA1/BARD1 RING-domain heterodimer\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4igk\",\n"
+ + " \"resolution\":1.75,\n"
+ + " \"title\":\"Structure of human BRCA1 BRCT in complex with ATRIP peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t2u\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1: structure of BRCA1 missense variant V1809F\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxb\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: T1700A\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1n5o\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Structural consequences of a cancer-causing BRCA1-BRCT missense mutation\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3coj\",\n"
+ + " \"resolution\":3.21,\n"
+ + " \"title\":\"Crystal Structure of the BRCT Domains of Human BRCA1 in Complex with a Phosphorylated Peptide from Human Acetyl-CoA Carboxylase 1\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"6g2i\",\n"
+ + " \"resolution\":5.9,\n"
+ + " \"title\":\"Filament of acetyl-CoA carboxylase and BRCT domains of BRCA1 (ACC-BRCT) at 5.9 A resolution\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4jlu\",\n"
+ + " \"resolution\":3.5,\n"
+ + " \"title\":\"Crystal structure of BRCA1 BRCT with doubly phosphorylated Abraxas\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4ofb\",\n"
+ + " \"resolution\":3.05,\n"
+ + " \"title\":\"Crystal structure of human BRCA1 BRCT in complex with nonphosphopeptide inhibitor\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxe\",\n"
+ + " \"resolution\":2.85,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: E1836K\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4u4a\",\n"
+ + " \"resolution\":3.51,\n"
+ + " \"title\":\"Complex Structure of BRCA1 BRCT with singly phospho Abraxas\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4y2g\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4y18\",\n"
+ + " \"resolution\":3.5,\n"
+ + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas double phosphorylated peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"2ing\",\n"
+ + " \"resolution\":3.6,\n"
+ + " \"title\":\"X-ray Structure of the BRCA1 BRCT mutant M1775K\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t15\",\n"
+ + " \"resolution\":1.85,\n"
+ + " \"title\":\"Crystal Structure of the Brca1 BRCT Domains in Complex with the Phosphorylated Interacting Region from Bach1 Helicase\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t29\",\n"
+ + " \"resolution\":2.3,\n"
+ + " \"title\":\"Crystal structure of the BRCA1 BRCT repeats bound to a phosphorylated BACH1 peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Solution NMR\"],\n"
+ + " \"pdb_id\":\"1jm7\",\n"
+ + " \"title\":\"Solution structure of the BRCA1/BARD1 RING-domain heterodimer\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t2v\",\n"
+ + " \"resolution\":3.3,\n"
+ + " \"title\":\"Structural basis of phospho-peptide recognition by the BRCT domain of BRCA1, structure with phosphopeptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4ifi\",\n"
+ + " \"resolution\":2.2,\n"
+ + " \"title\":\"Structure of human BRCA1 BRCT in complex with BAAT peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4igk\",\n"
+ + " \"resolution\":1.75,\n"
+ + " \"title\":\"Structure of human BRCA1 BRCT in complex with ATRIP peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k0k\",\n"
+ + " \"resolution\":2.7,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus.\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k16\",\n"
+ + " \"resolution\":3.0,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k15\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k0h\",\n"
+ + " \"resolution\":2.7,\n"
+ + " \"title\":\"The crystal structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1y98\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Structure of the BRCT repeats of BRCA1 bound to a CtIP phosphopeptide.\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3coj\",\n"
+ + " \"resolution\":3.21,\n"
+ + " \"title\":\"Crystal Structure of the BRCT Domains of Human BRCA1 in Complex with a Phosphorylated Peptide from Human Acetyl-CoA Carboxylase 1\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4y18\",\n"
+ + " \"resolution\":3.5,\n"
+ + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas double phosphorylated peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"6g2i\",\n"
+ + " \"resolution\":5.9,\n"
+ + " \"title\":\"Filament of acetyl-CoA carboxylase and BRCT domains of BRCA1 (ACC-BRCT) at 5.9 A resolution\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"}]\n"
+ + " }}" };
+
+ mocks[1] = new String[2];
+ try {
+ mocks[1][0] = readJsonStringFromFile("test/jalview/fts/threedbeacons/p01308_pdbfts_query.txt").trim();
+ mocks[1][1] = readJsonStringFromFile("test/jalview/fts/threedbeacons/p01308_pdbfts_resp.txt").trim();
+ } catch (Throwable e)
+ {
+ Assert.fail("Couldn't read mock data.",e);
+ }
+
+ FTSRestClient.createMockFTSRestClient((FTSRestClient) PDBFTSRestClient.getInstance(), mocks);
+ }
}
--- /dev/null
+/tdbJson.java
+/tdbresttest2.java
--- /dev/null
+package jalview.fts.threedbeacons;
+
+import static org.testng.Assert.assertNull;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+
+import java.io.IOException;
+import java.net.URL;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.testng.Assert;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
+import jalview.fts.core.FTSRestClient;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.pdb.PDBFTSRestClientTest;
+import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
+import jalview.gui.JvOptionPane;
+
+public class TDBeaconsFTSRestClientTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ private FTSRestClient ftsRestClient;
+
+ @BeforeMethod(alwaysRun = true)
+ public void setUp() throws Exception
+ {
+ ftsRestClient = new FTSRestClient()
+ {
+
+ @Override
+ public String getColumnDataConfigFileName()
+ {
+ return "/fts/tdbeacons_data_columns.txt";
+ }
+
+ @Override
+ public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
+ throws Exception
+ {
+ return null;
+ }
+ };
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void tearDown() throws Exception
+ {
+ }
+
+ @Test
+ public void getAllDefaulDisplayedDataColumns()
+ {
+ // to change when resources.tdbeacons_data_columns.txt is changed
+ Assert.assertNotNull(
+ ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
+ System.out
+ .println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
+ Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
+ .isEmpty());
+ Assert.assertEquals(
+ ftsRestClient.getAllDefaultDisplayedFTSDataColumns().size(),
+ 15);
+ }
+
+ @Test(groups = { "Functional" })
+ public void getPrimaryKeyColumIndexTest()
+ {
+ Collection<FTSDataColumnI> wantedFields = ftsRestClient
+ .getAllDefaultDisplayedFTSDataColumns();
+ int foundIndex = -1;
+ try
+ {
+ Assert.assertEquals(foundIndex, -1);
+ foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
+ false);
+ Assert.assertEquals(foundIndex, 12);
+ foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
+ true);
+ // 1+primary key index
+ Assert.assertEquals(foundIndex, 13);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDataColumnsFieldsAsCommaDelimitedString()
+ {
+ // to change when resources.tdbeacons_data_columns.txt is changed
+ Collection<FTSDataColumnI> wantedFields = ftsRestClient
+ .getAllDefaultDisplayedFTSDataColumns();
+ String actual = ftsRestClient
+ .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
+ Assert.assertEquals(actual,
+ "uniprot_start,uniprot_end,provider,model_identifier,model_category,model_title,resolution,confidence_avg_local_score,confidence_type,confidence_version,coverage,created,model_url,model_format,model_page_url");
+ }
+
+ @Test(groups = { "Functional" })
+ public void getAllFTSDataColumns()
+ {
+ Collection<FTSDataColumnI> allFields = ftsRestClient
+ .getAllFTSDataColumns();
+ Assert.assertNotNull(allFields);
+ // System.out.println(allFields.size());
+ Assert.assertEquals(allFields.size(), 20);
+ }
+
+ @Test(groups = { "Functional" })
+ public void getSearchableDataColumns()
+ {
+ // to change when resources.tdbeacons_data_columns.txt is changed
+ Collection<FTSDataColumnI> searchableFields = ftsRestClient
+ .getSearchableDataColumns();
+ Assert.assertNotNull(searchableFields);
+ // System.out.println(searchableFields.size());
+ Assert.assertEquals(searchableFields.size(), 1); // only 1: uniprot
+ // accession
+ }
+
+ @Test(groups = { "Functional" })
+ public void getPrimaryKeyColumn()
+ {
+ // to change when resources.tdbeacons_data_columns.txt is changed
+ FTSDataColumnI expectedPKColumn;
+ try
+ {
+ expectedPKColumn = ftsRestClient.getDataColumnByNameOrCode("Url");
+ Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
+ Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
+ expectedPKColumn);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDataColumnByNameOrCode()
+ {
+ try
+ {
+ FTSDataColumnI foundDataCol = ftsRestClient
+ .getDataColumnByNameOrCode("uniprot_accession");
+ Assert.assertNotNull(foundDataCol);
+ Assert.assertEquals(foundDataCol.getName(), "UniProt Accession");
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDataColumnGroupById()
+ {
+ FTSDataColumnGroupI foundDataColGroup;
+ try
+ {
+ foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2");
+ Assert.assertNotNull(foundDataColGroup);
+ Assert.assertEquals(foundDataColGroup.getName(), "Quality");
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void getDefaultResponsePageSize()
+ {
+ int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
+ Assert.assertEquals(defaultResSize, 100); // why 100 or 500 ? pdb is 100,
+ // uniprot 500
+ }
+
+ @Test(groups = { "Functional" })
+ public void getColumnMinWidthTest()
+ {
+ try
+ {
+ FTSDataColumnI foundDataCol = ftsRestClient
+ .getDataColumnByNameOrCode("uniprot_accession");
+ Assert.assertNotNull(foundDataCol);
+ int actualColMinWidth = foundDataCol.getMinWidth();
+ Assert.assertEquals(actualColMinWidth, 50);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+ // could add test for MaxWidth & PreferedWith
+
+ @Test(groups = { "Functional" })
+ public void getColumnClassTest()
+ {
+ try
+ {
+ FTSDataColumnI foundDataCol = ftsRestClient
+ .getDataColumnByNameOrCode("uniprot_accession");
+ Assert.assertNotNull(foundDataCol);
+ Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
+ String.class);
+ foundDataCol = ftsRestClient.getDataColumnByNameOrCode("id");
+ Assert.assertNotNull(foundDataCol);
+ Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
+ String.class);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Exception thrown while testing...");
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void coverageForEqualsAndHashFunction()
+ {
+ Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
+ Collection<FTSDataColumnI> searchableCols = ftsRestClient
+ .getSearchableDataColumns();
+ System.out.println(searchableCols);
+ for (FTSDataColumnI foundCol : searchableCols)
+ {
+ System.out.println(foundCol.toString());
+ uniqueSet.add(foundCol);
+ uniqueSet.add(foundCol);
+ }
+ Assert.assertTrue(!uniqueSet.isEmpty());
+ // Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB
+ }
+
+ @Test(groups = { "Functional" })
+ public void getTDBIdColumIndexTest()
+ {
+ List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ try
+ {
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("Model id"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("uniprot_accession"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("Title"));
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ try
+ {
+ assertEquals(4, TDBeaconsFTSRestClient.getInstance()
+ .getPrimaryKeyColumIndex(wantedFields, true));
+ // assertEquals(3, TDBeaconsFTSRestClient.getInstance()
+ // .getPrimaryKeyColumIndex(wantedFields, true));
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ private static String[][] mocks = { { "P38398.json",
+ "{\"uniprot_entry\":{\"sequence_length\":1863,\"ac\":\"P38398\",\"id\":\"BRCA1_HUMAN\"},\"structures\":[{\"model_identifier\":\"4igk\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2012-12-17\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.75,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4igk_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4igk\"},{\"model_identifier\":\"1t15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-15\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t15_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t15\"},{\"model_identifier\":\"4ifi\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2012-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.2,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ifi_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4ifi\"},{\"model_identifier\":\"1t29\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-20\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t29_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t29\"},{\"model_identifier\":\"3pxb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxb_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxb\"},{\"model_identifier\":\"4y2g\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2015-02-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y2g_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4y2g\"},{\"model_identifier\":\"1y98\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1y98_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1y98\"},{\"model_identifier\":\"1jnx\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2001-07-26\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jnx_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1jnx\"},{\"model_identifier\":\"3pxa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.55,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxa_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxa\"},{\"model_identifier\":\"3k0h\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-24\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.7,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k0h_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k0h\"},{\"model_identifier\":\"3k0k\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-24\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.7,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k0k_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k0k\"},{\"model_identifier\":\"1n5o\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2002-11-06\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1n5o_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1n5o\"},{\"model_identifier\":\"3pxc\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxc_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxc\"},{\"model_identifier\":\"3pxd\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxd_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxd\"},{\"model_identifier\":\"1t2u\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-22\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t2u_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t2u\"},{\"model_identifier\":\"3k15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-25\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k15_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k15\"},{\"model_identifier\":\"3pxe\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxe_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxe\"},{\"model_identifier\":\"3k16\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-25\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.0,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k16_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k16\"},{\"model_identifier\":\"4ofb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2014-01-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.05,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ofb_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4ofb\"},{\"model_identifier\":\"3coj\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2008-03-28\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.21,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3coj_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3coj\"},{\"model_identifier\":\"7lyb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2021-03-06\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":100,\"resolution\":3.28,\"coverage\":5.37,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7lyb_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/7lyb\"},{\"model_identifier\":\"1t2v\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-22\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t2v_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t2v\"},{\"model_identifier\":\"4y18\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2015-02-06\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y18_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4y18\"},{\"model_identifier\":\"4jlu\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2013-03-13\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4jlu_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4jlu\"},{\"model_identifier\":\"4u4a\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2014-07-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.51,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4u4a_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4u4a\"},{\"model_identifier\":\"2ing\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2006-10-07\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.6,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/2ing_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/2ing\"},{\"model_identifier\":\"7jzv\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2020-09-02\",\"sequence_identity\":99.0,\"uniprot_start\":2,\"uniprot_end\":104,\"resolution\":3.9,\"coverage\":5.53,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7jzv_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/7jzv\"},{\"model_identifier\":\"6g2i\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2018-03-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":5.9,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/6g2i_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/6g2i\"},{\"model_identifier\":\"1jm7\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2001-07-17\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":110,\"resolution\":null,\"coverage\":5.9,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jm7_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"SOLUTION NMR\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1jm7\"},{\"model_identifier\":\"1oqa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2003-03-07\",\"sequence_identity\":100.0,\"uniprot_start\":1755,\"uniprot_end\":1863,\"resolution\":null,\"coverage\":5.85,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1oqa_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"SOLUTION NMR\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1oqa\"},{\"model_identifier\":\"P38398_1646-1859:6g2i.1.K\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-11-05\",\"sequence_identity\":1.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"coverage\":0.115,\"confidence_version\":\"4.2.0\",\"confidence_avg_local_score\":0.776,\"model_url\":\"https://swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1646-1859&template=6g2i.1.K&provider=swissmodel\",\"model_format\":\"PDB\",\"model_page_url\":\"https://swissmodel.expasy.org/repository/uniprot/P38398?range=1646-1859&template=6g2i.1.K\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"P38398_1-103:1jm7.1.A\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-11-05\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":103,\"coverage\":0.055,\"confidence_version\":\"4.2.0\",\"confidence_avg_local_score\":0.655,\"model_url\":\"https://swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1-103&template=1jm7.1.A&provider=swissmodel\",\"model_format\":\"PDB\",\"model_page_url\":\"https://swissmodel.expasy.org/repository/uniprot/P38398?range=1-103&template=1jm7.1.A\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"AF-P38398-F1\",\"model_category\":\"DEEP-LEARNING\",\"provider\":\"AlphaFold DB\",\"created\":\"2021-07-01\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":1863,\"coverage\":100.0,\"model_url\":\"https://alphafold.ebi.ac.uk/files/AF-P38398-F1-model_v1.cif\",\"model_format\":\"MMCIF\",\"model_page_url\":\"https://alphafold.ebi.ac.uk/entry/P38398\"}]}" },
+ { "P01308.json",null}};
+
+ private static void setMockData()
+ {
+ try
+ {
+ mocks[1][1]= PDBFTSRestClientTest.readJsonStringFromFile("test/jalview/fts/threedbeacons/p01308_tdb_resp.txt");
+ } catch (IOException e)
+ {
+ Assert.fail("Couldn't read mock response data",e);
+ }
+ }
+
+ public static void setMock()
+ {
+ setMockData();
+ FTSRestClient.createMockFTSRestClient(
+ (FTSRestClient) TDBeaconsFTSRestClient.getInstance(),
+ mocks);
+ }
+
+ private static String dev_url = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+ private static String prod_url = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+
+ /**
+ * check that the mock request and response are the same as the response from
+ * a live 3D-beacons endpoint
+ *
+ * Note - servers often have rapidly changing ids / URIs so this might fail, but the overall structure will remain.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Network", "Integration" })
+ public void verifyMockTDBRequest() throws Exception
+ {
+ setMockData();
+ for (String[] otherMock:mocks)
+ {
+ verifyMockTDBRequest(otherMock[0],otherMock[1]);
+ }
+ }
+ private void verifyMockTDBRequest(String mockRequest, String _mockResponse) throws Exception
+ {
+ URL tdb_req = new URL(prod_url + mockRequest);
+ byte[] resp = tdb_req.openStream().readAllBytes();
+ String tresp = new String(resp, StandardCharsets.UTF_8);
+ assertEquals(_mockResponse.trim(), tresp.trim());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testMockTDBRequest()
+ {
+
+ setMock();
+ List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ try
+ {
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("Model Id"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("model_url"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("provider"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("model_category"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("qmean_avg_local_score"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("uniprot_start"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("uniprot_end"));
+ } catch (Exception e1)
+ {
+ e1.printStackTrace();
+ }
+ System.out.println("wantedFields >>" + wantedFields);
+
+ FTSRestRequest request = new FTSRestRequest();
+ FTSRestResponse response;
+
+ request.setResponseSize(100);
+ request.setFieldToSearchBy("");
+ request.setWantedFields(wantedFields);
+ // check 404 behaviour
+ request.setSearchTerm("P00000.json");
+
+ try
+ {
+ response = TDBeaconsFTSRestClient.getInstance()
+ .executeRequest(request);
+
+ assertNull(response);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Unexpected failure during mock 3DBeacons 404 test");
+ }
+
+ // check 200 behaviour
+ request.setSearchTerm("P38398.json");
+ System.out.println("request : " + request.getFieldToSearchBy());
+ // System.out.println(request.toString());
+
+ try
+ {
+ response = TDBeaconsFTSRestClient.getInstance()
+ .executeRequest(request);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Couldn't execute webservice call!");
+ return;
+ }
+ assertTrue(response.getSearchSummary() != null);
+ assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
+ System.out.println("Search summary : \n" + response.getSearchSummary());
+
+ // System.out.println(response.getSearchSummary().size());
+ }
+
+ @Test(groups = { "External", "Network" })
+ public void executeRequestTest()
+ {
+ List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ try
+ {
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("Model Id"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("model_url"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("provider"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("model_category"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("confidence_avg_local_score"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("uniprot_start"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("uniprot_end"));
+ } catch (Exception e1)
+ {
+ e1.printStackTrace();
+ }
+ System.out.println("wantedFields >>" + wantedFields);
+
+ FTSRestRequest request = new FTSRestRequest();
+ request.setResponseSize(100);
+ request.setFieldToSearchBy("");
+ request.setSearchTerm("P01318.json");
+ request.setWantedFields(wantedFields);
+ System.out.println("request : " + request.getFieldToSearchBy());
+ // System.out.println(request.toString());
+
+ FTSRestResponse response;
+ try
+ {
+ response = TDBeaconsFTSRestClient.getInstance()
+ .executeRequest(request);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ Assert.fail("Couldn't execute webservice call!");
+ return;
+ }
+ assertTrue(response.getSearchSummary() != null);
+ assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
+ System.out.println("Search summary : \n" + response.getSearchSummary());
+ // System.out.println(response.getSearchSummary().size());
+ }
+}
--- /dev/null
+package jalview.fts.threedbeacons;
+
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.fts.service.pdb.PDBFTSPanel;
+import jalview.fts.service.threedbeacons.TDBeaconsFTSPanel;
+import jalview.gui.JvOptionPane;
+
+import javax.swing.JComboBox;
+import javax.swing.JInternalFrame;
+
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import junit.extensions.PA;
+
+
+public class TDBeaconsPanelTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @BeforeMethod(alwaysRun = true)
+ public void setUp() throws Exception
+ {
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void tearDown() throws Exception
+ {
+ }
+
+ @Test(groups = { "Functional" })
+ public void populateCmbSearchTargetOptionsTest()
+ {
+ TDBeaconsFTSPanel searchPanel = new TDBeaconsFTSPanel(null);
+ assertTrue(searchPanel.getCmbSearchTarget().getItemCount() > 0);
+ searchPanel.populateCmbSearchTargetOptions();
+ }
+
+ @Test
+ public void getFTSframeTitleTest() {
+ TDBeaconsFTSPanel searchPanel = new TDBeaconsFTSPanel(null);
+ System.out.println(searchPanel.getFTSFrameTitle());
+ }
+
+ @Test
+ public void testgetUNIPROTid() {
+ String outcome = TDBeaconsFTSPanel.decodeSearchTerm("P01308");
+ System.out.println(outcome);
+ }
+//
+// @Test
+// public void queryTest() {
+// int outcome = TDBeaconsFTSPanel.executeParse("P01308");
+// //System.out.println("query outcome :" + outcome);
+// int expected_length = 110;
+// assertEquals(outcome, expected_length);
+// }
+}
--- /dev/null
+https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(5hpu+OR+2jmn+OR+4iuz+OR+6s34+OR+1efe+OR+6ce7+OR+1w8p+OR+1evr+OR+1hls+OR+5hpr+OR+7jp3+OR+3v19+OR+5bts+OR+3q6e+OR+2m1d+OR+2m1e+OR+2n2v+OR+2n2w+OR+2n2x+OR+1t1p+OR+1t1q+OR+2rn5+OR+2m2o+OR+4une+OR+3v1g+OR+2m2p+OR+4unh+OR+5t7r+OR+4ung+OR+4gbi+OR+4rxw+OR+4gbl+OR+4gbk+OR+4gbn+OR+3aiy+OR+1ioh+OR+1iog+OR+5wob+OR+4gbc+OR+2m2m+OR+2m2n+OR+5hqi+OR+2hiu+OR+6ce9+OR+4z76+OR+4z78+OR+4z77+OR+2kqp+OR+2kqq+OR+5en9+OR+6k59+OR+1mhj+OR+1mhi+OR+5hrq+OR+6ceb+OR+1jca+OR+4p65+OR+1k3m+OR+3kq6+OR+6s4i+OR+4f0o+OR+6s4j+OR+4f0n+OR+6gnq+OR+5ems+OR+2mvc+OR+2mvd+OR+1sf1+OR+3hyd+OR+2l1y+OR+1uz9+OR+2l1z+OR+7nhu+OR+3w80+OR+4aiy+OR+3utq+OR+3ilg+OR+5cjo+OR+4ak0+OR+6b3q+OR+4f1g+OR+4wdi+OR+1jco+OR+1vkt+OR+6tyh+OR+4iyd+OR+5ena+OR+4f1b+OR+4f1a+OR+4iyf+OR+4f1d+OR+4f1c+OR+4f1f+OR+4ajx+OR+4ajz+OR+1ben+OR+1tyl+OR+1tym+OR+2vk0+OR+6bfc+OR+2om0+OR+2om1+OR+3uts+OR+3utt+OR+3tt8+OR+2omh+OR+2omi+OR+3u4n+OR+6o17+OR+4fg3+OR+2vjz+OR+4oga+OR+2lgb+OR+6ck2+OR+2omg+OR+5uoz+OR+2oly+OR+1zeg+OR+2olz+OR+3inc+OR+1zeh+OR+4akj+OR+4f51+OR+3w7y+OR+3rov+OR+3w7z+OR+6b70+OR+5co9+OR+1j73+OR+5aiy+OR+5co2+OR+1os4+OR+5uqa+OR+1os3+OR+4f4t+OR+2jv1+OR+5co6+OR+4f4v+OR+7bw7+OR+5wdm+OR+7bw8+OR+1rwe+OR+2ceu+OR+2omq+OR+2r34+OR+2r35+OR+7s4y+OR+2r36+OR+5cny+OR+2juu+OR+2juv+OR+5mt9+OR+2jum+OR+3exx+OR+3ir0+OR+1htv+OR+5mt3+OR+7bwa+OR+3zqr+OR+6h3m+OR+1lkq+OR+5mam+OR+3zs2+OR+2mli+OR+1ai0+OR+5usp+OR+5uu2+OR+5uu4+OR+5uu3+OR+3e7y+OR+3e7z+OR+4ex0+OR+3jsd+OR+6gv0+OR+4ex1+OR+2kxk+OR+1sjt+OR+1q4v+OR+1sju+OR+5uru+OR+5urt+OR+6jk8+OR+1xda+OR+6z7y+OR+1hui+OR+5hyj+OR+6z7w+OR+4ey9+OR+4eww+OR+1a7f+OR+2k91+OR+4nib+OR+1b9e+OR+4ewx+OR+4ewz+OR+4ey1+OR+1jk8+OR+5uss+OR+5usv+OR+3zu1+OR+6p4z+OR+4efx+OR+6x4x+OR+1xw7+OR+2kjj+OR+1kmf+OR+4eyd+OR+1fu2+OR+4exx+OR+2wc0+OR+2ws6+OR+1qj0+OR+2ws7+OR+2c8q+OR+2c8r+OR+5udp+OR+5boq+OR+4f8f+OR+2ws0+OR+2ws1+OR+1guj+OR+2ws4+OR+1lph+OR+2wby+OR+1qiz+OR+1qiy+OR+3i40+OR+2k9r+OR+6sof+OR+2wru+OR+4fka+OR+4eyp+OR+2wrv+OR+2wrw+OR+2wrx+OR+1xgl+OR+5bpo+OR+1aiy+OR+5c0d+OR+2kju+OR+4eyn+OR+3fq9+OR+3i3z+OR+3p33+OR+1hiq+OR+2mpg+OR+5mwq+OR+2mpi+OR+1mso+OR+2h67+OR+6vep+OR+5bqq+OR+6ves+OR+4y19+OR+6vet+OR+1fub+OR+6ver+OR+6tc2+OR+1t0c+OR+1ev6+OR+1ev3+OR+2aiy+OR+3zi3+OR+5viz+OR+2g54+OR+4y1a+OR+6nwv+OR+5mhd+OR+2g56+OR+3bxq+OR+4cy7+OR+1hit+OR+1his+OR+2hh4+OR+6u46+OR+3w11+OR+2w44+OR+3w12+OR+3w13+OR+6hn5+OR+2hho+OR+5e7w+OR+1t1k+OR+4xc4+OR+6jr3+OR+1trz+OR+2qiu+OR+1g7b+OR+1g7a+OR+4cxl+OR+3p2x+OR+4cxn+OR+1znj)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort=
--- /dev/null
+{
+ "responseHeader":{
+ "status":0,
+ "QTime":4,
+ "params":{
+ "q":"(5hpu OR 2jmn OR 4iuz OR 6s34 OR 1efe OR 6ce7 OR 1w8p OR 1evr OR 1hls OR 5hpr OR 7jp3 OR 3v19 OR 5bts OR 3q6e OR 2m1d OR 2m1e OR 2n2v OR 2n2w OR 2n2x OR 1t1p OR 1t1q OR 2rn5 OR 2m2o OR 4une OR 3v1g OR 2m2p OR 4unh OR 5t7r OR 4ung OR 4gbi OR 4rxw OR 4gbl OR 4gbk OR 4gbn OR 3aiy OR 1ioh OR 1iog OR 5wob OR 4gbc OR 2m2m OR 2m2n OR 5hqi OR 2hiu OR 6ce9 OR 4z76 OR 4z78 OR 4z77 OR 2kqp OR 2kqq OR 5en9 OR 6k59 OR 1mhj OR 1mhi OR 5hrq OR 6ceb OR 1jca OR 4p65 OR 1k3m OR 3kq6 OR 6s4i OR 4f0o OR 6s4j OR 4f0n OR 6gnq OR 5ems OR 2mvc OR 2mvd OR 1sf1 OR 3hyd OR 2l1y OR 1uz9 OR 2l1z OR 7nhu OR 3w80 OR 4aiy OR 3utq OR 3ilg OR 5cjo OR 4ak0 OR 6b3q OR 4f1g OR 4wdi OR 1jco OR 1vkt OR 6tyh OR 4iyd OR 5ena OR 4f1b OR 4f1a OR 4iyf OR 4f1d OR 4f1c OR 4f1f OR 4ajx OR 4ajz OR 1ben OR 1tyl OR 1tym OR 2vk0 OR 6bfc OR 2om0 OR 2om1 OR 3uts OR 3utt OR 3tt8 OR 2omh OR 2omi OR 3u4n OR 6o17 OR 4fg3 OR 2vjz OR 4oga OR 2lgb OR 6ck2 OR 2omg OR 5uoz OR 2oly OR 1zeg OR 2olz OR 3inc OR 1zeh OR 4akj OR 4f51 OR 3w7y OR 3rov OR 3w7z OR 6b70 OR 5co9 OR 1j73 OR 5aiy OR 5co2 OR 1os4 OR 5uqa OR 1os3 OR 4f4t OR 2jv1 OR 5co6 OR 4f4v OR 7bw7 OR 5wdm OR 7bw8 OR 1rwe OR 2ceu OR 2omq OR 2r34 OR 2r35 OR 7s4y OR 2r36 OR 5cny OR 2juu OR 2juv OR 5mt9 OR 2jum OR 3exx OR 3ir0 OR 1htv OR 5mt3 OR 7bwa OR 3zqr OR 6h3m OR 1lkq OR 5mam OR 3zs2 OR 2mli OR 1ai0 OR 5usp OR 5uu2 OR 5uu4 OR 5uu3 OR 3e7y OR 3e7z OR 4ex0 OR 3jsd OR 6gv0 OR 4ex1 OR 2kxk OR 1sjt OR 1q4v OR 1sju OR 5uru OR 5urt OR 6jk8 OR 1xda OR 6z7y OR 1hui OR 5hyj OR 6z7w OR 4ey9 OR 4eww OR 1a7f OR 2k91 OR 4nib OR 1b9e OR 4ewx OR 4ewz OR 4ey1 OR 1jk8 OR 5uss OR 5usv OR 3zu1 OR 6p4z OR 4efx OR 6x4x OR 1xw7 OR 2kjj OR 1kmf OR 4eyd OR 1fu2 OR 4exx OR 2wc0 OR 2ws6 OR 1qj0 OR 2ws7 OR 2c8q OR 2c8r OR 5udp OR 5boq OR 4f8f OR 2ws0 OR 2ws1 OR 1guj OR 2ws4 OR 1lph OR 2wby OR 1qiz OR 1qiy OR 3i40 OR 2k9r OR 6sof OR 2wru OR 4fka OR 4eyp OR 2wrv OR 2wrw OR 2wrx OR 1xgl OR 5bpo OR 1aiy OR 5c0d OR 2kju OR 4eyn OR 3fq9 OR 3i3z OR 3p33 OR 1hiq OR 2mpg OR 5mwq OR 2mpi OR 1mso OR 2h67 OR 6vep OR 5bqq OR 6ves OR 4y19 OR 6vet OR 1fub OR 6ver OR 6tc2 OR 1t0c OR 1ev6 OR 1ev3 OR 2aiy OR 3zi3 OR 5viz OR 2g54 OR 4y1a OR 6nwv OR 5mhd OR 2g56 OR 3bxq OR 4cy7 OR 1hit OR 1his OR 2hh4 OR 6u46 OR 3w11 OR 2w44 OR 3w12 OR 3w13 OR 6hn5 OR 2hho OR 5e7w OR 1t1k OR 4xc4 OR 6jr3 OR 1trz OR 2qiu OR 1g7b OR 1g7a OR 4cxl OR 3p2x OR 4cxn OR 1znj) AND molecule_sequence:['' TO *] AND status:REL",
+ "fl":"pdb_id,title,experimental_method,resolution",
+ "start":"0",
+ "sort":"",
+ "rows":"500",
+ "wt":"json"}},
+ "response":{"numFound":641,"start":0,"docs":[
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3hyd",
+ "resolution":1.0,
+ "title":"LVEALYL peptide derived from human insulin chain B, residues 11-17"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1t0c",
+ "title":"Solution Structure of Human Proinsulin C-Peptide"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"6u46",
+ "title":"Solution Structure of a Heat-Resistant Long-Acting Insulin Analog"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2omq",
+ "resolution":2.0,
+ "title":"VEALYL peptide derived from human insulin chain B, residues 12-17"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1sju",
+ "title":"MINI-PROINSULIN, SINGLE CHAIN INSULIN ANALOG MUTANT: DES B30, HIS(B 10)ASP, PRO(B 28)ASP AND PEPTIDE BOND BETWEEN LYS B 29 AND GLY A 1, NMR, 20 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1efe",
+ "title":"AN ACTIVE MINI-PROINSULIN, M2PI"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5wdm",
+ "resolution":2.803,
+ "title":"An ultra-stable single-chain insulin analog resists thermal inactivation and exhibits biological signaling duration equivalent to the native protein"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1his",
+ "title":"Structure and dynamics of des-pentapeptide-insulin in solution: the molten-globule hypothesis."},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1his",
+ "title":"Structure and dynamics of des-pentapeptide-insulin in solution: the molten-globule hypothesis."},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"6k59",
+ "title":"Structure of Glargine insulin in 20% acetic acid-d4 (pH 1.9)"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"6k59",
+ "title":"Structure of Glargine insulin in 20% acetic acid-d4 (pH 1.9)"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1hit",
+ "title":"Receptor binding redefined by a structural switch in a mutant Human Insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1hit",
+ "title":"Receptor binding redefined by a structural switch in a mutant Human Insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1vkt",
+ "title":"HUMAN INSULIN TWO DISULFIDE MODEL, NMR, 10 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2m1e",
+ "title":"Biosynthetic engineered B28K-B29P human insulin monomer structure in in water solutions."},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2m2o",
+ "title":"Structure of [D-HisB24] insulin analogue at pH 1.9"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2m2p",
+ "title":"Structure of [D-HisB24] insulin analogue at pH 8.0"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2m1d",
+ "title":"Biosynthetic engineered B28K-B29P human insulin monomer structure in in water/acetonitrile solutions."},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2c8q",
+ "resolution":1.95,
+ "title":"insuline(1sec) and UV laser excited fluorescence"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2c8q",
+ "resolution":1.95,
+ "title":"insuline(1sec) and UV laser excited fluorescence"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2c8r",
+ "resolution":1.5,
+ "title":"insuline(60sec) and UV laser excited fluorescence"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2c8r",
+ "resolution":1.5,
+ "title":"insuline(60sec) and UV laser excited fluorescence"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1hiq",
+ "title":"PARADOXICAL STRUCTURE AND FUNCTION IN A MUTANT HUMAN INSULIN ASSOCIATED WITH DIABETES MELLITUS"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1hiq",
+ "title":"PARADOXICAL STRUCTURE AND FUNCTION IN A MUTANT HUMAN INSULIN ASSOCIATED WITH DIABETES MELLITUS"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"7nhu",
+ "resolution":1.4,
+ "title":"Crystal structure of desB30 insulin produced by cell free protein synthesis"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"7nhu",
+ "resolution":1.4,
+ "title":"Crystal structure of desB30 insulin produced by cell free protein synthesis"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6o17",
+ "resolution":1.58,
+ "title":"Recombinant Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6o17",
+ "resolution":1.58,
+ "title":"Recombinant Human Insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2mvc",
+ "title":"Solution structure of human insulin at pH 1.9"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2mvd",
+ "title":"Solution structure of [GlnB22]-insulin mutant at pH 1.9"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2mvd",
+ "title":"Solution structure of [GlnB22]-insulin mutant at pH 1.9"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2m2n",
+ "title":"Structure of [L-HisB24] insulin analogue at pH 8.0"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2m2n",
+ "title":"Structure of [L-HisB24] insulin analogue at pH 8.0"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1vkt",
+ "title":"HUMAN INSULIN TWO DISULFIDE MODEL, NMR, 10 STRUCTURES"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2ws4",
+ "resolution":1.9,
+ "title":"Semi-synthetic analogue of human insulin ProB26-DTI in monomer form"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2m1e",
+ "title":"Biosynthetic engineered B28K-B29P human insulin monomer structure in in water solutions."},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2m2o",
+ "title":"Structure of [D-HisB24] insulin analogue at pH 1.9"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2m2p",
+ "title":"Structure of [D-HisB24] insulin analogue at pH 8.0"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2m1d",
+ "title":"Biosynthetic engineered B28K-B29P human insulin monomer structure in in water/acetonitrile solutions."},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1k3m",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT ILE-A2-ALA, HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1k3m",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT ILE-A2-ALA, HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1lkq",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT ILE-A2-GLY, VAL-A3-GLY, HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO, 20 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1sjt",
+ "title":"MINI-PROINSULIN, TWO CHAIN INSULIN ANALOG MUTANT: DES B30, HIS(B 10)ASP, PRO(B 28)ASP, NMR, 20 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1sjt",
+ "title":"MINI-PROINSULIN, TWO CHAIN INSULIN ANALOG MUTANT: DES B30, HIS(B 10)ASP, PRO(B 28)ASP, NMR, 20 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1lkq",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT ILE-A2-GLY, VAL-A3-GLY, HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO, 20 STRUCTURES"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3ilg",
+ "resolution":1.9,
+ "title":"Crystal structure of humnan insulin Sr+2 complex"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"5mwq",
+ "title":"Biosynthetic engineered A21K-B31K-B32R human insulin monomer structure in water/acetonitrile solution"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2mvc",
+ "title":"Solution structure of human insulin at pH 1.9"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5ena",
+ "resolution":1.35,
+ "title":"Xray crystal structure of isotope-labeled human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5viz",
+ "resolution":1.7,
+ "title":"X-Ray structure of Insulin Glargine"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5viz",
+ "resolution":1.7,
+ "title":"X-Ray structure of Insulin Glargine"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5en9",
+ "resolution":1.5,
+ "title":"High resolution x-ray crystal structure of isotope-labeled ester-insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3i40",
+ "resolution":1.85,
+ "title":"Human insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2kjj",
+ "title":"Dynamics of insulin probed by 1H-NMR amide proton exchange anomalous flexibility of the receptor-binding surface"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2kjj",
+ "title":"Dynamics of insulin probed by 1H-NMR amide proton exchange anomalous flexibility of the receptor-binding surface"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2juu",
+ "title":"allo-ThrA3 DKP-insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2jum",
+ "title":"ThrA3-DKP-insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2jum",
+ "title":"ThrA3-DKP-insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2jv1",
+ "title":"NMR structure of human insulin monomer in 35% CD3CN zinc free, 50 structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1iog",
+ "title":"INSULIN MUTANT A3 GLY,(B1, B10, B16, B27)GLU, DES-B30, NMR, 19 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1jco",
+ "title":"Solution structure of the monomeric [Thr(B27)->Pro,Pro(B28)->Thr] insulin mutant (PT insulin)"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1xgl",
+ "title":"HUMAN INSULIN DISULFIDE ISOMER, NMR, 10 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1xgl",
+ "title":"HUMAN INSULIN DISULFIDE ISOMER, NMR, 10 STRUCTURES"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2r35",
+ "resolution":2.08,
+ "title":"Crystal structure of RB human arg-insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2qiu",
+ "resolution":2.0,
+ "title":"Structure of Human Arg-Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2ws4",
+ "resolution":1.9,
+ "title":"Semi-synthetic analogue of human insulin ProB26-DTI in monomer form"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2wrw",
+ "resolution":2.41,
+ "title":"Semi-synthetic highly active analogue of human insulin D-ProB26-DTI- NH2"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2wrw",
+ "resolution":2.41,
+ "title":"Semi-synthetic highly active analogue of human insulin D-ProB26-DTI- NH2"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2l1z",
+ "title":"NMR Structure of human insulin mutant GLY-B20-D-ALA, GLY-B23-D-ALA PRO-B28-LYS, LYS-B29-PRO, 20 Structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2l1z",
+ "title":"NMR Structure of human insulin mutant GLY-B20-D-ALA, GLY-B23-D-ALA PRO-B28-LYS, LYS-B29-PRO, 20 Structures"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2r34",
+ "resolution":2.25,
+ "title":"Crystal structure of MN human arg-insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1kmf",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT ILE-A2-ALLO-ILE, HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1kmf",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT ILE-A2-ALLO-ILE, HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1ioh",
+ "title":"INSULIN MUTANT A8 HIS,(B1, B10, B16, B27)GLU, DES-B30, NMR, 26 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1hui",
+ "title":"INSULIN MUTANT (B1, B10, B16, B27)GLU, DES-B30, NMR, 25 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1hui",
+ "title":"INSULIN MUTANT (B1, B10, B16, B27)GLU, DES-B30, NMR, 25 STRUCTURES"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1os4",
+ "resolution":2.25,
+ "title":"Dehydrated T6 human insulin at 295 K"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1a7f",
+ "title":"INSULIN MUTANT B16 GLU, B24 GLY, DES-B30, NMR, 20 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2kju",
+ "title":"NMR structure of human insulin mutant glu-b21-d-glu, his-b10 asp pro-b28-lys, lys-b29-pro, 20 structures"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3ilg",
+ "resolution":1.9,
+ "title":"Crystal structure of humnan insulin Sr+2 complex"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1t1k",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ALA, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1t1k",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ALA, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5t7r",
+ "resolution":1.55,
+ "title":"A6-A11 trans-dicarba human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5t7r",
+ "resolution":1.55,
+ "title":"A6-A11 trans-dicarba human insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"5mwq",
+ "title":"Biosynthetic engineered A21K-B31K-B32R human insulin monomer structure in water/acetonitrile solution"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6jr3",
+ "resolution":14.5,
+ "title":"Crystal structure of insulin hexamer fitted into cryo EM density map where each dimer was kept as rigid body"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6jr3",
+ "resolution":14.5,
+ "title":"Crystal structure of insulin hexamer fitted into cryo EM density map where each dimer was kept as rigid body"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"6x4x",
+ "title":"B24Y DKP insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"6x4x",
+ "title":"B24Y DKP insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5ena",
+ "resolution":1.35,
+ "title":"Xray crystal structure of isotope-labeled human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3u4n",
+ "resolution":1.98,
+ "title":"A novel covalently linked insulin dimer"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3u4n",
+ "resolution":1.98,
+ "title":"A novel covalently linked insulin dimer"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3zi3",
+ "resolution":1.7,
+ "title":"Crystal structure of the B24His-insulin - human analogue"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3zi3",
+ "resolution":1.7,
+ "title":"Crystal structure of the B24His-insulin - human analogue"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5en9",
+ "resolution":1.5,
+ "title":"High resolution x-ray crystal structure of isotope-labeled ester-insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"7jp3",
+ "resolution":1.95,
+ "title":"Des-B29,B30-insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3i40",
+ "resolution":1.85,
+ "title":"Human insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2hho",
+ "title":"NMR structure of human insulin mutant GLY-B8-SER, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2juu",
+ "title":"allo-ThrA3 DKP-insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2h67",
+ "title":"NMR structure of human insulin mutant HIS-B5-ALA, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2h67",
+ "title":"NMR structure of human insulin mutant HIS-B5-ALA, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2jv1",
+ "title":"NMR structure of human insulin monomer in 35% CD3CN zinc free, 50 structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2juv",
+ "title":"AbaA3-DKP-insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2juv",
+ "title":"AbaA3-DKP-insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2ws0",
+ "resolution":2.1,
+ "title":"Semi-synthetic analogue of human insulin NMeAlaB26-insulin at pH 7.5"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1iog",
+ "title":"INSULIN MUTANT A3 GLY,(B1, B10, B16, B27)GLU, DES-B30, NMR, 19 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1jco",
+ "title":"Solution structure of the monomeric [Thr(B27)->Pro,Pro(B28)->Thr] insulin mutant (PT insulin)"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1t1p",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-THR, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1t1p",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-THR, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1t1q",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ABA, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1t1q",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ABA, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1sf1",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN under Amyloidogenic Condition, 15 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1sf1",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN under Amyloidogenic Condition, 15 STRUCTURES"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2r35",
+ "resolution":2.08,
+ "title":"Crystal structure of RB human arg-insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2qiu",
+ "resolution":2.0,
+ "title":"Structure of Human Arg-Insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2rn5",
+ "title":"Humal Insulin Mutant B31Lys-B32Arg"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2rn5",
+ "title":"Humal Insulin Mutant B31Lys-B32Arg"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2lgb",
+ "title":"Modified A22Gly-B31Arg Human Insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2lgb",
+ "title":"Modified A22Gly-B31Arg Human Insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1ioh",
+ "title":"INSULIN MUTANT A8 HIS,(B1, B10, B16, B27)GLU, DES-B30, NMR, 26 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1a7f",
+ "title":"INSULIN MUTANT B16 GLU, B24 GLY, DES-B30, NMR, 20 STRUCTURES"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1mso",
+ "resolution":1.0,
+ "title":"T6 Human Insulin at 1.0 A Resolution"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1os4",
+ "resolution":2.25,
+ "title":"Dehydrated T6 human insulin at 295 K"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1hls",
+ "title":"NMR STRUCTURE OF THE HUMAN INSULIN-HIS(B16)"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1hls",
+ "title":"NMR STRUCTURE OF THE HUMAN INSULIN-HIS(B16)"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3i3z",
+ "resolution":1.6,
+ "title":"Human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3i3z",
+ "resolution":1.6,
+ "title":"Human insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2kju",
+ "title":"NMR structure of human insulin mutant glu-b21-d-glu, his-b10 asp pro-b28-lys, lys-b29-pro, 20 structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2aiy",
+ "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 20 STRUCTURES"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6ves",
+ "resolution":1.85,
+ "title":"Human insulin analog: [GluB10,HisA8,ArgA9]-DOI"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6ves",
+ "resolution":1.85,
+ "title":"Human insulin analog: [GluB10,HisA8,ArgA9]-DOI"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6s34",
+ "resolution":1.35,
+ "title":"Zinc free, dimeric human insulin determined to 1.35 Angstrom resolution"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6s34",
+ "resolution":1.35,
+ "title":"Zinc free, dimeric human insulin determined to 1.35 Angstrom resolution"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ung",
+ "resolution":1.81,
+ "title":"Human insulin B26Asn mutant crystal structure"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4unh",
+ "resolution":2.75,
+ "title":"Human insulin B26Gly mutant crystal structure"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4unh",
+ "resolution":2.75,
+ "title":"Human insulin B26Gly mutant crystal structure"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2mpg",
+ "title":"Solution structure of the [AibB8,LysB28,ProB29]-insulin analogue"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4iyd",
+ "resolution":1.66,
+ "title":"Insulin glargine crystal structure 1"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4iyd",
+ "resolution":1.66,
+ "title":"Insulin glargine crystal structure 1"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3w7z",
+ "resolution":1.15,
+ "title":"1.15A structure of human 2Zn insulin at 293K"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3w7z",
+ "resolution":1.15,
+ "title":"1.15A structure of human 2Zn insulin at 293K"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3w7y",
+ "resolution":0.92,
+ "title":"0.92A structure of 2Zn human insulin at 100K"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3w7y",
+ "resolution":0.92,
+ "title":"0.92A structure of 2Zn human insulin at 100K"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ak0",
+ "resolution":2.28,
+ "title":"Ligand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ak0",
+ "resolution":2.28,
+ "title":"Ligand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5uoz",
+ "resolution":1.1746387,
+ "title":"Insulin with proline analog FyP at position B28 in the T2 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5uoz",
+ "resolution":1.1746387,
+ "title":"Insulin with proline analog FyP at position B28 in the T2 state"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2hiu",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN IN 20% ACETIC ACID, ZINC-FREE, 10 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2hiu",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN IN 20% ACETIC ACID, ZINC-FREE, 10 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2m2m",
+ "title":"Structure of [L-HisB24] insulin analogue at pH 1.9"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2m2m",
+ "title":"Structure of [L-HisB24] insulin analogue at pH 1.9"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2hho",
+ "title":"NMR structure of human insulin mutant GLY-B8-SER, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2k91",
+ "title":"Enhancing the activity of insulin by stereospecific unfolding"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2k91",
+ "title":"Enhancing the activity of insulin by stereospecific unfolding"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2hh4",
+ "title":"NMR structure of human insulin mutant GLY-B8-D-SER, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2hh4",
+ "title":"NMR structure of human insulin mutant GLY-B8-D-SER, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2ws0",
+ "resolution":2.1,
+ "title":"Semi-synthetic analogue of human insulin NMeAlaB26-insulin at pH 7.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1os3",
+ "resolution":1.95,
+ "title":"Dehydrated T6 human insulin at 100 K"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1os3",
+ "resolution":1.95,
+ "title":"Dehydrated T6 human insulin at 100 K"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"3aiy",
+ "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, REFINED AVERAGE STRUCTURE"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"3aiy",
+ "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, REFINED AVERAGE STRUCTURE"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3inc",
+ "resolution":1.85,
+ "title":"Crystal structure of human insulin with Ni+2 complex"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3inc",
+ "resolution":1.85,
+ "title":"Crystal structure of human insulin with Ni+2 complex"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2kxk",
+ "title":"Human Insulin Mutant A22Gly-B31Lys-B32Arg"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4cxn",
+ "resolution":1.7,
+ "title":"Crystal structure of human insulin analogue (NMe-AlaB8)-insulin crystal form I"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4cxn",
+ "resolution":1.7,
+ "title":"Crystal structure of human insulin analogue (NMe-AlaB8)-insulin crystal form I"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2r34",
+ "resolution":2.25,
+ "title":"Crystal structure of MN human arg-insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2kxk",
+ "title":"Human Insulin Mutant A22Gly-B31Lys-B32Arg"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2wrx",
+ "resolution":1.5,
+ "title":"Semi-synthetic analogue of human insulin NMeAlaB26-insulin at pH 3.0"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2wrx",
+ "resolution":1.5,
+ "title":"Semi-synthetic analogue of human insulin NMeAlaB26-insulin at pH 3.0"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1mhi",
+ "title":"THREE-DIMENSIONAL SOLUTION STRUCTURE OF AN INSULIN DIMER. A STUDY OF THE B9(ASP) MUTANT OF HUMAN INSULIN USING NUCLEAR MAGNETIC RESONANCE DISTANCE GEOMETRY AND RESTRAINED MOLECULAR DYNAMICS"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1mhi",
+ "title":"THREE-DIMENSIONAL SOLUTION STRUCTURE OF AN INSULIN DIMER. A STUDY OF THE B9(ASP) MUTANT OF HUMAN INSULIN USING NUCLEAR MAGNETIC RESONANCE DISTANCE GEOMETRY AND RESTRAINED MOLECULAR DYNAMICS"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1mhj",
+ "title":"SOLUTION STRUCTURE OF THE SUPERACTIVE MONOMERIC DES-[PHE(B25)] HUMAN INSULIN MUTANT. ELUCIDATION OF THE STRUCTURAL BASIS FOR THE MONOMERIZATION OF THE DES-[PHE(B25)] INSULIN AND THE DIMERIZATION OF NATIVE INSULIN"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1mhj",
+ "title":"SOLUTION STRUCTURE OF THE SUPERACTIVE MONOMERIC DES-[PHE(B25)] HUMAN INSULIN MUTANT. ELUCIDATION OF THE STRUCTURAL BASIS FOR THE MONOMERIZATION OF THE DES-[PHE(B25)] INSULIN AND THE DIMERIZATION OF NATIVE INSULIN"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1aiy",
+ "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 10 STRUCTURES"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1mso",
+ "resolution":1.0,
+ "title":"T6 Human Insulin at 1.0 A Resolution"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2g56",
+ "resolution":2.2,
+ "title":"crystal structure of human insulin-degrading enzyme in complex with insulin B chain"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2aiy",
+ "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 20 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2kqq",
+ "title":"NMR structure of human insulin mutant gly-b8-d-ala, his-b10-asp, pro-b28-lys, lys-b29-pro, 20 structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2l1y",
+ "title":"NMR Structure of human insulin mutant GLY-B20-D-ALA, GLY-B23-D-ALA PRO-B28-LYS, LYS-B29-PRO, 20 Structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2n2v",
+ "title":"Solution structure of [B26-B29 triazole cross-linked]-insulin analogue at pH 1.9"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2n2w",
+ "title":"Solution structure of [B26-B29 triazole cross-linked]-insulin analogue at pH 8.0"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4une",
+ "resolution":1.59,
+ "title":"Human insulin B26Phe mutant crystal structure"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4une",
+ "resolution":1.59,
+ "title":"Human insulin B26Phe mutant crystal structure"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ung",
+ "resolution":1.81,
+ "title":"Human insulin B26Asn mutant crystal structure"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2mpi",
+ "title":"Solution structure of B24G insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2mpi",
+ "title":"Solution structure of B24G insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2mpg",
+ "title":"Solution structure of the [AibB8,LysB28,ProB29]-insulin analogue"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2mli",
+ "title":"NMR structure of B25-(alpha, beta)-dehydro-phenylalanine insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3w80",
+ "resolution":1.4,
+ "title":"Crystal structure of dodecamer human insulin with double C-axis length of the hexamer 2 Zn insulin cell"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3w80",
+ "resolution":1.4,
+ "title":"Crystal structure of dodecamer human insulin with double C-axis length of the hexamer 2 Zn insulin cell"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"4aiy",
+ "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 'GREEN' SUBSTATE, AVERAGE STRUCTURE"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"4aiy",
+ "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 'GREEN' SUBSTATE, AVERAGE STRUCTURE"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ewx",
+ "resolution":2.201,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3tt8",
+ "resolution":1.12,
+ "title":"Crystal Structure Analysis of Cu Human Insulin Derivative"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3tt8",
+ "resolution":1.12,
+ "title":"Crystal Structure Analysis of Cu Human Insulin Derivative"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4iyf",
+ "resolution":1.8,
+ "title":"Insulin glargine crystal structure 2"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4iyf",
+ "resolution":1.8,
+ "title":"Insulin glargine crystal structure 2"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"5aiy",
+ "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 'RED' SUBSTATE, AVERAGE STRUCTURE"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"5aiy",
+ "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 'RED' SUBSTATE, AVERAGE STRUCTURE"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"5mhd",
+ "title":"Biosynthetic engineered A22S-B3K-B31R human insulin monomer structure in water/acetonitrile solutions."},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"5mhd",
+ "title":"Biosynthetic engineered A22S-B3K-B31R human insulin monomer structure in water/acetonitrile solutions."},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2n2x",
+ "title":"Solution structure of [GlyB24,B27-B29 triazole cross-linked]-insulin analogue at pH 1.9"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5hqi",
+ "resolution":0.97,
+ "title":"Insulin with proline analog HzP at position B28 in the T2 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5hqi",
+ "resolution":0.97,
+ "title":"Insulin with proline analog HzP at position B28 in the T2 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4eww",
+ "resolution":2.3,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2wru",
+ "resolution":1.57,
+ "title":"Semi-synthetic highly active analogue of human insulin NMeAlaB26-DTI- NH2"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2wru",
+ "resolution":1.57,
+ "title":"Semi-synthetic highly active analogue of human insulin NMeAlaB26-DTI- NH2"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f1a",
+ "resolution":1.8,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f1a",
+ "resolution":1.8,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f51",
+ "resolution":1.637,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f4t",
+ "resolution":1.637,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f0o",
+ "resolution":1.672,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2ws1",
+ "resolution":1.6,
+ "title":"Semi-synthetic analogue of human insulin NMeTyrB26-insulin in monomer form"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2ws1",
+ "resolution":1.6,
+ "title":"Semi-synthetic analogue of human insulin NMeTyrB26-insulin in monomer form"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4fka",
+ "resolution":1.08,
+ "title":"High resolution structure of the manganese derivative of insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f1g",
+ "resolution":1.637,
+ "title":"Human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f8f",
+ "resolution":1.676,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f1d",
+ "resolution":1.637,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f0n",
+ "resolution":1.679,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f0n",
+ "resolution":1.679,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f1b",
+ "resolution":1.591,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f1c",
+ "resolution":1.7,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f1f",
+ "resolution":1.684,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f4v",
+ "resolution":1.637,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1aiy",
+ "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 10 STRUCTURES"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1htv",
+ "resolution":1.9,
+ "title":"CRYSTAL STRUCTURE OF DESTRIPEPTIDE (B28-B30) INSULIN"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1htv",
+ "resolution":1.9,
+ "title":"CRYSTAL STRUCTURE OF DESTRIPEPTIDE (B28-B30) INSULIN"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1ai0",
+ "title":"R6 HUMAN INSULIN HEXAMER (NON-SYMMETRIC), NMR, 10 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1ai0",
+ "title":"R6 HUMAN INSULIN HEXAMER (NON-SYMMETRIC), NMR, 10 STRUCTURES"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3bxq",
+ "resolution":1.3,
+ "title":"The structure of a mutant insulin uncouples receptor binding from protein allostery. An electrostatic block to the TR transition"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1jca",
+ "resolution":2.5,
+ "title":"Non-standard Design of Unstable Insulin Analogues with Enhanced Activity"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2kqq",
+ "title":"NMR structure of human insulin mutant gly-b8-d-ala, his-b10-asp, pro-b28-lys, lys-b29-pro, 20 structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2l1y",
+ "title":"NMR Structure of human insulin mutant GLY-B20-D-ALA, GLY-B23-D-ALA PRO-B28-LYS, LYS-B29-PRO, 20 Structures"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6ver",
+ "resolution":1.047,
+ "title":"Human insulin analog: [GluB10,TyrB20]-DOI"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6ver",
+ "resolution":1.047,
+ "title":"Human insulin analog: [GluB10,TyrB20]-DOI"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5bts",
+ "resolution":1.77,
+ "title":"Structural and biophysical characterization of a covalent insulin dimer formed during storage of neutral formulation of human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5bts",
+ "resolution":1.77,
+ "title":"Structural and biophysical characterization of a covalent insulin dimer formed during storage of neutral formulation of human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5bpo",
+ "resolution":1.9,
+ "title":"Human insulin with intra-chain chemical crosslink between modified B27 and B29"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5urt",
+ "resolution":1.18,
+ "title":"Insulin with proline analog DhP at position B28 in the T2 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5usp",
+ "resolution":1.174,
+ "title":"Insulin with proline analog Pip at position B28 in the T2 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5usp",
+ "resolution":1.174,
+ "title":"Insulin with proline analog Pip at position B28 in the T2 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6h3m",
+ "resolution":1.821,
+ "title":"The crystal structure of a human seleno-insulin analog"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6h3m",
+ "resolution":1.821,
+ "title":"The crystal structure of a human seleno-insulin analog"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4rxw",
+ "resolution":1.73,
+ "title":"Crystal Structure of the cobalt human insulin derivative"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4rxw",
+ "resolution":1.73,
+ "title":"Crystal Structure of the cobalt human insulin derivative"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2n2v",
+ "title":"Solution structure of [B26-B29 triazole cross-linked]-insulin analogue at pH 1.9"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2n2w",
+ "title":"Solution structure of [B26-B29 triazole cross-linked]-insulin analogue at pH 8.0"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4eyd",
+ "resolution":1.471,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4eyd",
+ "resolution":1.471,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4eyn",
+ "resolution":1.532,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4eyn",
+ "resolution":1.532,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ey1",
+ "resolution":1.471,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ewx",
+ "resolution":2.201,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4eyp",
+ "resolution":1.591,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4exx",
+ "resolution":1.55,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4exx",
+ "resolution":1.55,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5usv",
+ "resolution":1.3,
+ "title":"Insulin with proline analog AzeP at position B28 in the T2 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5usv",
+ "resolution":1.3,
+ "title":"Insulin with proline analog AzeP at position B28 in the T2 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5uu2",
+ "resolution":1.223,
+ "title":"Insulin with proline analog ThioP at position B28 in the T2 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ex1",
+ "resolution":1.657,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2n2x",
+ "title":"Solution structure of [GlyB24,B27-B29 triazole cross-linked]-insulin analogue at pH 1.9"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ey9",
+ "resolution":1.471,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ey9",
+ "resolution":1.471,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3q6e",
+ "resolution":2.05,
+ "title":"Human insulin in complex with cucurbit[7]uril"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3q6e",
+ "resolution":2.05,
+ "title":"Human insulin in complex with cucurbit[7]uril"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ex0",
+ "resolution":1.86,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ex0",
+ "resolution":1.86,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4eww",
+ "resolution":2.3,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ewz",
+ "resolution":1.791,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ewz",
+ "resolution":1.791,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5c0d",
+ "resolution":1.68,
+ "title":"HLA-A02 carrying AQWGPDPAAA"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3ir0",
+ "resolution":2.2,
+ "title":"Crystal Structure of Human Insulin complexed with Cu+2 metal ion"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3ir0",
+ "resolution":2.2,
+ "title":"Crystal Structure of Human Insulin complexed with Cu+2 metal ion"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3exx",
+ "resolution":1.35,
+ "title":"Structure of the T6 human insulin derivative with nickel at 1.35 A resolution"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3exx",
+ "resolution":1.35,
+ "title":"Structure of the T6 human insulin derivative with nickel at 1.35 A resolution"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2wrv",
+ "resolution":2.15,
+ "title":"Semi-synthetic highly active analogue of human insulin NMeHisB26-DTI- NH2"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2wrv",
+ "resolution":2.15,
+ "title":"Semi-synthetic highly active analogue of human insulin NMeHisB26-DTI- NH2"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2vk0",
+ "resolution":2.2,
+ "title":"Crystal structure form ultalente insulin microcrystals"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1b9e",
+ "resolution":2.5,
+ "title":"HUMAN INSULIN MUTANT SERB9GLU"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1b9e",
+ "resolution":2.5,
+ "title":"HUMAN INSULIN MUTANT SERB9GLU"},
+ {
+ "experimental_method":["X-ray powder diffraction"],
+ "pdb_id":"1fub",
+ "title":"FIRST PROTEIN STRUCTURE DETERMINED FROM X-RAY POWDER DIFFRACTION DATA"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f51",
+ "resolution":1.637,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f4t",
+ "resolution":1.637,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f0o",
+ "resolution":1.672,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2vjz",
+ "resolution":1.8,
+ "title":"Crystal structure form ultalente insulin microcrystals"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4fka",
+ "resolution":1.08,
+ "title":"High resolution structure of the manganese derivative of insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f1g",
+ "resolution":1.637,
+ "title":"Human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2r36",
+ "resolution":2.0,
+ "title":"Crystal structure of ni human ARG-insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4gbi",
+ "resolution":2.502,
+ "title":"Crystal structure of aspart insulin at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f8f",
+ "resolution":1.676,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f1d",
+ "resolution":1.637,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4gbc",
+ "resolution":1.778,
+ "title":"Crystal structure of aspart insulin at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4gbn",
+ "resolution":1.872,
+ "title":"Crystal structure of aspart insulin at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4cxl",
+ "resolution":1.5,
+ "title":"Human insulin analogue (D-ProB8)-insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4cxl",
+ "resolution":1.5,
+ "title":"Human insulin analogue (D-ProB8)-insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f1b",
+ "resolution":1.591,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f1c",
+ "resolution":1.7,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f1f",
+ "resolution":1.684,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f4v",
+ "resolution":1.637,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2ceu",
+ "resolution":1.8,
+ "title":"Despentapeptide insulin in acetic acid (pH 2)"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2ceu",
+ "resolution":1.8,
+ "title":"Despentapeptide insulin in acetic acid (pH 2)"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3bxq",
+ "resolution":1.3,
+ "title":"The structure of a mutant insulin uncouples receptor binding from protein allostery. An electrostatic block to the TR transition"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1jca",
+ "resolution":2.5,
+ "title":"Non-standard Design of Unstable Insulin Analogues with Enhanced Activity"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5cny",
+ "resolution":1.7,
+ "title":"Crystal Structure of human zinc insulin at pH 5.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5bpo",
+ "resolution":1.9,
+ "title":"Human insulin with intra-chain chemical crosslink between modified B27 and B29"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5urt",
+ "resolution":1.18,
+ "title":"Insulin with proline analog DhP at position B28 in the T2 state"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2mli",
+ "title":"NMR structure of B25-(alpha, beta)-dehydro-phenylalanine insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4iuz",
+ "resolution":1.6,
+ "title":"High resolution crystal structure of racemic ester insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ey1",
+ "resolution":1.471,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4eyp",
+ "resolution":1.591,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5uu2",
+ "resolution":1.223,
+ "title":"Insulin with proline analog ThioP at position B28 in the T2 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ex1",
+ "resolution":1.657,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2omi",
+ "resolution":2.24,
+ "title":"Structure of human insulin cocrystallized with protamine"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2k9r",
+ "title":"Enhancing the activity of insulin by stereospecific unfolding"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2k9r",
+ "title":"Enhancing the activity of insulin by stereospecific unfolding"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2g54",
+ "resolution":2.25,
+ "title":"Crystal structure of Zn-bound human insulin-degrading enzyme in complex with insulin B chain"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2vk0",
+ "resolution":2.2,
+ "title":"Crystal structure form ultalente insulin microcrystals"},
+ {
+ "experimental_method":["X-ray powder diffraction"],
+ "pdb_id":"1fub",
+ "title":"FIRST PROTEIN STRUCTURE DETERMINED FROM X-RAY POWDER DIFFRACTION DATA"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2vjz",
+ "resolution":1.8,
+ "title":"Crystal structure form ultalente insulin microcrystals"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2r36",
+ "resolution":2.0,
+ "title":"Crystal structure of ni human ARG-insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4gbk",
+ "resolution":2.4,
+ "title":"Crystal structure of aspart insulin at pH 8.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4gbk",
+ "resolution":2.4,
+ "title":"Crystal structure of aspart insulin at pH 8.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4gbi",
+ "resolution":2.502,
+ "title":"Crystal structure of aspart insulin at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4gbc",
+ "resolution":1.778,
+ "title":"Crystal structure of aspart insulin at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4cy7",
+ "resolution":1.4,
+ "title":"Crystal structure of human insulin analogue (NMe-AlaB8)-insulin crystal form II"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4gbn",
+ "resolution":1.872,
+ "title":"Crystal structure of aspart insulin at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4gbl",
+ "resolution":2.5,
+ "title":"Crystal structure of aspart insulin at pH 8.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4gbl",
+ "resolution":2.5,
+ "title":"Crystal structure of aspart insulin at pH 8.5"},
+ {
+ "experimental_method":["X-ray powder diffraction"],
+ "pdb_id":"1fu2",
+ "title":"FIRST PROTEIN STRUCTURE DETERMINED FROM X-RAY POWDER DIFFRACTION DATA"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1ev3",
+ "resolution":1.78,
+ "title":"Structure of the rhombohedral form of the M-cresol/insulin R6 hexamer"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1j73",
+ "resolution":2.0,
+ "title":"Crystal structure of an unstable insulin analog with native activity."},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1j73",
+ "resolution":2.0,
+ "title":"Crystal structure of an unstable insulin analog with native activity."},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6s4i",
+ "resolution":1.511,
+ "title":"Crystal structure of zinc free A14E, B25H, B29K(N(eps)-[2-(2-[2-(2-[2-(Octadecandioyl-gamma-Glu)amino]ethoxy)ethoxy]acetylamino)ethoxy]ethoxy)acetyl]), desB30 human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6s4i",
+ "resolution":1.511,
+ "title":"Crystal structure of zinc free A14E, B25H, B29K(N(eps)-[2-(2-[2-(2-[2-(Octadecandioyl-gamma-Glu)amino]ethoxy)ethoxy]acetylamino)ethoxy]ethoxy)acetyl]), desB30 human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6p4z",
+ "resolution":1.8,
+ "title":"Structure of gadolinium-caged cobalt (III) insulin hexamer"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5co9",
+ "resolution":1.92,
+ "title":"Crystal structure of human zinc insulin at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5cny",
+ "resolution":1.7,
+ "title":"Crystal Structure of human zinc insulin at pH 5.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5co2",
+ "resolution":1.7,
+ "title":"Crystalization of human zinc insulin at pH 5.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5co2",
+ "resolution":1.7,
+ "title":"Crystalization of human zinc insulin at pH 5.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5boq",
+ "resolution":1.7,
+ "title":"Human insulin with intra-chain chemical crosslink between modified B24 and B29"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5boq",
+ "resolution":1.7,
+ "title":"Human insulin with intra-chain chemical crosslink between modified B24 and B29"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6vet",
+ "resolution":1.46,
+ "title":"Human insulin analog: [GluB10,HisA8,ArgA9,TyrB20]-DOI"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6vet",
+ "resolution":1.46,
+ "title":"Human insulin analog: [GluB10,HisA8,ArgA9,TyrB20]-DOI"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6gv0",
+ "resolution":1.26,
+ "title":"Insulin glulisine"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4iuz",
+ "resolution":1.6,
+ "title":"High resolution crystal structure of racemic ester insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4efx",
+ "resolution":1.98,
+ "title":"Highly biologically active insulin with additional disulfide bond"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4efx",
+ "resolution":1.98,
+ "title":"Highly biologically active insulin with additional disulfide bond"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6ce7",
+ "resolution":7.4,
+ "title":"Insulin Receptor ectodomain in complex with one insulin molecule"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2jmn",
+ "title":"NMR structure of human insulin mutant His-B10-Asp, Pro-B28-Lys, Lys-B29-Pro, 20 structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2jmn",
+ "title":"NMR structure of human insulin mutant His-B10-Asp, Pro-B28-Lys, Lys-B29-Pro, 20 structures"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3utq",
+ "resolution":1.67,
+ "title":"Human HLA-A*0201-ALWGPDPAAA"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2omi",
+ "resolution":2.24,
+ "title":"Structure of human insulin cocrystallized with protamine"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3e7y",
+ "resolution":1.6,
+ "title":"Structure of human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3e7y",
+ "resolution":1.6,
+ "title":"Structure of human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1ev6",
+ "resolution":1.9,
+ "title":"Structure of the monoclinic form of the M-cresol/insulin R6 hexamer"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1trz",
+ "resolution":1.6,
+ "title":"CRYSTALLOGRAPHIC EVIDENCE FOR DUAL COORDINATION AROUND ZINC IN THE T3R3 HUMAN INSULIN HEXAMER"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1trz",
+ "resolution":1.6,
+ "title":"CRYSTALLOGRAPHIC EVIDENCE FOR DUAL COORDINATION AROUND ZINC IN THE T3R3 HUMAN INSULIN HEXAMER"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2ws7",
+ "resolution":2.59,
+ "title":"Semi-synthetic analogue of human insulin ProB26-DTI"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4nib",
+ "resolution":1.4,
+ "title":"Crystal structure of human insulin mutant B20 D-ala, B23 D-ala"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4nib",
+ "resolution":1.4,
+ "title":"Crystal structure of human insulin mutant B20 D-ala, B23 D-ala"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4cy7",
+ "resolution":1.4,
+ "title":"Crystal structure of human insulin analogue (NMe-AlaB8)-insulin crystal form II"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1qj0",
+ "resolution":2.4,
+ "title":"HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR"},
+ {
+ "experimental_method":["X-ray powder diffraction"],
+ "pdb_id":"1fu2",
+ "title":"FIRST PROTEIN STRUCTURE DETERMINED FROM X-RAY POWDER DIFFRACTION DATA"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1evr",
+ "resolution":1.9,
+ "title":"The structure of the resorcinol/insulin R6 hexamer"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1ev6",
+ "resolution":1.9,
+ "title":"Structure of the monoclinic form of the M-cresol/insulin R6 hexamer"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1guj",
+ "resolution":1.62,
+ "title":"Insulin at pH 2: structural analysis of the conditions promoting insulin fibre formation."},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1guj",
+ "resolution":1.62,
+ "title":"Insulin at pH 2: structural analysis of the conditions promoting insulin fibre formation."},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1ev3",
+ "resolution":1.78,
+ "title":"Structure of the rhombohedral form of the M-cresol/insulin R6 hexamer"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2w44",
+ "resolution":2.0,
+ "title":"Structure DeltaA1-A4 insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1uz9",
+ "resolution":1.6,
+ "title":"Crystallographic and solution studies of N-lithocholyl insulin: a new generation of prolonged-acting insulins."},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1uz9",
+ "resolution":1.6,
+ "title":"Crystallographic and solution studies of N-lithocholyl insulin: a new generation of prolonged-acting insulins."},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3e7z",
+ "resolution":1.7,
+ "title":"Structure of human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3e7z",
+ "resolution":1.7,
+ "title":"Structure of human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6gnq",
+ "resolution":2.2,
+ "title":"Monoclinic crystalline form of human insulin, complexed with meta-cresol"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"7s4y",
+ "resolution":1.71,
+ "title":"Serial Macromolecular Crystallography at ALBA Synchrotron Light Source - Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"7s4y",
+ "resolution":1.71,
+ "title":"Serial Macromolecular Crystallography at ALBA Synchrotron Light Source - Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5co6",
+ "resolution":1.8,
+ "title":"Crystal structure of human zinc insulin at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5co6",
+ "resolution":1.8,
+ "title":"Crystal structure of human zinc insulin at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6p4z",
+ "resolution":1.8,
+ "title":"Structure of gadolinium-caged cobalt (III) insulin hexamer"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5co9",
+ "resolution":1.92,
+ "title":"Crystal structure of human zinc insulin at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6s4j",
+ "resolution":1.5,
+ "title":"Crystal structure of zinc free A14E, B25H, B29K(N(eps)-[2-(2-[2-(2-[2-(Octadecandioyl-gamma-Glu)amino]ethoxy)ethoxy]acetylamino)ethoxy]ethoxy)acetyl]), desB27, desB30 human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6s4j",
+ "resolution":1.5,
+ "title":"Crystal structure of zinc free A14E, B25H, B29K(N(eps)-[2-(2-[2-(2-[2-(Octadecandioyl-gamma-Glu)amino]ethoxy)ethoxy]acetylamino)ethoxy]ethoxy)acetyl]), desB27, desB30 human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6gv0",
+ "resolution":1.26,
+ "title":"Insulin glulisine"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3zu1",
+ "resolution":1.6,
+ "title":"Structure of LysB29(Nepsilon omega-carboxyheptadecanoyl) des(B30) Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3zu1",
+ "resolution":1.6,
+ "title":"Structure of LysB29(Nepsilon omega-carboxyheptadecanoyl) des(B30) Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5ems",
+ "resolution":2.3,
+ "title":"Crystal Structure of an iodinated insulin analog"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6ce7",
+ "resolution":7.4,
+ "title":"Insulin Receptor ectodomain in complex with one insulin molecule"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1jk8",
+ "resolution":2.4,
+ "title":"Crystal structure of a human insulin peptide-HLA-DQ8 complex"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2wby",
+ "resolution":2.6,
+ "title":"Crystal structure of human insulin-degrading enzyme in complex with insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2wby",
+ "resolution":2.6,
+ "title":"Crystal structure of human insulin-degrading enzyme in complex with insulin"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6hn5",
+ "resolution":3.2,
+ "title":"Leucine-zippered human insulin receptor ectodomain with single bound insulin - \"upper\" membrane-distal part"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2om1",
+ "resolution":1.97,
+ "title":"Structure of human insulin in presence of thiocyanate at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2om0",
+ "resolution":2.05,
+ "title":"Structure of human insulin in presence of urea at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2om0",
+ "resolution":2.05,
+ "title":"Structure of human insulin in presence of urea at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3p33",
+ "resolution":2.3,
+ "title":"Insulin fibrillation is the Janus face of induced fit. A chiral clamp stabilizes the native state at the expense of activity"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2omg",
+ "resolution":1.52,
+ "title":"Structure of human insulin cocrystallized with protamine and urea"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2olz",
+ "resolution":1.7,
+ "title":"Structure of human insulin in presence of thiocyanate at pH 7.0"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2olz",
+ "resolution":1.7,
+ "title":"Structure of human insulin in presence of thiocyanate at pH 7.0"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1ben",
+ "resolution":1.4,
+ "title":"INSULIN COMPLEXED WITH 4-HYDROXYBENZAMIDE"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1g7a",
+ "resolution":1.2,
+ "title":"1.2 A structure of T3R3 human insulin at 100 K"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1g7a",
+ "resolution":1.2,
+ "title":"1.2 A structure of T3R3 human insulin at 100 K"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1w8p",
+ "resolution":2.08,
+ "title":"Structural properties of the B25Tyr-NMe-B26Phe insulin mutant."},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1w8p",
+ "resolution":2.08,
+ "title":"Structural properties of the B25Tyr-NMe-B26Phe insulin mutant."},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1rwe",
+ "resolution":1.8,
+ "title":"Enhancing the activity of insulin at receptor edge: crystal structure and photo-cross-linking of A8 analogues"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1rwe",
+ "resolution":1.8,
+ "title":"Enhancing the activity of insulin at receptor edge: crystal structure and photo-cross-linking of A8 analogues"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1znj",
+ "resolution":2.0,
+ "title":"INSULIN, MONOCLINIC CRYSTAL FORM"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1znj",
+ "resolution":2.0,
+ "title":"INSULIN, MONOCLINIC CRYSTAL FORM"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1xw7",
+ "resolution":2.3,
+ "title":"Diabetes-Associated Mutations in Human Insulin: Crystal Structure and Photo-Cross-Linking Studies of A-Chain Variant Insulin Wakayama"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1xw7",
+ "resolution":2.3,
+ "title":"Diabetes-Associated Mutations in Human Insulin: Crystal Structure and Photo-Cross-Linking Studies of A-Chain Variant Insulin Wakayama"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4fg3",
+ "resolution":2.001,
+ "title":"Crystal Structure Analysis of the Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4fg3",
+ "resolution":2.001,
+ "title":"Crystal Structure Analysis of the Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2ws7",
+ "resolution":2.59,
+ "title":"Semi-synthetic analogue of human insulin ProB26-DTI"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1lph",
+ "resolution":2.3,
+ "title":"LYS(B28)PRO(B29)-HUMAN INSULIN"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1qj0",
+ "resolution":2.4,
+ "title":"HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1g7b",
+ "resolution":1.3,
+ "title":"1.3 A STRUCTURE OF T3R3 HUMAN INSULIN AT 100 K"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1g7b",
+ "resolution":1.3,
+ "title":"1.3 A STRUCTURE OF T3R3 HUMAN INSULIN AT 100 K"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1evr",
+ "resolution":1.9,
+ "title":"The structure of the resorcinol/insulin R6 hexamer"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2w44",
+ "resolution":2.0,
+ "title":"Structure DeltaA1-A4 insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6gnq",
+ "resolution":2.2,
+ "title":"Monoclinic crystalline form of human insulin, complexed with meta-cresol"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5uru",
+ "resolution":2.41,
+ "title":"Insulin with proline analog DhP at position B28 in the R6 state"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"7bw7",
+ "resolution":4.1,
+ "title":"Cryo-EM Structure for the Ectodomain of the Full-length Human Insulin Receptor in Complex with 1 Insulin."},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6ck2",
+ "resolution":2.25,
+ "title":"Insulin analog containing a YB26W mutation"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6nwv",
+ "resolution":1.601,
+ "title":"Insulin Lispro Analog"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5hrq",
+ "resolution":1.28,
+ "title":"Insulin with proline analog HzP at position B28 in the R6 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3zqr",
+ "resolution":1.9,
+ "title":"NMePheB25 insulin analogue crystal structure"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3zqr",
+ "resolution":1.9,
+ "title":"NMePheB25 insulin analogue crystal structure"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ajx",
+ "resolution":1.2,
+ "title":"Ligand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ajx",
+ "resolution":1.2,
+ "title":"Ligand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4akj",
+ "resolution":2.01,
+ "title":"Ligand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ajz",
+ "resolution":1.8,
+ "title":"Ligand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3v19",
+ "resolution":2.0,
+ "title":"Forestalling insulin fibrillation by insertion of a chiral clamp mechanism-based application of protein engineering to global health"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3v19",
+ "resolution":2.0,
+ "title":"Forestalling insulin fibrillation by insertion of a chiral clamp mechanism-based application of protein engineering to global health"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3zs2",
+ "resolution":1.97,
+ "title":"TyrB25,NMePheB26,LysB28,ProB29-insulin analogue crystal structure"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3zs2",
+ "resolution":1.97,
+ "title":"TyrB25,NMePheB26,LysB28,ProB29-insulin analogue crystal structure"},
+ {
+ "experimental_method":["X-ray diffraction"],
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+ "experimental_method":["X-ray diffraction"],
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+ {
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+ "pdb_id":"5uu3",
+ "resolution":2.25,
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+ {
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+ "title":"Insulin with proline analog PiP at position B28 in the R6 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5uss",
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+ "title":"Insulin with proline analog PiP at position B28 in the R6 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5udp",
+ "resolution":1.348,
+ "title":"High resolution x-ray crystal structure of synthetic insulin lispro"},
+ {
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+ "pdb_id":"5udp",
+ "resolution":1.348,
+ "title":"High resolution x-ray crystal structure of synthetic insulin lispro"},
+ {
+ "experimental_method":["X-ray diffraction"],
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+ "resolution":1.88,
+ "title":"Human insulin in complex with serotonin and arginine"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5ems",
+ "resolution":2.3,
+ "title":"Crystal Structure of an iodinated insulin analog"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5hpr",
+ "resolution":1.33,
+ "title":"Insulin with proline analog HyP at position B28 in the T2 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5hpr",
+ "resolution":1.33,
+ "title":"Insulin with proline analog HyP at position B28 in the T2 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3kq6",
+ "resolution":1.9,
+ "title":"Enhancing the Therapeutic Properties of a Protein by a Designed Zinc-Binding Site, Structural principles of a novel long-acting insulin analog"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3kq6",
+ "resolution":1.9,
+ "title":"Enhancing the Therapeutic Properties of a Protein by a Designed Zinc-Binding Site, Structural principles of a novel long-acting insulin analog"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5mt3",
+ "resolution":2.02,
+ "title":"Human insulin in complex with serotonin and arginine"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6hn5",
+ "resolution":3.2,
+ "title":"Leucine-zippered human insulin receptor ectodomain with single bound insulin - \"upper\" membrane-distal part"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4wdi",
+ "resolution":2.313,
+ "title":"Weak TCR binding to an unstable insulin epitope drives type 1 diabetes"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2wc0",
+ "resolution":2.8,
+ "title":"crystal structure of human insulin degrading enzyme in complex with iodinated insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2wc0",
+ "resolution":2.8,
+ "title":"crystal structure of human insulin degrading enzyme in complex with iodinated insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6z7y",
+ "resolution":2.2,
+ "title":"Human insulin in complex with the analytical antibody OXI-005 Fab"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6z7y",
+ "resolution":2.2,
+ "title":"Human insulin in complex with the analytical antibody OXI-005 Fab"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6sof",
+ "resolution":4.3,
+ "title":"human insulin receptor ectodomain bound by 4 insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3p2x",
+ "resolution":2.0,
+ "title":"Insulin fibrillation is the Janus face of induced fit. A chiaral clamp stabilizes the native state at the expense of activity"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3p2x",
+ "resolution":2.0,
+ "title":"Insulin fibrillation is the Janus face of induced fit. A chiaral clamp stabilizes the native state at the expense of activity"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3jsd",
+ "resolution":2.5,
+ "title":"Insulin's biosynthesis and activity have opposing structural requirements: a new factor in neonatal diabetes mellitus"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3jsd",
+ "resolution":2.5,
+ "title":"Insulin's biosynthesis and activity have opposing structural requirements: a new factor in neonatal diabetes mellitus"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2om1",
+ "resolution":1.97,
+ "title":"Structure of human insulin in presence of thiocyanate at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2omh",
+ "resolution":1.36,
+ "title":"Structure of human insulin cocrystallized with ARG-12 peptide in presence of urea"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2omh",
+ "resolution":1.36,
+ "title":"Structure of human insulin cocrystallized with ARG-12 peptide in presence of urea"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3fq9",
+ "resolution":1.35,
+ "title":"Design of an insulin analog with enhanced receptor-binding selectivity. Rationale, structure, and therapeutic implications"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3fq9",
+ "resolution":1.35,
+ "title":"Design of an insulin analog with enhanced receptor-binding selectivity. Rationale, structure, and therapeutic implications"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3p33",
+ "resolution":2.3,
+ "title":"Insulin fibrillation is the Janus face of induced fit. A chiral clamp stabilizes the native state at the expense of activity"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2omg",
+ "resolution":1.52,
+ "title":"Structure of human insulin cocrystallized with protamine and urea"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1ben",
+ "resolution":1.4,
+ "title":"INSULIN COMPLEXED WITH 4-HYDROXYBENZAMIDE"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1qiz",
+ "resolution":2.0,
+ "title":"HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR COMPLEXED WITH RESORCINOL"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1qiz",
+ "resolution":2.0,
+ "title":"HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR COMPLEXED WITH RESORCINOL"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4p65",
+ "resolution":1.5,
+ "title":"Crystal structure of an cyclohexylalanine substituted insulin analog."},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4p65",
+ "resolution":1.5,
+ "title":"Crystal structure of an cyclohexylalanine substituted insulin analog."},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1lph",
+ "resolution":2.3,
+ "title":"LYS(B28)PRO(B29)-HUMAN INSULIN"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2oly",
+ "resolution":1.7,
+ "title":"Structure of human insulin in presence of urea at pH 7.0"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6tyh",
+ "resolution":1.600019,
+ "title":"Four-Disulfide Insulin Analog A22/B22"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6tyh",
+ "resolution":1.600019,
+ "title":"Four-Disulfide Insulin Analog A22/B22"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5uru",
+ "resolution":2.41,
+ "title":"Insulin with proline analog DhP at position B28 in the R6 state"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"7bw8",
+ "resolution":3.8,
+ "title":"Cryo-EM Structure for the Insulin Binding Region in the Ectodomain of the Full-length Human Insulin Receptor in Complex with 1 Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6ck2",
+ "resolution":2.25,
+ "title":"Insulin analog containing a YB26W mutation"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6bfc",
+ "resolution":3.7,
+ "title":"Cryo-EM structure of human insulin degrading enzyme in complex with insulin"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6b3q",
+ "resolution":3.7,
+ "title":"Cryo-EM structure of human insulin degrading enzyme in complex with insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6nwv",
+ "resolution":1.601,
+ "title":"Insulin Lispro Analog"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"7bwa",
+ "resolution":4.9,
+ "title":"Cryo-EM Structure for the Ectodomain of the Full-length Human Insulin Receptor in Complex with 2 Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5hpu",
+ "resolution":2.2,
+ "title":"Insulin with proline analog HyP at position B28 in the R6 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5hpu",
+ "resolution":2.2,
+ "title":"Insulin with proline analog HyP at position B28 in the R6 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5hrq",
+ "resolution":1.28,
+ "title":"Insulin with proline analog HzP at position B28 in the R6 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4akj",
+ "resolution":2.01,
+ "title":"Ligand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4ajz",
+ "resolution":1.8,
+ "title":"Ligand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5uu3",
+ "resolution":2.25,
+ "title":"Insulin with proline analog DfP at position B28 in the R6 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5uu4",
+ "resolution":1.973,
+ "title":"Insulin with proline analog ThioP at position B28 in the R6 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5uu4",
+ "resolution":1.973,
+ "title":"Insulin with proline analog ThioP at position B28 in the R6 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5mam",
+ "resolution":2.2,
+ "title":"Human insulin in complex with serotonin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5mam",
+ "resolution":2.2,
+ "title":"Human insulin in complex with serotonin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5mt3",
+ "resolution":2.02,
+ "title":"Human insulin in complex with serotonin and arginine"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5mt9",
+ "resolution":1.88,
+ "title":"Human insulin in complex with serotonin and arginine"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5bqq",
+ "resolution":1.54,
+ "title":"Human insulin with intra-chain chemical crosslink between modified B27 and B30"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1q4v",
+ "resolution":2.0,
+ "title":"CRYSTAL STRUCTURE OF ALLO-ILEA2-INSULIN, AN INACTIVE CHIRAL ANALOGUE: IMPLICATIONS FOR THE MECHANISM OF RECEPTOR"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4xc4",
+ "resolution":1.499,
+ "title":"Insulin co-crystallizes in the presence of it beta-cell chaperone sulfatide"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4xc4",
+ "resolution":1.499,
+ "title":"Insulin co-crystallizes in the presence of it beta-cell chaperone sulfatide"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6z7y",
+ "resolution":2.2,
+ "title":"Human insulin in complex with the analytical antibody OXI-005 Fab"}]
+ }}
--- /dev/null
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ENSEMBLE","provider":"PED","created":"2020-10-01","uniprot_start":90,"uniprot_end":110,"model_url":"https://proteinensemble.org/api/ensemble/PED00096e000","model_format":"PDB","model_page_url":"https://proteinensemble.org/PED00096","number_of_conformers":35,"ensemble_sample_url":"https://proteinensemble.org/api/ensemble_sample/PED00096e000","ensemble_sample_format":"MMCIF"},{"model_identifier":"PED00101e000","model_category":"CONFORMATIONAL ENSEMBLE","provider":"PED","created":"2020-10-01","uniprot_start":26,"uniprot_end":53,"model_url":"https://proteinensemble.org/api/ensemble/PED00101e000","model_format":"PDB","model_page_url":"https://proteinensemble.org/PED00101","number_of_conformers":25,"ensemble_sample_url":"https://proteinensemble.org/api/ensemble_sample/PED00101e000","ensemble_sample_format":"MMCIF"},{"model_identifier":"PED00101e000","model_category":"CONFORMATIONAL ENSEMBLE","provider":"PED","created":"2020-10-01","uniprot_start":90,"uniprot_end":110,"model_url":"https://proteinensemble.org/api/ensemble/PED00101e000","model_format":"PDB","model_page_url":"https://proteinensemble.org/PED00101","number_of_conformers":25,"ensemble_sample_url":"https://proteinensemble.org/api/ensemble_sample/PED00101e000","ensemble_sample_format":"MMCIF"},{"model_identifier":"PED00102e000","model_category":"CONFORMATIONAL ENSEMBLE","provider":"PED","created":"2020-10-01","uniprot_start":25,"uniprot_end":54,"model_url":"https://proteinensemble.org/api/ensemble/PED00102e000","model_format":"PDB","model_page_url":"https://proteinensemble.org/PED00102","number_of_conformers":40,"ensemble_sample_url":"https://proteinensemble.org/api/ensemble_sample/PED00102e000","ensemble_sample_format":"MMCIF"},{"model_identifier":"PED00102e000","model_category":"CONFORMATIONAL ENSEMBLE","provider":"PED","created":"2020-10-01","uniprot_start":90,"uniprot_end":110,"model_url":"https://proteinensemble.org/api/ensemble/PED00102e000","model_format":"PDB","model_page_url":"https://proteinensemble.org/PED00102","number_of_conformers":40,"ensemble_sample_url":"https://proteinensemble.org/api/ensemble_sample/PED00102e000","ensemble_sample_format":"MMCIF"},{"model_identifier":"PED00103e000","model_category":"CONFORMATIONAL ENSEMBLE","provider":"PED","created":"2020-10-01","uniprot_start":25,"uniprot_end":54,"model_url":"https://proteinensemble.org/api/ensemble/PED00103e000","model_format":"PDB","model_page_url":"https://proteinensemble.org/PED00103","number_of_conformers":30,"ensemble_sample_url":"https://proteinensemble.org/api/ensemble_sample/PED00103e000","ensemble_sample_format":"MMCIF"},{"model_identifier":"PED00103e000","model_category":"CONFORMATIONAL ENSEMBLE","provider":"PED","created":"2020-10-01","uniprot_start":90,"uniprot_end":110,"model_url":"https://proteinensemble.org/api/ensemble/PED00103e000","model_format":"PDB","model_page_url":"https://proteinensemble.org/PED00103","number_of_conformers":30,"ensemble_sample_url":"https://proteinensemble.org/api/ensemble_sample/PED00103e000","ensemble_sample_format":"MMCIF"},{"model_identifier":"PED00104e000","model_category":"CONFORMATIONAL ENSEMBLE","provider":"PED","created":"2020-10-01","uniprot_start":90,"uniprot_end":110,"model_url":"https://proteinensemble.org/api/ensemble/PED00104e000","model_format":"PDB","model_page_url":"https://proteinensemble.org/PED00104","number_of_conformers":50,"ensemble_sample_url":"https://proteinensemble.org/api/ensemble_sample/PED00104e000","ensemble_sample_format":"MMCIF"},{"model_identifier":"PED00104e000","model_category":"CONFORMATIONAL ENSEMBLE","provider":"PED","created":"2020-10-01","uniprot_start":25,"uniprot_end":54,"model_url":"https://proteinensemble.org/api/ensemble/PED00104e000","model_format":"PDB","model_page_url":"https://proteinensemble.org/PED00104","number_of_conformers":50,"ensemble_sample_url":"https://proteinensemble.org/api/ensemble_sample/PED00104e000","ensemble_sample_format":"MMCIF"},{"model_identifier":"P01308_25-110:2lwz.1.A","model_category":"TEMPLATE-BASED","provider":"SWISS-MODEL","created":"2021-11-05","sequence_identity":1.0,"uniprot_start":25,"uniprot_end":110,"coverage":0.782,"confidence_version":"4.2.0","confidence_avg_local_score":0.524,"model_url":"https://swissmodel.expasy.org/3d-beacons/uniprot/P01308.pdb?range=25-110&template=2lwz.1.A&provider=swissmodel","model_format":"PDB","model_page_url":"https://swissmodel.expasy.org/repository/uniprot/P01308?range=25-110&template=2lwz.1.A","confidence_type":"QMEANDisCo"},{"model_identifier":"AF-P01308-F1","model_category":"DEEP-LEARNING","provider":"AlphaFold DB","created":"2021-07-01","sequence_identity":1.0,"uniprot_start":1,"uniprot_end":110,"coverage":100.0,"model_url":"https://alphafold.ebi.ac.uk/files/AF-P01308-F1-model_v1.cif","model_format":"MMCIF","model_page_url":"https://alphafold.ebi.ac.uk/entry/P01308"},{"model_identifier":"2400","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2018-11-11","uniprot_start":25,"uniprot_end":110,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDE25_fit1_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDE25"},{"model_identifier":"2396","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2018-11-11","uniprot_start":25,"uniprot_end":110,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDE25_fit2_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDE25"},{"model_identifier":"2452","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2019-04-07","uniprot_start":25,"uniprot_end":110,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDEV5_fit2_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDEV5"},{"model_identifier":"2453","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2019-04-07","uniprot_start":25,"uniprot_end":110,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDEV5_fit3_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDEV5"},{"model_identifier":"2456","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2019-04-07","uniprot_start":25,"uniprot_end":110,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDEW5_fit2_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDEW5"},{"model_identifier":"2457","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2019-04-07","uniprot_start":25,"uniprot_end":110,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDEW5_fit3_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDEW5"},{"model_identifier":"2459","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2019-04-07","uniprot_start":25,"uniprot_end":110,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDEX5_fit2_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDEX5"},{"model_identifier":"2460","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2019-04-07","uniprot_start":25,"uniprot_end":110,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDEX5_fit3_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDEX5"},{"model_identifier":"2462","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2019-04-07","uniprot_start":25,"uniprot_end":609,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDEY5_fit2_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDEY5"},{"model_identifier":"2463","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2019-04-07","uniprot_start":25,"uniprot_end":609,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDEY5_fit3_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDEY5"},{"model_identifier":"2465","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2019-04-07","uniprot_start":25,"uniprot_end":609,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDEZ5_fit2_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDEZ5"},{"model_identifier":"2467","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2019-04-07","uniprot_start":25,"uniprot_end":609,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDEZ5_fit3_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDEZ5"},{"model_identifier":"2469","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2019-04-07","uniprot_start":25,"uniprot_end":609,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDE26_fit2_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDE26"},{"model_identifier":"2470","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2019-04-07","uniprot_start":25,"uniprot_end":609,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDE26_fit3_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDE26"},{"model_identifier":"4420","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2020-12-18","uniprot_start":25,"uniprot_end":110,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDJY3_fit1_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDJY3"},{"model_identifier":"4421","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2020-12-18","uniprot_start":25,"uniprot_end":110,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDJY3_fit1_model2.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDJY3"},{"model_identifier":"4422","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2020-12-18","uniprot_start":25,"uniprot_end":110,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDJZ3_fit1_model1.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDJZ3"},{"model_identifier":"4423","model_category":"EXPERIMENTALLY DETERMINED","provider":"SASBDB","created":"2020-12-18","uniprot_start":25,"uniprot_end":110,"model_url":"https://www.sasbdb.org/media/pdb_file/SASDJZ3_fit1_model2.pdb","model_format":"PDB","model_page_url":"https://www.sasbdb.org/data/SASDJZ3"}]}
\ No newline at end of file
*/
package jalview.gui;
-import jalview.bin.Cache;
-
import java.awt.Dimension;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.bin.Console;
+
public class JAL1353bugdemo
{
@Test(groups = { "Functional" }, enabled = false)
public void test()
{
- Cache.initLogger();
+ Console.initLogger();
// final Desktop foo = new Desktop();
final JFrame cfoo = new JFrame("Crash Java");
final JDesktopPane foo = new JDesktopPane();
import org.testng.annotations.Test;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
public void setUp() throws IOException
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.initLogger();
+ Console.initLogger();
String inMenuString = ("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
+ SEQUENCE_ID
*/
package jalview.gui;
-import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.Assert.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.fts.api.FTSData;
-import jalview.jbgui.GStructureChooser.FilterOption;
-import jalview.ws.params.InvalidArgumentException;
-
import java.util.Collection;
import java.util.Vector;
+import org.junit.Assert;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.core.FTSRestClient;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.fts.service.pdb.PDBFTSRestClientTest;
+import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
+import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
+import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
+import jalview.jbgui.FilterOption;
import junit.extensions.PA;
+@Test(singleThreaded = true)
public class StructureChooserTest
{
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- Sequence seq;
+ Sequence seq,upSeq,upSeq_nocanonical;
@BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
pdbIds.add(dbRef);
seq.setPDBId(pdbIds);
+
+ // Uniprot sequence for 3D-Beacons mocks
+ upSeq = new Sequence("P38398",
+ "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
+ + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
+ + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
+ + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
+ + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
+ + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
+ + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
+ + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
+ + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
+ + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
+ + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
+ + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
+ + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
+ + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
+ + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
+ + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
+ + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
+ + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
+ + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
+ + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
+ + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
+ + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
+ + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
+ + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
+ + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
+ + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
+ + "", 1,
+1863);
+ upSeq.setDescription("Breast cancer type 1 susceptibility protein");
+ upSeq_nocanonical = new Sequence(upSeq);
+ upSeq.createDatasetSequence();
+ upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
+
+ upSeq_nocanonical.createDatasetSequence();
+ // not a canonical reference
+ upSeq_nocanonical.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,false));
+
}
@AfterMethod(alwaysRun = true)
public void tearDown() throws Exception
{
seq = null;
- }
-
- @Test(groups = { "Functional" })
- public void buildQueryTest()
- {
- String query = StructureChooser.buildQuery(seq);
- assertEquals("pdb_id:1tim", query);
- System.out.println("seq >>>> " + seq);
- seq.getAllPDBEntries().clear();
- query = StructureChooser.buildQuery(seq);
- assertEquals(
- "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
- query);
- seq.setDBRefs(null);
- query = StructureChooser.buildQuery(seq);
- assertEquals("text:4kqy", query);
-
- DBRefEntry uniprotDBRef = new DBRefEntry();
- uniprotDBRef.setAccessionId("P12345");
- uniprotDBRef.setSource(DBRefSource.UNIPROT);
- seq.addDBRef(uniprotDBRef);
-
- DBRefEntry pdbDBRef = new DBRefEntry();
- pdbDBRef.setAccessionId("1XYZ");
- pdbDBRef.setSource(DBRefSource.PDB);
- seq.addDBRef(pdbDBRef);
-
- for (int x = 1; x < 5; x++)
- {
- DBRefEntry dbRef = new DBRefEntry();
- dbRef.setAccessionId("XYZ_" + x);
- seq.addDBRef(dbRef);
- }
- query = StructureChooser.buildQuery(seq);
- assertEquals(
- "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
- query);
+ upSeq=null;
+ upSeq_nocanonical=null;
}
@Test(groups = { "Functional" })
public void populateFilterComboBoxTest() throws InterruptedException
{
+ TDBeaconsFTSRestClientTest.setMock();
+ PDBFTSRestClientTest.setMock();
+
SequenceI[] selectedSeqs = new SequenceI[] { seq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+ ThreadwaitFor(200, sc);
+
+ // if structures are not discovered then don't
+ // populate filter options
sc.populateFilterComboBox(false, false);
int optionsSize = sc.getCmbFilterOption().getItemCount();
- assertEquals(2, optionsSize); // if structures are not discovered then don't
- // populate filter options
+ System.out.println("Items (no data, no cache): ");
+ StringBuilder items = new StringBuilder();
+ for (int p=0;p<optionsSize;p++)
+ {
+ items.append
+ ("- ").append(sc.getCmbFilterOption().getItemAt(p).getName()).append("\n");
+
+ }
+ // report items when this fails - seems to be a race condition
+ Assert.assertEquals(items.toString(),optionsSize,2);
sc.populateFilterComboBox(true, false);
optionsSize = sc.getCmbFilterOption().getItemCount();
FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
.getSelectedItem();
assertEquals("Cached Structures", filterOpt.getName());
+ FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
+ FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void displayTDBQueryTest() throws InterruptedException
+ {
+ TDBeaconsFTSRestClientTest.setMock();
+ PDBFTSRestClientTest.setMock();
+
+ SequenceI[] selectedSeqs = new SequenceI[] { upSeq_nocanonical };
+ StructureChooser sc = new StructureChooser(selectedSeqs, upSeq_nocanonical, null);
+ // mock so should be quick. Exceptions from mocked PDBFTS are expected too
+ ThreadwaitFor(500, sc);
+
+ assertTrue(sc.isCanQueryTDB() && sc.isNotQueriedTDBYet());
}
@Test(groups = { "Network" })
public void fetchStructuresInfoTest()
{
+ FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
+ PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
SequenceI[] selectedSeqs = new SequenceI[] { seq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+ // not mocked, wait for 2s
+ ThreadwaitFor(2000, sc);
+
sc.fetchStructuresMetaData();
Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
"discoveredStructuresSet");
assertNotNull(ss);
assertTrue(ss.size() > 0);
+ }
+ @Test(groups = { "Functional" })
+ public void fetchStructuresInfoMockedTest()
+ {
+ TDBeaconsFTSRestClientTest.setMock();
+ PDBFTSRestClientTest.setMock();
+ SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
+ StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+ ThreadwaitFor(500, sc);
+
+ sc.fetchStructuresMetaData();
+ Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
+ "discoveredStructuresSet");
+ assertNotNull(ss);
+ assertTrue(ss.size() > 0);
}
+ private void ThreadwaitFor(int i, StructureChooser sc)
+ {
+ long timeout = i+System.currentTimeMillis();
+ while (!sc.isDialogVisible() && timeout > System.currentTimeMillis())
+ {
+ try {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+
+ }
+ }
+
+ }
+
+
@Test(groups = { "Functional" })
public void sanitizeSeqNameTest()
{
String name = "ab_cdEF|fwxyz012349";
- assertEquals(name, StructureChooser.sanitizeSeqName(name));
+ assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove a [nn] substring
name = "abcde12[345]fg";
- assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name));
+ assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove characters other than a-zA-Z0-9 | or _
name = "ab[cd],.\t£$*!- \\\"@:e";
- assertEquals("abcde", StructureChooser.sanitizeSeqName(name));
+ assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
name = "abcde12[345a]fg";
- assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name));
+ assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
}
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui.structurechooser;
+
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Vector;
+
+import org.junit.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.fts.service.pdb.PDBFTSRestClientTest;
+import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
+import jalview.gui.JvOptionPane;
+import jalview.gui.StructureChooser;
+import jalview.jbgui.FilterOption;
+
+public class StructureChooserQuerySourceTest
+{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ Sequence seq,upSeq,upSeq_insulin;
+
+ // same set up as for structurechooser test
+
+@BeforeMethod(alwaysRun = true)
+ public void setUp() throws Exception
+ {
+ seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
+ 26);
+ seq.createDatasetSequence();
+ for (int x = 1; x < 5; x++)
+ {
+ DBRefEntry dbRef = new DBRefEntry();
+ dbRef.setAccessionId("XYZ_" + x);
+ seq.addDBRef(dbRef);
+ }
+
+ PDBEntry dbRef = new PDBEntry();
+ dbRef.setId("1tim");
+
+ Vector<PDBEntry> pdbIds = new Vector<>();
+ pdbIds.add(dbRef);
+
+ seq.setPDBId(pdbIds);
+
+ // Uniprot sequence for 3D-Beacons mocks
+ upSeq = new Sequence("P38398",
+ "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
+ + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
+ + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
+ + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
+ + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
+ + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
+ + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
+ + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
+ + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
+ + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
+ + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
+ + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
+ + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
+ + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
+ + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
+ + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
+ + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
+ + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
+ + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
+ + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
+ + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
+ + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
+ + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
+ + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
+ + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
+ + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
+ + "", 1,
+1863);
+ upSeq.createDatasetSequence();
+ upSeq.setDescription("Breast cancer type 1 susceptibility protein");
+ upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
+
+ upSeq_insulin=new Sequence("INS_HUMAN",
+ "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGP"
+ + "GAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN");
+ upSeq_insulin.createDatasetSequence();
+ upSeq_insulin.setDescription("Insulin");
+ upSeq_insulin.addDBRef(new DBRefEntry("UNIPROT","0","P01308",null,true));
+ }
+
+@AfterMethod(alwaysRun = true)
+ public void tearDown() throws Exception
+ {
+ seq = null;
+ upSeq=null;
+ }
+
+ @SuppressWarnings("deprecation")
+ @Test(groups = { "Functional" })
+ public void buildPDBQueryTest()
+ {
+ System.out.println("seq >>>> " + seq);
+
+ StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
+ AssertJUnit.assertTrue(scquery instanceof PDBStructureChooserQuerySource);
+ String query = scquery.buildQuery(seq);
+ AssertJUnit.assertEquals("pdb_id:1tim", query);
+ seq.getAllPDBEntries().clear();
+ query = scquery.buildQuery(seq);
+ AssertJUnit.assertEquals(
+ "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
+ query);
+ seq.setDBRefs(null);
+ query = scquery.buildQuery(seq);
+ System.out.println(query);
+ AssertJUnit.assertEquals("text:4kqy", query);
+
+ DBRefEntry uniprotDBRef = new DBRefEntry();
+ uniprotDBRef.setAccessionId("P12345");
+ uniprotDBRef.setSource(DBRefSource.UNIPROT);
+ seq.addDBRef(uniprotDBRef);
+
+ DBRefEntry pdbDBRef = new DBRefEntry();
+ pdbDBRef.setAccessionId("1XYZ");
+ pdbDBRef.setSource(DBRefSource.PDB);
+ seq.addDBRef(pdbDBRef);
+
+ for (int x = 1; x < 5; x++)
+ {
+ DBRefEntry dbRef = new DBRefEntry();
+ dbRef.setAccessionId("XYZ_" + x);
+ seq.addDBRef(dbRef);
+ }
+ System.out.println("");
+ System.out.println(seq.getDBRefs());
+ System.out.println(query);
+ query = scquery.buildQuery(seq);
+ AssertJUnit.assertEquals(
+ "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
+ query);
+ }
+
+ @SuppressWarnings("deprecation")
+ @Test(groups = { "Functional" })
+ public void buildThreeDBQueryTest()
+ {
+ System.out.println("seq >>>> " + upSeq);
+ TDBeaconsFTSRestClientTest.setMock();
+ PDBFTSRestClientTest.setMock();
+ StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
+ // gets the lightweight proxy rather than the ThreeDBStructureChooserQuerySource
+ AssertJUnit.assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
+ String query = scquery.buildQuery(upSeq);
+ AssertJUnit.assertEquals("P38398", query);
+
+ // query shouldn't change regardless of additional entries
+ // because 3DBeacons requires canonical entries.
+ upSeq.getAllPDBEntries().clear();
+ query = scquery.buildQuery(upSeq);
+ AssertJUnit.assertEquals("P38398", query);
+ upSeq.setDBRefs(null);
+ query = scquery.buildQuery(upSeq);
+ /*
+ * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
+ * graceful behaviour would be to
+ * - pick one ? not possible
+ * - iterate through all until a 200 is obtained ?
+ * ---> ideal but could be costly
+ * ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
+ * ----> need a test to check that accessions can be promoted to canonical!
+ */
+ //FIXME - need to be able to use ID to query here ?
+ AssertJUnit.assertEquals(null, query);
+
+
+
+ // TODO:
+ /**
+ * set of sequences:
+ * - no protein -> TDB not applicable, query PDBe only (consider RNA or DNA - specific query adapter ?)
+ * - protein but no uniprot -> first consider trying to get uniprot refs (need a mark to say none are available)
+ * - protein and uniprot - no canonicals -> resolve to uniprot automatically to get canonicals
+ * - query uniprot against 3DBeacons
+ * --> decorate experimental structures with additional data from PDBe
+ * - query remaining against PDBe
+ * Ranking
+ * - 3D Beacons
+ * --> in memory ranking - no need to query twice
+ * Rank by
+ * - experimental > AlphaFold -> Model
+ * - start > end
+ * -> filters for
+ * -> experimental only
+ * -> experimental plus best models for other regions
+ * -> "best cover"
+ * -> need to be able to select correct reference (the longest one that covers all) for superposition
+ */
+//
+// DBRefEntry uniprotDBRef = new DBRefEntry();
+// uniprotDBRef.setAccessionId("P12345");
+// uniprotDBRef.setSource(DBRefSource.UNIPROT);
+// upSeq.addDBRef(uniprotDBRef);
+//
+// DBRefEntry pdbDBRef = new DBRefEntry();
+// pdbDBRef.setAccessionId("1XYZ");
+// pdbDBRef.setSource(DBRefSource.PDB);
+// upSeq.addDBRef(pdbDBRef);
+//
+// for (int x = 1; x < 5; x++)
+// {
+// DBRefEntry dbRef = new DBRefEntry();
+// dbRef.setAccessionId("XYZ_" + x);
+// seq.addDBRef(dbRef);
+// }
+// System.out.println("");
+// System.out.println(seq.getDBRefs());
+// System.out.println(query);
+// query = scquery.buildQuery(seq);
+// assertEquals(
+// "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
+// query);
+ }
+ @Test(groups= {"Functional"},dataProvider = "testUpSeqs")
+ public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
+ {
+ TDBeaconsFTSRestClientTest.setMock();
+ PDBFTSRestClientTest.setMock();
+ ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
+ PDBStructureChooserQuerySource pdbquery = new PDBStructureChooserQuerySource();
+
+
+
+ FTSRestResponse upResponse = null;
+ FTSRestResponse pdbResponse = null;
+ // TODO test available options
+ // Best coverage
+ // Best Alphafold Model
+ // Best model (by confidence score)
+ // Will also need to develop a more sophisticated filtering system
+ List<FilterOption> opts = tdbquery.getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
+ FilterOption opt_singlebest = opts.get(0);
+ FilterOption opt_manybest = opts.get(1);
+ assertEquals(opt_singlebest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
+ assertEquals(opt_manybest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
+
+ try {
+ upResponse = tdbquery.fetchStructuresMetaData(testUpSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_singlebest, false);
+ tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,opts,upResponse.getSearchSummary());
+ // test ranking without additional PDBe data
+ FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(testUpSeq, upResponse.getSearchSummary(), tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_singlebest.getValue(), false);
+ assertEquals(firstRanked.getNumberOfItemsFound(),1);
+ // many best response
+ upResponse = tdbquery.fetchStructuresMetaData(testUpSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_manybest, false);
+ assertTrue(firstRanked.getSearchSummary().size()<upResponse.getSearchSummary().size());
+ // NB Could have race condition here
+ String pdb_Query = tdbquery.buildPDBFTSQueryFor(upResponse);
+ assertTrue(pdb_Query.trim().length()>0);
+ pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery, upResponse);
+ assertTrue(pdbResponse.getNumberOfItemsFound()>0);
+ FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse, pdbResponse);
+ assertEquals(upResponse.getNumberOfItemsFound(),joinedResp.getNumberOfItemsFound());
+
+
+ } catch (Exception x)
+ {
+ x.printStackTrace();
+ Assert.fail("Unexpected Exception");
+ }
+ StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { testUpSeq});
+
+ }
+
+ @DataProvider(name = "testUpSeqs")
+ public Object[][] testUpSeqs() throws Exception
+ {
+ setUp();
+ return new Object[][] { {upSeq},{upSeq_insulin}};
+ }
+
+ @Test(groups = { "Functional" })
+ public void sanitizeSeqNameTest()
+ {
+ String name = "ab_cdEF|fwxyz012349";
+ AssertJUnit.assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
+
+ // remove a [nn] substring
+ name = "abcde12[345]fg";
+ AssertJUnit.assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+
+ // remove characters other than a-zA-Z0-9 | or _
+ name = "ab[cd],.\t£$*!- \\\"@:e";
+ AssertJUnit.assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+
+ name = "abcde12[345a]fg";
+ AssertJUnit.assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ }
+}
*/
package jalview.io;
+import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.gui.JvOptionPane;
-import jalview.io.AnnotationFile.ViewDef;
-
+import java.awt.Color;
import java.io.File;
import java.util.Hashtable;
+import java.util.List;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceGroup;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.AnnotationFile.ViewDef;
+
public class AnnotationFileIOTest
{
+ "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
+ annotFile + "'.");
}
+
+ @Test(groups="Functional")
+ public void testAnnotateAlignmentView()
+ {
+ long t1 = System.currentTimeMillis();
+ /*
+ * JAL-3779 test multiple groups of the same name get annotated
+ */
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq1\nQRSIL\n>Seq2\nFTHND\n>Seq3\nRPVSL\n",
+ DataSourceType.PASTE);
+ long t2 = System.currentTimeMillis();
+ System.err.println("t0: " + (t2 - t1));
+ // seq1 and seq3 are in distinct groups both named Group1
+ String annotationFile = "JALVIEW_ANNOTATION\nSEQUENCE_GROUP\tGroup1\t*\t*\t1\n"
+ + "SEQUENCE_GROUP\tGroup2\t*\t*\t2\n"
+ + "SEQUENCE_GROUP\tGroup1\t*\t*\t3\n"
+ + "PROPERTIES\tGroup1\toutlineColour=blue\tidColour=red\n";
+ new AnnotationFile().annotateAlignmentView(af.getViewport(), annotationFile, DataSourceType.PASTE);
+
+ AlignmentI al = af.getViewport().getAlignment();
+ List<SequenceGroup> groups = al.getGroups();
+ assertEquals(3, groups.size());
+ SequenceGroup sg = groups.get(0);
+ assertEquals("Group1", sg.getName());
+ assertTrue(sg.contains(al.getSequenceAt(0)));
+ assertEquals(Color.BLUE, sg.getOutlineColour());
+ assertEquals(Color.RED, sg.getIdColour());
+ sg = groups.get(1);
+ assertEquals("Group2", sg.getName());
+ assertTrue(sg.contains(al.getSequenceAt(1)));
+
+ /*
+ * the bug fix: a second group of the same name is also given properties
+ */
+ sg = groups.get(2);
+ assertEquals("Group1", sg.getName());
+ assertTrue(sg.contains(al.getSequenceAt(2)));
+ assertEquals(Color.BLUE, sg.getOutlineColour());
+ assertEquals(Color.RED, sg.getIdColour());
+ }
}
cleanupTmpFiles(newFile, suffix, digits);
}
- private void cleanupTmpFiles(String file, String mysuffix, int mydigits)
+ protected static void cleanupTmpFiles(String file, String mysuffix,
+ int mydigits)
{
File newfile = new File(file);
if (newfile.exists())
--- /dev/null
+package jalview.io;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.fail;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Set;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.bin.Console;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence.DBModList;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.util.MapList;
+
+public class EmblFlatFileTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Console.initLogger();
+ }
+
+ /**
+ * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
+ * one of them reverse strand
+ *
+ * @throws MalformedURLException
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testParse() throws MalformedURLException, IOException
+ {
+ File dataFile = new File("test/jalview/io/J03321.embl.txt");
+ FileParse fp = new FileParse(dataFile, DataSourceType.FILE);
+ EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
+ List<SequenceI> seqs = parser.getSeqs();
+
+ assertEquals(seqs.size(), 1);
+ SequenceI seq = seqs.get(0);
+ assertEquals(seq.getName(), "EmblTest|J03321");
+ assertEquals(seq.getLength(), 7502);
+ assertEquals(seq.getDescription(),
+ "Chlamydia trachomatis plasmid pCHL1, complete sequence");
+
+ /*
+ * should be 9 CDS features (one is a 'join' of two exons)
+ */
+ Set<String> featureTypes = seq.getFeatures().getFeatureTypes();
+ assertEquals(featureTypes.size(), 1);
+ assertTrue(featureTypes.contains("CDS"));
+
+ /*
+ * inspect some features (sorted just for convenience of test assertions)
+ */
+ List<SequenceFeature> features = seq.getFeatures()
+ .getAllFeatures("CDS");
+ SequenceFeatures.sortFeatures(features, true);
+ assertEquals(features.size(), 9);
+
+ SequenceFeature sf = features.get(0);
+ assertEquals(sf.getBegin(), 1);
+ assertEquals(sf.getEnd(), 437);
+ assertEquals(sf.getDescription(),
+ "Exon 2 for protein EMBLCDS:AAA91567.1");
+ assertEquals(sf.getFeatureGroup(), "EmblTest");
+ assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), 1);
+ assertEquals(sf.getValue("note"), "pGP7-D");
+ // this is the second exon of circular CDS!
+ assertEquals(sf.getValue("exon number"), 2);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+ assertEquals(sf.getValue("transl_table"), "11");
+
+ sf = features.get(1);
+ assertEquals(sf.getBegin(), 488);
+ assertEquals(sf.getEnd(), 1480);
+ assertEquals(sf.getDescription(),
+ "Exon 1 for protein EMBLCDS:AAA91568.1");
+ assertEquals(sf.getFeatureGroup(), "EmblTest");
+ assertEquals(sf.getEnaLocation(), "complement(488..1480)");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), -1); // reverse strand!
+ assertEquals(sf.getValue("note"), "pGP8-D");
+ assertEquals(sf.getValue("exon number"), 1);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+
+ sf = features.get(7);
+ assertEquals(sf.getBegin(), 6045);
+ assertEquals(sf.getEnd(), 6788);
+ assertEquals(sf.getDescription(),
+ "Exon 1 for protein EMBLCDS:AAA91574.1");
+ assertEquals(sf.getFeatureGroup(), "EmblTest");
+ assertEquals(sf.getEnaLocation(), "6045..6788");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), 1);
+ assertEquals(sf.getValue("note"), "pGP6-D (gtg start codon)");
+ assertEquals(sf.getValue("exon number"), 1);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+
+ /*
+ * CDS at 7022-7502 is the first exon of the circular CDS
+ */
+ sf = features.get(8);
+ assertEquals(sf.getBegin(), 7022);
+ assertEquals(sf.getEnd(), 7502);
+ assertEquals(sf.getDescription(),
+ "Exon 1 for protein EMBLCDS:AAA91567.1");
+ assertEquals(sf.getFeatureGroup(), "EmblTest");
+ assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), 1);
+ assertEquals(sf.getValue("note"), "pGP7-D");
+ assertEquals(sf.getValue("exon number"), 1);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+
+ /*
+ * Verify DBRefs, whether declared in the file or added by Jalview.
+ * There are 4 'direct' (DR) dbrefs, and numerous CDS /db_xref entries
+ * (some e.g. INTERPRO are duplicates). Jalview adds a dbref to 'self'.
+ * Sample a few here. Note DBRefEntry constructor capitalises source.
+ */
+ List<DBRefEntry> dbrefs = seq.getDBRefs();
+ assertEquals(dbrefs.size(), 32);
+ // xref to 'self':
+ DBRefEntry selfRef = new DBRefEntry("EMBLTEST", "1", "J03321");
+ int[] range = new int[] { 1, seq.getLength() };
+ selfRef.setMap(new Mapping(null, range, range, 1, 1));
+ assertTrue(dbrefs.contains(selfRef));
+
+ // 1st DR line; note trailing period is removed
+ assertTrue(dbrefs.contains(new DBRefEntry("MD5", "0",
+ "d4c4942a634e3df4995fd5ac75c26a61")));
+ // the 4th DR line:
+ assertTrue(
+ dbrefs.contains(new DBRefEntry("EUROPEPMC", "0", "PMC87941")));
+ // from the first CDS feature
+ assertTrue(dbrefs.contains(new DBRefEntry("GOA", "0", "P0CE19")));
+ // from the last CDS feature
+ assertTrue(
+ dbrefs.contains(new DBRefEntry("INTERPRO", "0", "IPR005350")));
+
+ /*
+ * verify mappings to, and sequences for, UNIPROT proteins
+ */
+ int uniprotCount = 0;
+ List<int[]> ranges;
+ for (DBRefEntry dbref : dbrefs)
+ {
+ if ("UNIPROT".equals(dbref.getSource()))
+ {
+ uniprotCount++;
+ Mapping mapping = dbref.getMap();
+ assertNotNull(mapping);
+ MapList map = mapping.getMap();
+ String mappedToName = mapping.getTo().getName();
+ if ("UNIPROT|P0CE16".equals(mappedToName))
+ {
+ assertEquals((ranges = map.getFromRanges()).size(), 1);
+ assertEquals(ranges.get(0)[0], 1579);
+ assertEquals(ranges.get(0)[1], 2931); // excludes stop 2934
+ assertEquals((ranges = map.getToRanges()).size(), 1);
+ assertEquals(ranges.get(0)[0], 1);
+ assertEquals(ranges.get(0)[1], 451);
+ // CDS /product carries over as protein product description
+ assertEquals(mapping.getTo().getDescription(),
+ "hypothetical protein");
+ }
+ else if ("UNIPROT|P0CE17".equals(mappedToName))
+ {
+ assertEquals((ranges = map.getFromRanges()).size(), 1);
+ assertEquals(ranges.get(0)[0], 2928);
+ assertEquals(ranges.get(0)[1], 3989); // excludes stop 3992
+ assertEquals((ranges = map.getToRanges()).size(), 1);
+ assertEquals(ranges.get(0)[0], 1);
+ assertEquals(ranges.get(0)[1], 354);
+ }
+ else if ("UNIPROT|P0CE18".equals(mappedToName))
+ {
+ assertEquals((ranges = map.getFromRanges()).size(), 1);
+ assertEquals(ranges.get(0)[0], 4054);
+ assertEquals(ranges.get(0)[1], 4845); // excludes stop 4848
+ assertEquals((ranges = map.getToRanges()).size(), 1);
+ assertEquals(ranges.get(0)[0], 1);
+ assertEquals(ranges.get(0)[1], 264);
+ }
+ else if ("UNIPROT|P0CE19".equals(mappedToName))
+ {
+ // join(7022..7502,1..437)
+ assertEquals((ranges = map.getFromRanges()).size(), 2);
+ assertEquals(ranges.get(0)[0], 7022);
+ assertEquals(ranges.get(0)[1], 7502);
+ assertEquals(ranges.get(1)[0], 1);
+ assertEquals(ranges.get(1)[1], 434); // excludes stop at 437
+ assertEquals((ranges = map.getToRanges()).size(), 1);
+ assertEquals(ranges.get(0)[0], 1);
+ assertEquals(ranges.get(0)[1], 305);
+ }
+ else if ("UNIPROT|P0CE20".equals(mappedToName))
+ {
+ // complement(488..1480)
+ assertEquals((ranges = map.getFromRanges()).size(), 1);
+ assertEquals(ranges.get(0)[0], 1480);
+ assertEquals(ranges.get(0)[1], 491); // // excludes stop at 488
+ assertEquals((ranges = map.getToRanges()).size(), 1);
+ assertEquals(ranges.get(0)[0], 1);
+ assertEquals(ranges.get(0)[1], 330);
+ }
+ else if (!"UNIPROT|P0CE23".equals(mappedToName)
+ && !"UNIPROT|P10559".equals(mappedToName)
+ && !"UNIPROT|P10560".equals(mappedToName))
+ {
+ fail("Unexpected UNIPROT dbref to " + mappedToName);
+ }
+ }
+ }
+ assertEquals(uniprotCount, 8);
+ }
+ /**
+ * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
+ * one of them reverse strand
+ *
+ * @throws MalformedURLException
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testParseToRNA() throws MalformedURLException, IOException
+ {
+ File dataFile = new File("test/jalview/io/J03321_rna.embl.txt");
+ FileParse fp = new FileParse(dataFile, DataSourceType.FILE);
+ EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
+ List<SequenceI> seqs = parser.getSeqs();
+ assertTrue(seqs.get(0).getSequenceAsString().indexOf("u")>-1);
+ }
+
+ @Test(groups = "Functional")
+ public void testParse_codonStartNot1()
+ {
+ // TODO verify CDS-to-protein mapping for CDS with /codon_start=2
+ // example: https://www.ebi.ac.uk/ena/browser/api/embl/EU498516
+ }
+
+ /**
+ * Test for the case that the EMBL CDS has no UNIPROT xref. In this case
+ * Jalview should synthesize an xref to EMBLCDSPROTEIN in the hope this will
+ * allow Get Cross-References.
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testParse_noUniprotXref() throws IOException
+ {
+ // MN908947 cut down to 40BP, one CDS, length 5 peptide for test purposes
+ // plus an additional (invented) test case:
+ // - multi-line /product qualifier including escaped quotes
+ String data = "ID MN908947; SV 3; linear; genomic RNA; STD; VRL; 20 BP.\n"
+ + "DE Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1,\n"
+ + "FT CDS 3..17\n"
+ + "FT /protein_id=\"QHD43415.1\"\n"
+ + "FT /product=\"orf1ab polyprotein\n"
+ + "FT \"\"foobar\"\" \"\n"
+ + "FT /translation=\"MRKLD\n"
+ + "SQ Sequence 7496 BP; 2450 A; 1290 C; 1434 G; 2322 T; 0 other;\n"
+ + " ggatGcgtaa gttagacgaa attttgtctt tgcgcacaga 40\n";
+ FileParse fp = new FileParse(data, DataSourceType.PASTE);
+ EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
+ List<SequenceI> seqs = parser.getSeqs();
+ assertEquals(seqs.size(), 1);
+ SequenceI seq = seqs.get(0);
+ DBModList<DBRefEntry> dbrefs = seq.getDBRefs();
+
+ /*
+ * dna should have dbref to itself, and to inferred EMBLCDSPROTEIN:QHD43415.1
+ */
+ assertEquals(dbrefs.size(), 2);
+
+ // dbref to self
+ DBRefEntry dbref = dbrefs.get(0);
+ assertEquals(dbref.getSource(), "EMBLTEST");
+ assertEquals(dbref.getAccessionId(), "MN908947");
+ Mapping mapping = dbref.getMap();
+ assertNull(mapping.getTo());
+ MapList map = mapping.getMap();
+ assertEquals(map.getFromLowest(), 1);
+ assertEquals(map.getFromHighest(), 40);
+ assertEquals(map.getToLowest(), 1);
+ assertEquals(map.getToHighest(), 40);
+ assertEquals(map.getFromRatio(), 1);
+ assertEquals(map.getToRatio(), 1);
+
+ // dbref to inferred EMBLCDSPROTEIN:
+ dbref = dbrefs.get(1);
+ assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
+ assertEquals(dbref.getAccessionId(), "QHD43415.1");
+ mapping = dbref.getMap();
+ SequenceI mapTo = mapping.getTo();
+ assertEquals(mapTo.getName(), "QHD43415.1");
+ // the /product qualifier transfers to protein product description
+ assertEquals(mapTo.getDescription(), "orf1ab polyprotein \"foobar\"");
+ assertEquals(mapTo.getSequenceAsString(), "MRKLD");
+ map = mapping.getMap();
+ assertEquals(map.getFromLowest(), 3);
+ assertEquals(map.getFromHighest(), 17);
+ assertEquals(map.getToLowest(), 1);
+ assertEquals(map.getToHighest(), 5);
+ assertEquals(map.getFromRatio(), 3);
+ assertEquals(map.getToRatio(), 1);
+ }
+
+ @Test(groups = "Functional")
+ public void testAdjustForProteinLength()
+ {
+ int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
+
+ // exact length match:
+ assertSame(exons, EmblFlatFile.adjustForProteinLength(6, exons));
+
+ // patch from JAL-3725 in EmblXmlSource propagated to Flatfile
+ // match if we assume exons include stop codon not in protein:
+ int[] truncated = EmblFlatFile.adjustForProteinLength(5, exons);
+ assertEquals(Arrays.toString(truncated), "[11, 15, 21, 25, 31, 35]");
+
+ // truncate last exon by 6bp
+ truncated = EmblFlatFile.adjustForProteinLength(4, exons);
+ assertEquals(Arrays.toString(truncated),"[11, 15, 21, 25, 31, 32]");
+
+ // remove last exon and truncate preceding by 1bp (so 3bp in total)
+ truncated = EmblFlatFile.adjustForProteinLength(3, exons);
+ assertEquals(Arrays.toString(truncated),"[11, 15, 21, 24]");
+
+ // exact removal of exon case:
+ exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
+ truncated = EmblFlatFile.adjustForProteinLength(4, exons);
+ assertEquals(Arrays.toString(truncated), "[11, 15, 21, 27]");
+
+ // what if exons are too short for protein?
+ truncated = EmblFlatFile.adjustForProteinLength(7, exons);
+ assertSame(exons, truncated);
+ }
+
+ @Test(groups = "Functional")
+ public void testRemoveQuotes()
+ {
+ assertNull(EmblFlatFile.removeQuotes(null));
+ assertEquals(EmblFlatFile.removeQuotes("No quotes here"), "No quotes here");
+ assertEquals(EmblFlatFile.removeQuotes("\"Enclosing quotes\""), "Enclosing quotes");
+ assertEquals(EmblFlatFile.removeQuotes("\"Escaped \"\"quotes\"\" example\""), "Escaped \"quotes\" example");
+ }
+}
package jalview.io;
+import java.util.Locale;
+
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotEquals;
public void testIsIdentifiable()
{
FileFormats formats = FileFormats.getInstance();
- assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Fasta
- .getName())));
- assertTrue(formats.isIdentifiable(formats.forName(FileFormat.MMCif
- .getName())));
- assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Jnet
- .getName())));
- assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Jalview
- .getName())));
+ assertTrue(formats
+ .isIdentifiable(formats.forName(FileFormat.Fasta.getName())));
+ assertTrue(formats
+ .isIdentifiable(formats.forName(FileFormat.MMCif.getName())));
+ assertTrue(formats
+ .isIdentifiable(formats.forName(FileFormat.Jnet.getName())));
+ assertTrue(formats
+ .isIdentifiable(formats.forName(FileFormat.Jalview.getName())));
+ // GenBank/ENA
assertFalse(formats.isIdentifiable(null));
/*
@Test(groups = "Functional")
public void testGetReadableFormats()
{
- String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+ String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
FileFormats formats = FileFormats.getInstance();
assertEquals(formats.getReadableFormats().toString(), expected);
}
public void testDeregisterFileFormat()
{
String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
- String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+ String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
FileFormats formats = FileFormats.getInstance();
assertEquals(formats.getWritableFormats(true).toString(), writable);
assertEquals(formats.getReadableFormats().toString(), readable);
formats.deregisterFileFormat(FileFormat.Fasta.getName());
writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
- readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+ readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
assertEquals(formats.getWritableFormats(true).toString(), writable);
assertEquals(formats.getReadableFormats().toString(), readable);
*/
formats.registerFileFormat(FileFormat.Fasta);
writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Fasta]";
- readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]";
+ readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]";
assertEquals(formats.getWritableFormats(true).toString(), writable);
assertEquals(formats.getReadableFormats().toString(), readable);
}
for (FileFormatI ff : FileFormat.values())
{
assertSame(ff, formats.forName(ff.getName()));
- assertSame(ff, formats.forName(ff.getName().toUpperCase()));
- assertSame(ff, formats.forName(ff.getName().toLowerCase()));
+ assertSame(ff, formats.forName(ff.getName().toUpperCase(Locale.ROOT)));
+ assertSame(ff, formats.forName(ff.getName().toLowerCase(Locale.ROOT)));
}
assertNull(formats.forName(null));
assertNull(formats.forName("rubbish"));
* verify the list of file formats registered matches the enum values
*/
FileFormats instance = FileFormats.getInstance();
- Iterator<FileFormatI> formats = instance.getFormats()
- .iterator();
+ Iterator<FileFormatI> formats = instance.getFormats().iterator();
FileFormatI[] builtIn = FileFormat.values();
for (FileFormatI ff : builtIn)
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.JvOptionPane;
/**
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- Cache.initLogger();
+ Console.initLogger();
}
/**
--- /dev/null
+package jalview.io;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertNull;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.List;
+import java.util.Set;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.bin.Console;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.util.MapList;
+
+public class GenBankFileTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Console.initLogger();
+ }
+
+ /**
+ * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
+ * one of them reverse strand
+ *
+ * @throws MalformedURLException
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testParse() throws MalformedURLException, IOException
+ {
+ File dataFile = new File("test/jalview/io/J03321.gb");
+ FileParse fp = new FileParse(dataFile.getAbsolutePath(),
+ DataSourceType.FILE);
+ EMBLLikeFlatFile parser = new GenBankFile(fp, "GenBankTest");
+ List<SequenceI> seqs = parser.getSeqs();
+
+ assertEquals(seqs.size(), 1);
+ SequenceI seq = seqs.get(0);
+ assertEquals(seq.getName(), "GenBankTest|J03321");
+ assertEquals(seq.getLength(), 7502);
+ assertEquals(seq.getDescription(),
+ "Chlamydia trachomatis plasmid pCHL1, complete sequence");
+
+ /*
+ * should be 9 CDS features (one is a 'join' of two exons)
+ */
+ Set<String> featureTypes = seq.getFeatures().getFeatureTypes();
+ assertEquals(featureTypes.size(), 1);
+ assertTrue(featureTypes.contains("CDS"));
+
+ /*
+ * inspect some features (sorted just for convenience of test assertions)
+ */
+ List<SequenceFeature> features = seq.getFeatures()
+ .getAllFeatures("CDS");
+ SequenceFeatures.sortFeatures(features, true);
+ assertEquals(features.size(), 9);
+
+ SequenceFeature sf = features.get(0);
+ assertEquals(sf.getBegin(), 1);
+ assertEquals(sf.getEnd(), 437);
+ assertEquals(sf.getDescription(),
+ "Exon 2 for protein EMBLCDS:AAA91567.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), 1);
+ assertEquals(sf.getValue("note"), "pGP7-D");
+ // this is the second exon of circular CDS!
+ assertEquals(sf.getValue("exon number"), 2);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+ assertEquals(sf.getValue("transl_table"), "11");
+
+ sf = features.get(1);
+ assertEquals(sf.getBegin(), 488);
+ assertEquals(sf.getEnd(), 1480);
+ assertEquals(sf.getDescription(),
+ "Exon 1 for protein EMBLCDS:AAA91568.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "complement(488..1480)");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), -1); // reverse strand!
+ assertEquals(sf.getValue("note"), "pGP8-D");
+ assertEquals(sf.getValue("exon number"), 1);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+
+ sf = features.get(7);
+ assertEquals(sf.getBegin(), 6045);
+ assertEquals(sf.getEnd(), 6788);
+ assertEquals(sf.getDescription(),
+ "Exon 1 for protein EMBLCDS:AAA91574.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "6045..6788");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), 1);
+ assertEquals(sf.getValue("note"), "pGP6-D (gtg start codon)");
+ assertEquals(sf.getValue("exon number"), 1);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+
+ /*
+ * CDS at 7022-7502 is the first exon of the circular CDS
+ */
+ sf = features.get(8);
+ assertEquals(sf.getBegin(), 7022);
+ assertEquals(sf.getEnd(), 7502);
+ assertEquals(sf.getDescription(),
+ "Exon 1 for protein EMBLCDS:AAA91567.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), 1);
+ assertEquals(sf.getValue("note"), "pGP7-D");
+ assertEquals(sf.getValue("exon number"), 1);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+
+ /*
+ * GenBank doesn't declare accession or CDS xrefs;
+ * dbrefs are added by Jalview for
+ * xref to self : 1
+ * protein products: 8
+ */
+ List<DBRefEntry> dbrefs = seq.getDBRefs();
+
+ assertEquals(dbrefs.size(), 9);
+ // xref to 'self':
+ DBRefEntry selfRef = new DBRefEntry("GENBANKTEST", "1", "J03321");
+ int[] range = new int[] { 1, seq.getLength() };
+ selfRef.setMap(new Mapping(null, range, range, 1, 1));
+ assertTrue(dbrefs.contains(selfRef));
+
+ /*
+ * dna should have dbref to itself, and to EMBLCDSPROTEIN
+ * for each /protein_id (synthesized as no UNIPROT xref)
+ */
+ // TODO check if we should synthesize EMBLCDSPROTEIN dbrefs
+ DBRefEntry dbref = dbrefs.get(0);
+ assertEquals(dbref.getSource(), "GENBANKTEST");
+ assertEquals(dbref.getAccessionId(), "J03321");
+ Mapping mapping = dbref.getMap();
+ assertNull(mapping.getTo());
+ MapList map = mapping.getMap();
+ assertEquals(map.getFromLowest(), 1);
+ assertEquals(map.getFromHighest(), 7502);
+ assertEquals(map.getToLowest(), 1);
+ assertEquals(map.getToHighest(), 7502);
+ assertEquals(map.getFromRatio(), 1);
+ assertEquals(map.getToRatio(), 1);
+
+ // dbref to inferred EMBLCDSPROTEIN for first CDS
+ dbref = dbrefs.get(1);
+ assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
+ assertEquals(dbref.getAccessionId(), "AAA91567.1");
+ mapping = dbref.getMap();
+ SequenceI mapTo = mapping.getTo();
+ assertEquals(mapTo.getName(), "AAA91567.1");
+ // the /product qualifier transfers to protein product description
+ assertEquals(mapTo.getDescription(), "hypothetical protein");
+ String seqString = mapTo.getSequenceAsString();
+ assertEquals(seqString.length(), 305);
+ assertTrue(seqString.startsWith("MGSMAF"));
+ assertTrue(seqString.endsWith("QTPTIL"));
+ map = mapping.getMap();
+ assertEquals(map.getFromLowest(), 1);
+ assertEquals(map.getFromHighest(), 7502);
+ assertEquals(map.getToLowest(), 1);
+ assertEquals(map.getToHighest(), 305);
+ assertEquals(map.getFromRatio(), 3);
+ assertEquals(map.getToRatio(), 1);
+
+ // dbref to inferred EMBLCDSPROTEIN for last CDS
+ dbref = dbrefs.get(8);
+ assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
+ assertEquals(dbref.getAccessionId(), "AAA91574.1");
+ mapping = dbref.getMap();
+ mapTo = mapping.getTo();
+ assertEquals(mapTo.getName(), "AAA91574.1");
+ // the /product qualifier transfers to protein product description
+ assertEquals(mapTo.getDescription(), "hypothetical protein");
+ seqString = mapTo.getSequenceAsString();
+ assertEquals(seqString.length(), 247);
+ assertTrue(seqString.startsWith("MNKLK"));
+ assertTrue(seqString.endsWith("FKQKS"));
+ map = mapping.getMap();
+ assertEquals(map.getFromLowest(), 6045);
+ assertEquals(map.getFromHighest(), 6785); // excludes stop at 6788
+ assertEquals(map.getToLowest(), 1);
+ assertEquals(map.getToHighest(), 247);
+ assertEquals(map.getFromRatio(), 3);
+ assertEquals(map.getToRatio(), 1);
+ }
+}
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.gui.JvOptionPane;
-
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import jalview.gui.JvOptionPane;
+
public class IdentifyFileTest
{
{ "examples/testdata/test.html", FileFormat.Html },
{ "examples/testdata/test.pileup", FileFormat.Pileup },
{ "examples/testdata/test.blc", FileFormat.BLC },
+ { "test/jalview/io/J03321.embl.txt", FileFormat.Embl },
+ { "test/jalview/io/J03321.gb", FileFormat.GenBank },
{ "examples/exampleFeatures.txt", FileFormat.Features },
{ "examples/testdata/simpleGff3.gff", FileFormat.Features },
{ "examples/testdata/test.jvp", FileFormat.Jalview },
--- /dev/null
+ID J03321; SV 1; circular; genomic DNA; STD; PRO; 7502 BP.
+XX
+AC J03321;
+XX
+DT 27-JUL-1990 (Rel. 24, Created)
+DT 10-APR-2020 (Rel. 144, Last updated, Version 9)
+XX
+DE Chlamydia trachomatis plasmid pCHL1, complete sequence.
+XX
+KW .
+XX
+OS Chlamydia trachomatis
+OC Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae;
+OC Chlamydia/Chlamydophila group; Chlamydia.
+OG Plasmid pCHL1
+XX
+RN [1]
+RP 1-7502
+RX DOI; 10.1016/0147-619X(90)90034-A.
+RX PUBMED; 2194229.
+RA Comanducci M., Ricci S., Cevenini R., Ratti G.;
+RT "Diversity of the Chlamydia trachomatis common plasmid in biovars with
+RT different pathogenicity";
+RL Plasmid 23(2):149-154(1990).
+XX
+RN [2]
+RP 1-7502
+RA Comanducci M., Ricci S., Cevenini R., Ratti G.;
+RT ;
+RL Submitted (23-JUN-2010) to the INSDC.
+RL Sclavo Research Centre, Siena, Italy
+XX
+DR MD5; d4c4942a634e3df4995fd5ac75c26a61.
+DR BioSample; SAMN14225621.
+DR EuropePMC; PMC4450983; 26031715.
+DR EuropePMC; PMC87941; 11283058.
+XX
+CC Draft entry and computer-readable sequence kindly submitted by
+CC G.Ratti, 28-MAR-1990.
+XX
+FH Key Location/Qualifiers
+FH
+FT source 1..7502
+FT /organism="Chlamydia trachomatis"
+FT /plasmid="pCHL1"
+FT /isolate="G0/86"
+FT /serotype="D"
+FT /mol_type="genomic DNA"
+FT /isolation_source="trachoma"
+FT /db_xref="taxon:813"
+XX next line artificially split for test purposes!
+FT CDS join(7022..7502,
+FT 1..437)
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP7-D"
+FT /db_xref="GOA:P0CE19"
+FT /db_xref="InterPro:IPR002104"
+FT /db_xref="InterPro:IPR011010"
+FT /db_xref="InterPro:IPR013762"
+FT /db_xref="UniProtKB/Swiss-Prot:P0CE19"
+FT /protein_id="AAA91567.1"
+FT /translation="MGSMAFHKSRLFLTFGDASEIWLSTLSYLTRKNYASGINFLVSLE
+FT ILDLSETLIKAISLDHSESLFKIKSLDVFNGKVVSEASKQARAACYISFTKFLYRLTKG
+FT YIKPAIPLKDFGNTTFFKIRDKIKTESISKQEWTVFFEALRIVNYRDYLIGKLIVQGIR
+FT KLDEILSLRTDDLFFASNQISFRIKKRQNKETKILITFPISLMEELQKYTCGRNGRVFV
+FT SKIGIPVTTSQVAHNFRLAEFHSAMKIKITPRVLRASALIHLKQIGLKDEEIMRISCLS
+FT SRQSVCSYCSGEEVIPLVQTPTIL"
+FT CDS complement(488..1480)
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP8-D"
+FT /db_xref="GOA:P0CE20"
+FT /db_xref="InterPro:IPR002104"
+FT /db_xref="InterPro:IPR011010"
+FT /db_xref="InterPro:IPR013762"
+FT /db_xref="UniProtKB/Swiss-Prot:P0CE20"
+FT /protein_id="AAA91568.1"
+FT /translation="MGKGILSLQQEMSLEYSEKSYQEVLKIRQESYWKRMKSFSLFEVI
+FT MHWTASLNKHTCRSYRGSFLSLEKIGLLSLDMNLQEFSLLNHNLILDAIKKVSSAKTSW
+FT TEGTKQVRAASYISLTRFLNRMTQGIVAIAQPSKQENSRTFFKTREIVKTDAMNSLQTA
+FT SFLKELKKINARDWLIAQTMLQGGKRSSEVLSLEISQICFQQATISFSQLKNRQTEKRI
+FT IITYPQKFMHFLQEYIGQRRGFVFVTRSGKMVGLRQIARTFSQAGLQAAIPFKITPHVL
+FT RATAVTEYKRLGCSDSDIMKVTGHATAKMIFAYDKSSREDNASKKMALI"
+FT CDS 1579..2934
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP1-D"
+FT /db_xref="GOA:P0CE16"
+FT /db_xref="InterPro:IPR003593"
+FT /db_xref="InterPro:IPR007693"
+FT /db_xref="InterPro:IPR007694"
+FT /db_xref="InterPro:IPR027417"
+FT /db_xref="InterPro:IPR036185"
+FT /db_xref="UniProtKB/Swiss-Prot:P0CE16"
+FT /protein_id="AAA91569.1"
+FT /translation="MKTRSEIENRMQDIEYALLGKALIFEDSTEYILRQLANYEFKCSH
+FT HKNIFIVFKHLKDNGLPITVDSAWEELLRRRIKDMDKSYLGLMLHDALSNDKLRSVSHT
+FT VFLDDLSVCSAEENLSNFIFRSFNEYNENPLRRSPFLLLERIKGRLDSAIAKTFSIRSA
+FT RGRSIYDIFSQSEIGVLARIKKRRVAFSENQNSFFDGFPTGYKDIDDKGVILAKGNFVI
+FT IAARPSIGKTALAIDMAINLAVTQQRRVGFLSLEMSAGQIVERIIANLTGISGEKLQRG
+FT DLSKEELFRVEEAGETVRESHFYICSDSQYKLNLIANQIRLLRKEDRVDVIFIDYLQLI
+FT NSSVGENRQNEIADISRTLRGLASELNIPIVCLSQLSRKVEDRANKVPMLSDLRDSGQI
+FT EQDADVILFINRKESSSNCEITVGKNRHGSVFSSVLHFDPKISKFSAIKKVW"
+FT CDS 2928..3992
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP2-D"
+FT /db_xref="InterPro:IPR040719"
+FT /db_xref="UniProtKB/Swiss-Prot:P0CE17"
+FT /protein_id="AAA91570.1"
+FT /translation="MVNYSNCHFIKSPIHLENQKFGRRPGQSIKISPKLAQNGMVEVIG
+FT LDFLSSHYHALAAIQRLLTATNYKGNTKGVVLSRESNSFQFEGWIPRIRFTKTEFLEAY
+FT GVKRYKTSRNKYEFSGKEAETALEALYHLGHQPFLIVATRTRWTNGTQIVDRYQTLSPI
+FT IRIYEGWEGLTDEENIDIDLTPFNSPPTRKHKGFVVEPCPILVDQIESYFVIKPANVYQ
+FT EIKMRFPNASKYAYTFIDWVITAAAKKRRKLTKDNSWPENLLLNVNVKSLAYILRMNRY
+FT ICTRNWKKIELAIDKCIEIAIQLGWLSRRKRIEFLDSSKLSKKEILYLNKERFEEITKK
+FT SKEQMEQLEQESIN"
+FT CDS 4054..4848
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP3-D"
+FT /db_xref="InterPro:IPR008444"
+FT /db_xref="InterPro:IPR033758"
+FT /db_xref="InterPro:IPR038264"
+FT /db_xref="PDB:6GJT"
+FT /db_xref="UniProtKB/Swiss-Prot:P0CE18"
+FT /protein_id="AAA91571.1"
+FT /translation="MGNSGFYLYNTENCVFADNIKVGQMTEPLKDQQIILGTTSTPVAA
+FT KMTASDGISLTVSNNSSTNASITIGLDAEKAYQLILEKLGDQILDGIADTIVDSTVQDI
+FT LDKIKTDPSLGLLKAFNNFPITNKIQCNGLFTPSNIETLLGGTEIGKFTVTPKSSGSMF
+FT LVSADIIASRMEGGVVLALVREGDSKPCAISYGYSSGIPNLCSLRTSITNTGLTPTTYS
+FT LRVGGLESGVVWVNALSNGNDILGITNTSNVSFLEVIPQTNA"
+FT CDS 4918..5226
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP4-D"
+FT /db_xref="UniProtKB/Swiss-Prot:P0CE23"
+FT /protein_id="AAA91572.1"
+FT /translation="MQNKRKVRDDFIKIVKDVKKDFPELDLKIRVNKEKVTFLNSPLEL
+FT YHKSVSLILGLLQQIENSLGLFPDSPVLEKLEDNSLKLKKALIMLILSRKDMFSKAE"
+FT CDS 5317..6048
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP5-D (gtg start codon)"
+FT /db_xref="GOA:P10559"
+FT /db_xref="InterPro:IPR025669"
+FT /db_xref="InterPro:IPR027417"
+FT /db_xref="UniProtKB/Swiss-Prot:P10559"
+FT /protein_id="AAA91573.1"
+FT /translation="MGCNLAQFLGKKVLLADLDPQSNLSSGLGASVRSDQKGLHDIVYT
+FT SNDLKSIICETKKDSVDLIPASFSSEQFRELDIHRGPSNNLKLFLNEYCAPFYDICIID
+FT TPPSLGGLTKEAFVAGDKLIACLTPEPFSILGLQKIREFLSSVGKPEEEHILGIALSFW
+FT DDRNSTNQMYIDIIESIYKNKLFSTKIRRDISLSRSLLKEDSVANVYPNSRAAEDILKL
+FT THEIANILHIEYERDYSQRTT"
+FT CDS 6045..6788
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP6-D (gtg start codon)"
+FT /db_xref="InterPro:IPR005350"
+FT /db_xref="UniProtKB/Swiss-Prot:P10560"
+FT /protein_id="AAA91574.1"
+FT /translation="MNKLKKEADVFFKKNQTAASLDFKKTLPSIELFSATLNSEESQSL
+FT DRLFLSESQNYSDEEFYQEDILAVKLLTGQIKSIQKQHVLLLGEKIYNARKILSKDHFS
+FT STTFSSWIELVFRTKSSAYNALAYYELFINLPNQTLQKEFQSIPYKSAYILAARKGDLK
+FT TKVDVIGKVCGMSNSSAIRVLDQFLPSSRNKDVRETIDKSDSEKNRQLSDFLIEILRIM
+FT CSGVSLSSYNENLLQQLFELFKQKS"
+FT repeat_region 6857..6945
+FT /note="four tandem 22bp repeats"
+XX
+SQ Sequence 7502 BP; 2460 A; 1285 C; 1433 G; 2324 T; 0 other;
+ ggatccgtaa gttagacgaa attttgtctt tgcgcacaga cgatctattt tttgcatcca 60
+ atcagatttc ctttcgcatt aaaaaaagac agaataaaga aaccaaaatt ctaatcacat 120
+ ttcctatcag cttaatggaa gagttgcaaa aatacacttg tgggagaaat gggagagtat 180
+ ttgtttctaa aatagggatt cctgtaacaa caagtcaggt tgcgcataat tttaggcttg 240
+ cagagttcca tagtgctatg aaaataaaaa ttactcccag agtacttcgt gcaagcgctt 300
+ tgattcattt aaagcaaata ggattaaaag atgaggaaat catgcgtatt tcctgtcttt 360
+ catcgagaca aagtgtgtgt tcttattgtt ctggggaaga ggtaattcct ctagtacaaa 420
+ cacccacaat attgtgatat aattaaaatt atattcatat tctgttgcca gaaaaaacac 480
+ ctttaggcta tattagagcc atcttctttg aagcgttgtc ttctcgagaa gatttatcgt 540
+ acgcaaatat catctttgcg gttgcgtgtc ctgtgacctt cattatgtcg gagtctgagc 600
+ accctaggcg tttgtactcc gtcacagcgg ttgctcgaag cacgtgcggg gttattttaa 660
+ aagggattgc agcttgtagt cctgcttgag agaacgtgcg ggcgatttgc cttaacccca 720
+ ccatttttcc ggagcgagtt acgaagacaa aacctcttcg ttgaccgatg tactcttgta 780
+ gaaagtgcat aaacttctga ggataagtta taataatcct cttttctgtc tgacggttct 840
+ taagctggga gaaagaaatg gtagcttgtt ggaaacaaat ctgactaatc tccaagctta 900
+ agacttcaga ggagcgttta cctccttgga gcattgtctg ggcgatcaac caatcccggg 960
+ cattgatttt ttttagctct tttaggaagg atgctgtttg caaactgttc atcgcatccg 1020
+ tttttactat ttccctggtt ttaaaaaatg ttcgactatt ttcttgttta gaaggttgcg 1080
+ ctatagcgac tattccttga gtcatcctgt ttaggaatct tgttaaggaa atatagcttg 1140
+ ctgctcgaac ttgtttagta ccttcggtcc aagaagtctt ggcagaggaa acttttttaa 1200
+ tcgcatctag gattagatta tgatttaaaa gggaaaactc ttgcagattc atatccaagg 1260
+ acaatagacc aatcttttct aaagacaaaa aagatcctcg atatgatcta caagtatgtt 1320
+ tgttgagtga tgcggtccaa tgcataataa cttcgaataa ggagaagctt ttcatgcgtt 1380
+ tccaatagga ttcttggcga atttttaaaa cttcctgata agacttttca ctatattcta 1440
+ acgacatttc ttgctgcaaa gataaaatcc ctttacccat gaaatccctc gtgatataac 1500
+ ctatccgtaa aatgtcctga ttagtgaaat aatcaggttg ttaacaggat agcacgctcg 1560
+ gtattttttt atataaacat gaaaactcgt tccgaaatag aaaatcgcat gcaagatatc 1620
+ gagtatgcgt tgttaggtaa agctctgata tttgaagact ctactgagta tattctgagg 1680
+ cagcttgcta attatgagtt taagtgttct catcataaaa acatattcat agtatttaaa 1740
+ cacttaaaag acaatggatt acctataact gtagactcgg cttgggaaga gcttttgcgg 1800
+ cgtcgtatca aagatatgga caaatcgtat ctcgggttaa tgttgcatga tgctttatca 1860
+ aatgacaagc ttagatccgt ttctcatacg gttttcctcg atgatttgag cgtgtgtagc 1920
+ gctgaagaaa atttgagtaa tttcattttc cgctcgttta atgagtacaa tgaaaatcca 1980
+ ttgcgtagat ctccgtttct attgcttgag cgtataaagg gaaggcttga tagtgctata 2040
+ gcaaagactt tttctattcg cagcgctaga ggccggtcta tttatgatat attctcacag 2100
+ tcagaaattg gagtgctggc tcgtataaaa aaaagacgag tagcgttctc tgagaatcaa 2160
+ aattctttct ttgatggctt cccaacagga tacaaggata ttgatgataa aggagttatc 2220
+ ttagctaaag gtaatttcgt gattatagca gctagaccat ctatagggaa aacagcttta 2280
+ gctatagaca tggcgataaa tcttgcggtt actcaacagc gtagagttgg tttcctatct 2340
+ ctagaaatga gcgcaggtca aattgttgag cggattattg ctaatttaac aggaatatct 2400
+ ggtgaaaaat tacaaagagg ggatctctct aaagaagaat tattccgagt agaagaagct 2460
+ ggagaaacgg ttagagaatc acatttttat atctgcagtg atagtcagta taagcttaac 2520
+ ttaatcgcga atcagatccg gttgctgaga aaagaagatc gagtagacgt aatatttatc 2580
+ gattacttgc agttgatcaa ctcatcggtt ggagaaaatc gtcaaaatga aatagcagat 2640
+ atatctagaa ccttaagagg tttagcctca gagctaaaca ttcctatagt ttgtttatcc 2700
+ caactatcta gaaaagttga ggatagagca aataaagttc ccatgctttc agatttgcga 2760
+ gacagcggtc aaatagagca agacgcagat gtgattttgt ttatcaatag gaaggaatcg 2820
+ tcttctaatt gtgagataac tgttgggaaa aatagacatg gatcggtttt ctcttcggta 2880
+ ttacatttcg atccaaaaat tagtaaattc tccgctatta aaaaagtatg gtaaattata 2940
+ gtaactgcca cttcatcaaa agtcctatcc accttgaaaa tcagaagttt ggaagaagac 3000
+ ctggtcaatc tattaagata tctcccaaat tggctcaaaa tgggatggta gaagttatag 3060
+ gtcttgattt tctttcatct cattaccatg cattagcagc tatccaaaga ttactgaccg 3120
+ caacgaatta caaggggaac acaaaagggg ttgttttatc cagagaatca aatagttttc 3180
+ aatttgaagg atggatacca agaatccgtt ttacaaaaac tgaattctta gaggcttatg 3240
+ gagttaagcg gtataaaaca tccagaaata agtatgagtt tagtggaaaa gaagctgaaa 3300
+ ctgctttaga agccttatac catttaggac atcaaccgtt tttaatagtg gcaactagaa 3360
+ ctcgatggac taatggaaca caaatagtag accgttacca aactctttct ccgatcatta 3420
+ ggatttacga aggatgggaa ggtttaactg acgaagaaaa tatagatata gacttaacac 3480
+ cttttaattc accacctaca cggaaacata aagggttcgt tgtagagcca tgtcctatct 3540
+ tggtagatca aatagaatcc tactttgtaa tcaagcctgc aaatgtatac caagaaataa 3600
+ aaatgcgttt cccaaatgca tcaaagtatg cttacacatt tatcgactgg gtgattacag 3660
+ cagctgcgaa aaagagacga aaattaacta aggataattc ttggccagaa aacttgttat 3720
+ taaacgttaa cgttaaaagt cttgcatata ttttaaggat gaatcggtac atctgtacaa 3780
+ ggaactggaa aaaaatcgag ttagctatcg ataaatgtat agaaatcgcc attcagcttg 3840
+ gctggttatc tagaagaaaa cgcattgaat ttctggattc ttctaaactc tctaaaaaag 3900
+ aaattctata tctaaataaa gagcgctttg aagaaataac taagaaatct aaagaacaaa 3960
+ tggaacaatt agaacaagaa tctattaatt aatagcaagc ttgaaactaa aaacctaatt 4020
+ tatttaaagc tcaaaataaa aaagagtttt aaaatgggaa attctggttt ttatttgtat 4080
+ aacactgaaa actgcgtctt tgctgataat atcaaagttg ggcaaatgac agagccgctc 4140
+ aaggaccagc aaataatcct tgggacaaca tcaacacctg tcgcagccaa aatgacagct 4200
+ tctgatggaa tatctttaac agtctccaat aattcatcaa ccaatgcttc tattacaatt 4260
+ ggtttggatg cggaaaaagc ttaccagctt attctagaaa agttgggaga tcaaattctt 4320
+ gatggaattg ctgatactat tgttgatagt acagtccaag atattttaga caaaatcaaa 4380
+ acagaccctt ctctaggttt gttgaaagct tttaacaact ttccaatcac taataaaatt 4440
+ caatgcaacg ggttattcac tcccagtaac attgaaactt tattaggagg aactgaaata 4500
+ ggaaaattca cagtcacacc caaaagctct gggagcatgt tcttagtctc agcagatatt 4560
+ attgcatcaa gaatggaagg cggcgttgtt ctagctttgg tacgagaagg tgattctaag 4620
+ ccctgcgcga ttagttatgg atactcatca ggcattccta atttatgtag tctaagaacc 4680
+ agtattacta atacaggatt gactccgaca acgtattcat tacgtgtagg cggtttagaa 4740
+ agcggtgtgg tatgggttaa tgccctttct aatggcaatg atattttagg aataacaaat 4800
+ acttctaatg tatctttttt agaggtaata cctcaaacaa acgcttaaac aatttttatt 4860
+ ggatttttct tataggtttt atatttagag aaaacagttc gaattacggg gtttgttatg 4920
+ caaaataaaa gaaaagtgag ggacgatttt attaaaattg ttaaagatgt gaaaaaagat 4980
+ ttccccgaat tagacctaaa aatacgagta aacaaggaaa aagtaacttt cttaaattct 5040
+ cccttagaac tctaccataa aagtgtctca ctaattctag gactgcttca acaaatagaa 5100
+ aactctttag gattattccc agactctcct gttcttgaaa aattagagga taacagttta 5160
+ aagctaaaaa aggctttgat tatgcttatc ttgtctagaa aagacatgtt ttccaaggct 5220
+ gaatagacaa cttactctaa cgttggagtt gatttgcaca ccttagtttt ttgctctttt 5280
+ aagggaggaa ctggaaaaac aacactttct ctaaacgtgg gatgcaactt ggcccaattt 5340
+ ttagggaaaa aagtgttact tgctgaccta gacccgcaat ccaatttatc ttctggattg 5400
+ ggggctagtg tcagaagtga ccaaaaaggc ttgcacgaca tagtatacac atcaaacgat 5460
+ ttaaaatcaa tcatttgcga aacaaaaaaa gatagtgtgg acctaattcc tgcatcattt 5520
+ tcatccgaac agtttagaga attggatatt catagaggac ctagtaacaa cttaaagtta 5580
+ tttctgaatg agtactgcgc tcctttttat gacatctgca taatagacac tccacctagc 5640
+ ctaggagggt taacgaaaga agcttttgtt gcaggagaca aattaattgc ttgtttaact 5700
+ ccagaacctt tttctattct agggttacaa aagatacgtg aattcttaag ttcggtcgga 5760
+ aaacctgaag aagaacacat tcttggaata gctttgtctt tttgggatga tcgtaactcg 5820
+ actaaccaaa tgtatataga cattatcgag tctatttaca aaaacaagct tttttcaaca 5880
+ aaaattcgtc gagatatttc tctcagccgt tctcttctta aagaagattc tgtagctaat 5940
+ gtctatccaa attctagggc cgcagaagat attctgaagt taacgcatga aatagcaaat 6000
+ attttgcata tcgaatatga acgagattac tctcagagga caacgtgaac aaactaaaaa 6060
+ aagaagcgga tgtctttttt aaaaaaaatc aaactgccgc ttctctagat tttaagaaga 6120
+ cgcttccctc cattgaacta ttctcagcaa ctttgaattc tgaggaaagt cagagtttgg 6180
+ atcgattatt tttatcagag tcccaaaact attcggatga agaattttat caagaagaca 6240
+ tcctagcggt aaaactgctt actggtcaga taaaatccat acagaagcaa cacgtacttc 6300
+ ttttaggaga aaaaatctat aatgctagaa aaatcctgag taaggatcac ttctcctcaa 6360
+ caactttttc atcttggata gagttagttt ttagaactaa gtcttctgct tacaatgctc 6420
+ ttgcatatta cgagcttttt ataaacctcc ccaaccaaac tctacaaaaa gagtttcaat 6480
+ cgatccccta taaatccgca tatattttgg ccgctagaaa aggcgattta aaaaccaagg 6540
+ tcgatgtgat agggaaagta tgtggaatgt cgaactcatc ggcgataagg gtgttggatc 6600
+ aatttcttcc ttcatctaga aacaaagacg ttagagaaac gatagataag tctgattcag 6660
+ agaagaatcg ccaattatct gatttcttaa tagagatact tcgcatcatg tgttccggag 6720
+ tttctttgtc ctcctataac gaaaatcttc tacaacagct ttttgaactt tttaagcaaa 6780
+ agagctgatc ctccgtcagc tcatatatat atatctatta tatatatata tttagggatt 6840
+ tgatttcacg agagagattt gcaactcttg gtggtagact ttgcaactct tggtggtaga 6900
+ ctttgcaact cttggtggta gactttgcaa ctcttggtgg tagacttggt cataatggac 6960
+ ttttgttaaa aaatttatta aaatcttaga gctccgattt tgaatagctt tggttaagaa 7020
+ aatgggctcg atggctttcc ataaaagtag attgttttta acttttgggg acgcgtcgga 7080
+ aatttggtta tctactttat cttatctaac tagaaaaaat tatgcgtctg ggattaactt 7140
+ tcttgtttct ttagagattc tggatttatc ggaaaccttg ataaaggcta tttctcttga 7200
+ ccacagcgaa tctttgttta aaatcaagtc tctagatgtt tttaatggaa aagttgtttc 7260
+ agaggcatct aaacaggcta gagcggcatg ctacatatct ttcacaaagt ttttgtatag 7320
+ attgaccaag ggatatatta aacccgctat tccattgaaa gattttggaa acactacatt 7380
+ ttttaaaatc cgagacaaaa tcaaaacaga atcgatttct aagcaggaat ggacagtttt 7440
+ ttttgaagcg ctccggatag tgaattatag agactattta atcggtaaat tgattgtaca 7500
+ ag 7502
+//
--- /dev/null
+LOCUS CH1L1CG 7502 bp DNA circular BCT 06-APR-2020
+DEFINITION Chlamydia trachomatis plasmid pCHL1, complete sequence.
+ACCESSION J03321
+VERSION J03321.1
+DBLINK BioSample: SAMN14225621
+KEYWORDS .
+SOURCE Chlamydia trachomatis
+ ORGANISM Chlamydia trachomatis
+ Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae;
+ Chlamydia/Chlamydophila group; Chlamydia.
+REFERENCE 1 (bases 1 to 7502)
+ AUTHORS Comanducci,M., Ricci,S., Cevenini,R. and Ratti,G.
+ TITLE Diversity of the Chlamydia trachomatis common plasmid in biovars
+ with different pathogenicity
+ JOURNAL Plasmid 23 (2), 149-154 (1990)
+ PUBMED 2194229
+REFERENCE 2 (bases 1 to 7502)
+ AUTHORS Comanducci,M., Ricci,S., Cevenini,R. and Ratti,G.
+ TITLE Direct Submission
+ JOURNAL Submitted (23-JUN-2010) Sclavo Research Centre, Siena, Italy
+COMMENT Draft entry and computer-readable sequence kindly submitted by
+ G.Ratti, 28-MAR-1990.
+ ! CDS location split below (and this line added), for Jalview test purposes !
+FEATURES Location/Qualifiers
+ source 1..7502
+ /organism="Chlamydia trachomatis"
+ /mol_type="genomic DNA"
+ /serotype="D"
+ /isolate="G0/86"
+ /isolation_source="trachoma"
+ /db_xref="taxon:813"
+ /plasmid="pCHL1"
+ CDS join(7022..7502,
+ 1..437)
+ /note="pGP7-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91567.1"
+ /translation="MGSMAFHKSRLFLTFGDASEIWLSTLSYLTRKNYASGINFLVSL
+ EILDLSETLIKAISLDHSESLFKIKSLDVFNGKVVSEASKQARAACYISFTKFLYRLT
+ KGYIKPAIPLKDFGNTTFFKIRDKIKTESISKQEWTVFFEALRIVNYRDYLIGKLIVQ
+ GIRKLDEILSLRTDDLFFASNQISFRIKKRQNKETKILITFPISLMEELQKYTCGRNG
+ RVFVSKIGIPVTTSQVAHNFRLAEFHSAMKIKITPRVLRASALIHLKQIGLKDEEIMR
+ ISCLSSRQSVCSYCSGEEVIPLVQTPTIL"
+ CDS complement(488..1480)
+ /note="pGP8-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91568.1"
+ /translation="MGKGILSLQQEMSLEYSEKSYQEVLKIRQESYWKRMKSFSLFEV
+ IMHWTASLNKHTCRSYRGSFLSLEKIGLLSLDMNLQEFSLLNHNLILDAIKKVSSAKT
+ SWTEGTKQVRAASYISLTRFLNRMTQGIVAIAQPSKQENSRTFFKTREIVKTDAMNSL
+ QTASFLKELKKINARDWLIAQTMLQGGKRSSEVLSLEISQICFQQATISFSQLKNRQT
+ EKRIIITYPQKFMHFLQEYIGQRRGFVFVTRSGKMVGLRQIARTFSQAGLQAAIPFKI
+ TPHVLRATAVTEYKRLGCSDSDIMKVTGHATAKMIFAYDKSSREDNASKKMALI"
+ CDS 1579..2934
+ /note="pGP1-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91569.1"
+ /translation="MKTRSEIENRMQDIEYALLGKALIFEDSTEYILRQLANYEFKCS
+ HHKNIFIVFKHLKDNGLPITVDSAWEELLRRRIKDMDKSYLGLMLHDALSNDKLRSVS
+ HTVFLDDLSVCSAEENLSNFIFRSFNEYNENPLRRSPFLLLERIKGRLDSAIAKTFSI
+ RSARGRSIYDIFSQSEIGVLARIKKRRVAFSENQNSFFDGFPTGYKDIDDKGVILAKG
+ NFVIIAARPSIGKTALAIDMAINLAVTQQRRVGFLSLEMSAGQIVERIIANLTGISGE
+ KLQRGDLSKEELFRVEEAGETVRESHFYICSDSQYKLNLIANQIRLLRKEDRVDVIFI
+ DYLQLINSSVGENRQNEIADISRTLRGLASELNIPIVCLSQLSRKVEDRANKVPMLSD
+ LRDSGQIEQDADVILFINRKESSSNCEITVGKNRHGSVFSSVLHFDPKISKFSAIKKV
+ W"
+ CDS 2928..3992
+ /note="pGP2-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91570.1"
+ /translation="MVNYSNCHFIKSPIHLENQKFGRRPGQSIKISPKLAQNGMVEVI
+ GLDFLSSHYHALAAIQRLLTATNYKGNTKGVVLSRESNSFQFEGWIPRIRFTKTEFLE
+ AYGVKRYKTSRNKYEFSGKEAETALEALYHLGHQPFLIVATRTRWTNGTQIVDRYQTL
+ SPIIRIYEGWEGLTDEENIDIDLTPFNSPPTRKHKGFVVEPCPILVDQIESYFVIKPA
+ NVYQEIKMRFPNASKYAYTFIDWVITAAAKKRRKLTKDNSWPENLLLNVNVKSLAYIL
+ RMNRYICTRNWKKIELAIDKCIEIAIQLGWLSRRKRIEFLDSSKLSKKEILYLNKERF
+ EEITKKSKEQMEQLEQESIN"
+ CDS 4054..4848
+ /note="pGP3-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91571.1"
+ /translation="MGNSGFYLYNTENCVFADNIKVGQMTEPLKDQQIILGTTSTPVA
+ AKMTASDGISLTVSNNSSTNASITIGLDAEKAYQLILEKLGDQILDGIADTIVDSTVQ
+ DILDKIKTDPSLGLLKAFNNFPITNKIQCNGLFTPSNIETLLGGTEIGKFTVTPKSSG
+ SMFLVSADIIASRMEGGVVLALVREGDSKPCAISYGYSSGIPNLCSLRTSITNTGLTP
+ TTYSLRVGGLESGVVWVNALSNGNDILGITNTSNVSFLEVIPQTNA"
+ CDS 4918..5226
+ /note="pGP4-D"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91572.1"
+ /translation="MQNKRKVRDDFIKIVKDVKKDFPELDLKIRVNKEKVTFLNSPLE
+ LYHKSVSLILGLLQQIENSLGLFPDSPVLEKLEDNSLKLKKALIMLILSRKDMFSKAE
+ "
+ CDS 5317..6048
+ /note="pGP5-D (gtg start codon)"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91573.1"
+ /translation="MGCNLAQFLGKKVLLADLDPQSNLSSGLGASVRSDQKGLHDIVY
+ TSNDLKSIICETKKDSVDLIPASFSSEQFRELDIHRGPSNNLKLFLNEYCAPFYDICI
+ IDTPPSLGGLTKEAFVAGDKLIACLTPEPFSILGLQKIREFLSSVGKPEEEHILGIAL
+ SFWDDRNSTNQMYIDIIESIYKNKLFSTKIRRDISLSRSLLKEDSVANVYPNSRAAED
+ ILKLTHEIANILHIEYERDYSQRTT"
+ CDS 6045..6788
+ /note="pGP6-D (gtg start codon)"
+ /codon_start=1
+ /transl_table=11
+ /product="hypothetical protein"
+ /protein_id="AAA91574.1"
+ /translation="MNKLKKEADVFFKKNQTAASLDFKKTLPSIELFSATLNSEESQS
+ LDRLFLSESQNYSDEEFYQEDILAVKLLTGQIKSIQKQHVLLLGEKIYNARKILSKDH
+ FSSTTFSSWIELVFRTKSSAYNALAYYELFINLPNQTLQKEFQSIPYKSAYILAARKG
+ DLKTKVDVIGKVCGMSNSSAIRVLDQFLPSSRNKDVRETIDKSDSEKNRQLSDFLIEI
+ LRIMCSGVSLSSYNENLLQQLFELFKQKS"
+ repeat_region 6857..6945
+ /note="four tandem 22bp repeats"
+ORIGIN
+ 1 ggatccgtaa gttagacgaa attttgtctt tgcgcacaga cgatctattt tttgcatcca
+ 61 atcagatttc ctttcgcatt aaaaaaagac agaataaaga aaccaaaatt ctaatcacat
+ 121 ttcctatcag cttaatggaa gagttgcaaa aatacacttg tgggagaaat gggagagtat
+ 181 ttgtttctaa aatagggatt cctgtaacaa caagtcaggt tgcgcataat tttaggcttg
+ 241 cagagttcca tagtgctatg aaaataaaaa ttactcccag agtacttcgt gcaagcgctt
+ 301 tgattcattt aaagcaaata ggattaaaag atgaggaaat catgcgtatt tcctgtcttt
+ 361 catcgagaca aagtgtgtgt tcttattgtt ctggggaaga ggtaattcct ctagtacaaa
+ 421 cacccacaat attgtgatat aattaaaatt atattcatat tctgttgcca gaaaaaacac
+ 481 ctttaggcta tattagagcc atcttctttg aagcgttgtc ttctcgagaa gatttatcgt
+ 541 acgcaaatat catctttgcg gttgcgtgtc ctgtgacctt cattatgtcg gagtctgagc
+ 601 accctaggcg tttgtactcc gtcacagcgg ttgctcgaag cacgtgcggg gttattttaa
+ 661 aagggattgc agcttgtagt cctgcttgag agaacgtgcg ggcgatttgc cttaacccca
+ 721 ccatttttcc ggagcgagtt acgaagacaa aacctcttcg ttgaccgatg tactcttgta
+ 781 gaaagtgcat aaacttctga ggataagtta taataatcct cttttctgtc tgacggttct
+ 841 taagctggga gaaagaaatg gtagcttgtt ggaaacaaat ctgactaatc tccaagctta
+ 901 agacttcaga ggagcgttta cctccttgga gcattgtctg ggcgatcaac caatcccggg
+ 961 cattgatttt ttttagctct tttaggaagg atgctgtttg caaactgttc atcgcatccg
+ 1021 tttttactat ttccctggtt ttaaaaaatg ttcgactatt ttcttgttta gaaggttgcg
+ 1081 ctatagcgac tattccttga gtcatcctgt ttaggaatct tgttaaggaa atatagcttg
+ 1141 ctgctcgaac ttgtttagta ccttcggtcc aagaagtctt ggcagaggaa acttttttaa
+ 1201 tcgcatctag gattagatta tgatttaaaa gggaaaactc ttgcagattc atatccaagg
+ 1261 acaatagacc aatcttttct aaagacaaaa aagatcctcg atatgatcta caagtatgtt
+ 1321 tgttgagtga tgcggtccaa tgcataataa cttcgaataa ggagaagctt ttcatgcgtt
+ 1381 tccaatagga ttcttggcga atttttaaaa cttcctgata agacttttca ctatattcta
+ 1441 acgacatttc ttgctgcaaa gataaaatcc ctttacccat gaaatccctc gtgatataac
+ 1501 ctatccgtaa aatgtcctga ttagtgaaat aatcaggttg ttaacaggat agcacgctcg
+ 1561 gtattttttt atataaacat gaaaactcgt tccgaaatag aaaatcgcat gcaagatatc
+ 1621 gagtatgcgt tgttaggtaa agctctgata tttgaagact ctactgagta tattctgagg
+ 1681 cagcttgcta attatgagtt taagtgttct catcataaaa acatattcat agtatttaaa
+ 1741 cacttaaaag acaatggatt acctataact gtagactcgg cttgggaaga gcttttgcgg
+ 1801 cgtcgtatca aagatatgga caaatcgtat ctcgggttaa tgttgcatga tgctttatca
+ 1861 aatgacaagc ttagatccgt ttctcatacg gttttcctcg atgatttgag cgtgtgtagc
+ 1921 gctgaagaaa atttgagtaa tttcattttc cgctcgttta atgagtacaa tgaaaatcca
+ 1981 ttgcgtagat ctccgtttct attgcttgag cgtataaagg gaaggcttga tagtgctata
+ 2041 gcaaagactt tttctattcg cagcgctaga ggccggtcta tttatgatat attctcacag
+ 2101 tcagaaattg gagtgctggc tcgtataaaa aaaagacgag tagcgttctc tgagaatcaa
+ 2161 aattctttct ttgatggctt cccaacagga tacaaggata ttgatgataa aggagttatc
+ 2221 ttagctaaag gtaatttcgt gattatagca gctagaccat ctatagggaa aacagcttta
+ 2281 gctatagaca tggcgataaa tcttgcggtt actcaacagc gtagagttgg tttcctatct
+ 2341 ctagaaatga gcgcaggtca aattgttgag cggattattg ctaatttaac aggaatatct
+ 2401 ggtgaaaaat tacaaagagg ggatctctct aaagaagaat tattccgagt agaagaagct
+ 2461 ggagaaacgg ttagagaatc acatttttat atctgcagtg atagtcagta taagcttaac
+ 2521 ttaatcgcga atcagatccg gttgctgaga aaagaagatc gagtagacgt aatatttatc
+ 2581 gattacttgc agttgatcaa ctcatcggtt ggagaaaatc gtcaaaatga aatagcagat
+ 2641 atatctagaa ccttaagagg tttagcctca gagctaaaca ttcctatagt ttgtttatcc
+ 2701 caactatcta gaaaagttga ggatagagca aataaagttc ccatgctttc agatttgcga
+ 2761 gacagcggtc aaatagagca agacgcagat gtgattttgt ttatcaatag gaaggaatcg
+ 2821 tcttctaatt gtgagataac tgttgggaaa aatagacatg gatcggtttt ctcttcggta
+ 2881 ttacatttcg atccaaaaat tagtaaattc tccgctatta aaaaagtatg gtaaattata
+ 2941 gtaactgcca cttcatcaaa agtcctatcc accttgaaaa tcagaagttt ggaagaagac
+ 3001 ctggtcaatc tattaagata tctcccaaat tggctcaaaa tgggatggta gaagttatag
+ 3061 gtcttgattt tctttcatct cattaccatg cattagcagc tatccaaaga ttactgaccg
+ 3121 caacgaatta caaggggaac acaaaagggg ttgttttatc cagagaatca aatagttttc
+ 3181 aatttgaagg atggatacca agaatccgtt ttacaaaaac tgaattctta gaggcttatg
+ 3241 gagttaagcg gtataaaaca tccagaaata agtatgagtt tagtggaaaa gaagctgaaa
+ 3301 ctgctttaga agccttatac catttaggac atcaaccgtt tttaatagtg gcaactagaa
+ 3361 ctcgatggac taatggaaca caaatagtag accgttacca aactctttct ccgatcatta
+ 3421 ggatttacga aggatgggaa ggtttaactg acgaagaaaa tatagatata gacttaacac
+ 3481 cttttaattc accacctaca cggaaacata aagggttcgt tgtagagcca tgtcctatct
+ 3541 tggtagatca aatagaatcc tactttgtaa tcaagcctgc aaatgtatac caagaaataa
+ 3601 aaatgcgttt cccaaatgca tcaaagtatg cttacacatt tatcgactgg gtgattacag
+ 3661 cagctgcgaa aaagagacga aaattaacta aggataattc ttggccagaa aacttgttat
+ 3721 taaacgttaa cgttaaaagt cttgcatata ttttaaggat gaatcggtac atctgtacaa
+ 3781 ggaactggaa aaaaatcgag ttagctatcg ataaatgtat agaaatcgcc attcagcttg
+ 3841 gctggttatc tagaagaaaa cgcattgaat ttctggattc ttctaaactc tctaaaaaag
+ 3901 aaattctata tctaaataaa gagcgctttg aagaaataac taagaaatct aaagaacaaa
+ 3961 tggaacaatt agaacaagaa tctattaatt aatagcaagc ttgaaactaa aaacctaatt
+ 4021 tatttaaagc tcaaaataaa aaagagtttt aaaatgggaa attctggttt ttatttgtat
+ 4081 aacactgaaa actgcgtctt tgctgataat atcaaagttg ggcaaatgac agagccgctc
+ 4141 aaggaccagc aaataatcct tgggacaaca tcaacacctg tcgcagccaa aatgacagct
+ 4201 tctgatggaa tatctttaac agtctccaat aattcatcaa ccaatgcttc tattacaatt
+ 4261 ggtttggatg cggaaaaagc ttaccagctt attctagaaa agttgggaga tcaaattctt
+ 4321 gatggaattg ctgatactat tgttgatagt acagtccaag atattttaga caaaatcaaa
+ 4381 acagaccctt ctctaggttt gttgaaagct tttaacaact ttccaatcac taataaaatt
+ 4441 caatgcaacg ggttattcac tcccagtaac attgaaactt tattaggagg aactgaaata
+ 4501 ggaaaattca cagtcacacc caaaagctct gggagcatgt tcttagtctc agcagatatt
+ 4561 attgcatcaa gaatggaagg cggcgttgtt ctagctttgg tacgagaagg tgattctaag
+ 4621 ccctgcgcga ttagttatgg atactcatca ggcattccta atttatgtag tctaagaacc
+ 4681 agtattacta atacaggatt gactccgaca acgtattcat tacgtgtagg cggtttagaa
+ 4741 agcggtgtgg tatgggttaa tgccctttct aatggcaatg atattttagg aataacaaat
+ 4801 acttctaatg tatctttttt agaggtaata cctcaaacaa acgcttaaac aatttttatt
+ 4861 ggatttttct tataggtttt atatttagag aaaacagttc gaattacggg gtttgttatg
+ 4921 caaaataaaa gaaaagtgag ggacgatttt attaaaattg ttaaagatgt gaaaaaagat
+ 4981 ttccccgaat tagacctaaa aatacgagta aacaaggaaa aagtaacttt cttaaattct
+ 5041 cccttagaac tctaccataa aagtgtctca ctaattctag gactgcttca acaaatagaa
+ 5101 aactctttag gattattccc agactctcct gttcttgaaa aattagagga taacagttta
+ 5161 aagctaaaaa aggctttgat tatgcttatc ttgtctagaa aagacatgtt ttccaaggct
+ 5221 gaatagacaa cttactctaa cgttggagtt gatttgcaca ccttagtttt ttgctctttt
+ 5281 aagggaggaa ctggaaaaac aacactttct ctaaacgtgg gatgcaactt ggcccaattt
+ 5341 ttagggaaaa aagtgttact tgctgaccta gacccgcaat ccaatttatc ttctggattg
+ 5401 ggggctagtg tcagaagtga ccaaaaaggc ttgcacgaca tagtatacac atcaaacgat
+ 5461 ttaaaatcaa tcatttgcga aacaaaaaaa gatagtgtgg acctaattcc tgcatcattt
+ 5521 tcatccgaac agtttagaga attggatatt catagaggac ctagtaacaa cttaaagtta
+ 5581 tttctgaatg agtactgcgc tcctttttat gacatctgca taatagacac tccacctagc
+ 5641 ctaggagggt taacgaaaga agcttttgtt gcaggagaca aattaattgc ttgtttaact
+ 5701 ccagaacctt tttctattct agggttacaa aagatacgtg aattcttaag ttcggtcgga
+ 5761 aaacctgaag aagaacacat tcttggaata gctttgtctt tttgggatga tcgtaactcg
+ 5821 actaaccaaa tgtatataga cattatcgag tctatttaca aaaacaagct tttttcaaca
+ 5881 aaaattcgtc gagatatttc tctcagccgt tctcttctta aagaagattc tgtagctaat
+ 5941 gtctatccaa attctagggc cgcagaagat attctgaagt taacgcatga aatagcaaat
+ 6001 attttgcata tcgaatatga acgagattac tctcagagga caacgtgaac aaactaaaaa
+ 6061 aagaagcgga tgtctttttt aaaaaaaatc aaactgccgc ttctctagat tttaagaaga
+ 6121 cgcttccctc cattgaacta ttctcagcaa ctttgaattc tgaggaaagt cagagtttgg
+ 6181 atcgattatt tttatcagag tcccaaaact attcggatga agaattttat caagaagaca
+ 6241 tcctagcggt aaaactgctt actggtcaga taaaatccat acagaagcaa cacgtacttc
+ 6301 ttttaggaga aaaaatctat aatgctagaa aaatcctgag taaggatcac ttctcctcaa
+ 6361 caactttttc atcttggata gagttagttt ttagaactaa gtcttctgct tacaatgctc
+ 6421 ttgcatatta cgagcttttt ataaacctcc ccaaccaaac tctacaaaaa gagtttcaat
+ 6481 cgatccccta taaatccgca tatattttgg ccgctagaaa aggcgattta aaaaccaagg
+ 6541 tcgatgtgat agggaaagta tgtggaatgt cgaactcatc ggcgataagg gtgttggatc
+ 6601 aatttcttcc ttcatctaga aacaaagacg ttagagaaac gatagataag tctgattcag
+ 6661 agaagaatcg ccaattatct gatttcttaa tagagatact tcgcatcatg tgttccggag
+ 6721 tttctttgtc ctcctataac gaaaatcttc tacaacagct ttttgaactt tttaagcaaa
+ 6781 agagctgatc ctccgtcagc tcatatatat atatctatta tatatatata tttagggatt
+ 6841 tgatttcacg agagagattt gcaactcttg gtggtagact ttgcaactct tggtggtaga
+ 6901 ctttgcaact cttggtggta gactttgcaa ctcttggtgg tagacttggt cataatggac
+ 6961 ttttgttaaa aaatttatta aaatcttaga gctccgattt tgaatagctt tggttaagaa
+ 7021 aatgggctcg atggctttcc ataaaagtag attgttttta acttttgggg acgcgtcgga
+ 7081 aatttggtta tctactttat cttatctaac tagaaaaaat tatgcgtctg ggattaactt
+ 7141 tcttgtttct ttagagattc tggatttatc ggaaaccttg ataaaggcta tttctcttga
+ 7201 ccacagcgaa tctttgttta aaatcaagtc tctagatgtt tttaatggaa aagttgtttc
+ 7261 agaggcatct aaacaggcta gagcggcatg ctacatatct ttcacaaagt ttttgtatag
+ 7321 attgaccaag ggatatatta aacccgctat tccattgaaa gattttggaa acactacatt
+ 7381 ttttaaaatc cgagacaaaa tcaaaacaga atcgatttct aagcaggaat ggacagtttt
+ 7441 ttttgaagcg ctccggatag tgaattatag agactattta atcggtaaat tgattgtaca
+ 7501 ag
+//
+
--- /dev/null
+ID J03321; SV 1; circular; genomic DNA; STD; PRO; 7502 BP.
+XX
+AC J03321;
+XX
+DT 27-JUL-1990 (Rel. 24, Created)
+DT 10-APR-2020 (Rel. 144, Last updated, Version 9)
+XX
+DE Chlamydia trachomatis plasmid pCHL1, complete sequence.
+XX
+KW .
+XX
+OS Chlamydia trachomatis
+OC Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae;
+OC Chlamydia/Chlamydophila group; Chlamydia.
+OG Plasmid pCHL1
+XX
+RN [1]
+RP 1-7502
+RX DOI; 10.1016/0147-619X(90)90034-A.
+RX PUBMED; 2194229.
+RA Comanducci M., Ricci S., Cevenini R., Ratti G.;
+RT "Diversity of the Chlamydia trachomatis common plasmid in biovars with
+RT different pathogenicity";
+RL Plasmid 23(2):149-154(1990).
+XX
+RN [2]
+RP 1-7502
+RA Comanducci M., Ricci S., Cevenini R., Ratti G.;
+RT ;
+RL Submitted (23-JUN-2010) to the INSDC.
+RL Sclavo Research Centre, Siena, Italy
+XX
+DR MD5; d4c4942a634e3df4995fd5ac75c26a61.
+DR BioSample; SAMN14225621.
+DR EuropePMC; PMC4450983; 26031715.
+DR EuropePMC; PMC87941; 11283058.
+XX
+CC Draft entry and computer-readable sequence kindly submitted by
+CC G.Ratti, 28-MAR-1990.
+XX
+FH Key Location/Qualifiers
+FH
+FT source 1..7502
+FT /organism="Chlamydia trachomatis"
+FT /plasmid="pCHL1"
+FT /isolate="G0/86"
+FT /serotype="D"
+FT /mol_type="genomic RNA"
+FT /isolation_source="trachoma"
+FT /db_xref="taxon:813"
+XX next line artificially split for test purposes!
+FT CDS join(7022..7502,
+FT 1..437)
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP7-D"
+FT /db_xref="GOA:P0CE19"
+FT /db_xref="InterPro:IPR002104"
+FT /db_xref="InterPro:IPR011010"
+FT /db_xref="InterPro:IPR013762"
+FT /db_xref="UniProtKB/Swiss-Prot:P0CE19"
+FT /protein_id="AAA91567.1"
+FT /translation="MGSMAFHKSRLFLTFGDASEIWLSTLSYLTRKNYASGINFLVSLE
+FT ILDLSETLIKAISLDHSESLFKIKSLDVFNGKVVSEASKQARAACYISFTKFLYRLTKG
+FT YIKPAIPLKDFGNTTFFKIRDKIKTESISKQEWTVFFEALRIVNYRDYLIGKLIVQGIR
+FT KLDEILSLRTDDLFFASNQISFRIKKRQNKETKILITFPISLMEELQKYTCGRNGRVFV
+FT SKIGIPVTTSQVAHNFRLAEFHSAMKIKITPRVLRASALIHLKQIGLKDEEIMRISCLS
+FT SRQSVCSYCSGEEVIPLVQTPTIL"
+FT CDS complement(488..1480)
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP8-D"
+FT /db_xref="GOA:P0CE20"
+FT /db_xref="InterPro:IPR002104"
+FT /db_xref="InterPro:IPR011010"
+FT /db_xref="InterPro:IPR013762"
+FT /db_xref="UniProtKB/Swiss-Prot:P0CE20"
+FT /protein_id="AAA91568.1"
+FT /translation="MGKGILSLQQEMSLEYSEKSYQEVLKIRQESYWKRMKSFSLFEVI
+FT MHWTASLNKHTCRSYRGSFLSLEKIGLLSLDMNLQEFSLLNHNLILDAIKKVSSAKTSW
+FT TEGTKQVRAASYISLTRFLNRMTQGIVAIAQPSKQENSRTFFKTREIVKTDAMNSLQTA
+FT SFLKELKKINARDWLIAQTMLQGGKRSSEVLSLEISQICFQQATISFSQLKNRQTEKRI
+FT IITYPQKFMHFLQEYIGQRRGFVFVTRSGKMVGLRQIARTFSQAGLQAAIPFKITPHVL
+FT RATAVTEYKRLGCSDSDIMKVTGHATAKMIFAYDKSSREDNASKKMALI"
+FT CDS 1579..2934
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP1-D"
+FT /db_xref="GOA:P0CE16"
+FT /db_xref="InterPro:IPR003593"
+FT /db_xref="InterPro:IPR007693"
+FT /db_xref="InterPro:IPR007694"
+FT /db_xref="InterPro:IPR027417"
+FT /db_xref="InterPro:IPR036185"
+FT /db_xref="UniProtKB/Swiss-Prot:P0CE16"
+FT /protein_id="AAA91569.1"
+FT /translation="MKTRSEIENRMQDIEYALLGKALIFEDSTEYILRQLANYEFKCSH
+FT HKNIFIVFKHLKDNGLPITVDSAWEELLRRRIKDMDKSYLGLMLHDALSNDKLRSVSHT
+FT VFLDDLSVCSAEENLSNFIFRSFNEYNENPLRRSPFLLLERIKGRLDSAIAKTFSIRSA
+FT RGRSIYDIFSQSEIGVLARIKKRRVAFSENQNSFFDGFPTGYKDIDDKGVILAKGNFVI
+FT IAARPSIGKTALAIDMAINLAVTQQRRVGFLSLEMSAGQIVERIIANLTGISGEKLQRG
+FT DLSKEELFRVEEAGETVRESHFYICSDSQYKLNLIANQIRLLRKEDRVDVIFIDYLQLI
+FT NSSVGENRQNEIADISRTLRGLASELNIPIVCLSQLSRKVEDRANKVPMLSDLRDSGQI
+FT EQDADVILFINRKESSSNCEITVGKNRHGSVFSSVLHFDPKISKFSAIKKVW"
+FT CDS 2928..3992
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP2-D"
+FT /db_xref="InterPro:IPR040719"
+FT /db_xref="UniProtKB/Swiss-Prot:P0CE17"
+FT /protein_id="AAA91570.1"
+FT /translation="MVNYSNCHFIKSPIHLENQKFGRRPGQSIKISPKLAQNGMVEVIG
+FT LDFLSSHYHALAAIQRLLTATNYKGNTKGVVLSRESNSFQFEGWIPRIRFTKTEFLEAY
+FT GVKRYKTSRNKYEFSGKEAETALEALYHLGHQPFLIVATRTRWTNGTQIVDRYQTLSPI
+FT IRIYEGWEGLTDEENIDIDLTPFNSPPTRKHKGFVVEPCPILVDQIESYFVIKPANVYQ
+FT EIKMRFPNASKYAYTFIDWVITAAAKKRRKLTKDNSWPENLLLNVNVKSLAYILRMNRY
+FT ICTRNWKKIELAIDKCIEIAIQLGWLSRRKRIEFLDSSKLSKKEILYLNKERFEEITKK
+FT SKEQMEQLEQESIN"
+FT CDS 4054..4848
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP3-D"
+FT /db_xref="InterPro:IPR008444"
+FT /db_xref="InterPro:IPR033758"
+FT /db_xref="InterPro:IPR038264"
+FT /db_xref="PDB:6GJT"
+FT /db_xref="UniProtKB/Swiss-Prot:P0CE18"
+FT /protein_id="AAA91571.1"
+FT /translation="MGNSGFYLYNTENCVFADNIKVGQMTEPLKDQQIILGTTSTPVAA
+FT KMTASDGISLTVSNNSSTNASITIGLDAEKAYQLILEKLGDQILDGIADTIVDSTVQDI
+FT LDKIKTDPSLGLLKAFNNFPITNKIQCNGLFTPSNIETLLGGTEIGKFTVTPKSSGSMF
+FT LVSADIIASRMEGGVVLALVREGDSKPCAISYGYSSGIPNLCSLRTSITNTGLTPTTYS
+FT LRVGGLESGVVWVNALSNGNDILGITNTSNVSFLEVIPQTNA"
+FT CDS 4918..5226
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP4-D"
+FT /db_xref="UniProtKB/Swiss-Prot:P0CE23"
+FT /protein_id="AAA91572.1"
+FT /translation="MQNKRKVRDDFIKIVKDVKKDFPELDLKIRVNKEKVTFLNSPLEL
+FT YHKSVSLILGLLQQIENSLGLFPDSPVLEKLEDNSLKLKKALIMLILSRKDMFSKAE"
+FT CDS 5317..6048
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP5-D (gtg start codon)"
+FT /db_xref="GOA:P10559"
+FT /db_xref="InterPro:IPR025669"
+FT /db_xref="InterPro:IPR027417"
+FT /db_xref="UniProtKB/Swiss-Prot:P10559"
+FT /protein_id="AAA91573.1"
+FT /translation="MGCNLAQFLGKKVLLADLDPQSNLSSGLGASVRSDQKGLHDIVYT
+FT SNDLKSIICETKKDSVDLIPASFSSEQFRELDIHRGPSNNLKLFLNEYCAPFYDICIID
+FT TPPSLGGLTKEAFVAGDKLIACLTPEPFSILGLQKIREFLSSVGKPEEEHILGIALSFW
+FT DDRNSTNQMYIDIIESIYKNKLFSTKIRRDISLSRSLLKEDSVANVYPNSRAAEDILKL
+FT THEIANILHIEYERDYSQRTT"
+FT CDS 6045..6788
+FT /codon_start=1
+FT /transl_table=11
+FT /product="hypothetical protein"
+FT /note="pGP6-D (gtg start codon)"
+FT /db_xref="InterPro:IPR005350"
+FT /db_xref="UniProtKB/Swiss-Prot:P10560"
+FT /protein_id="AAA91574.1"
+FT /translation="MNKLKKEADVFFKKNQTAASLDFKKTLPSIELFSATLNSEESQSL
+FT DRLFLSESQNYSDEEFYQEDILAVKLLTGQIKSIQKQHVLLLGEKIYNARKILSKDHFS
+FT STTFSSWIELVFRTKSSAYNALAYYELFINLPNQTLQKEFQSIPYKSAYILAARKGDLK
+FT TKVDVIGKVCGMSNSSAIRVLDQFLPSSRNKDVRETIDKSDSEKNRQLSDFLIEILRIM
+FT CSGVSLSSYNENLLQQLFELFKQKS"
+FT repeat_region 6857..6945
+FT /note="four tandem 22bp repeats"
+XX
+SQ Sequence 7502 BP; 2460 A; 1285 C; 1433 G; 2324 T; 0 other;
+ ggatccgtaa gttagacgaa attttgtctt tgcgcacaga cgatctattt tttgcatcca 60
+ atcagatttc ctttcgcatt aaaaaaagac agaataaaga aaccaaaatt ctaatcacat 120
+ ttcctatcag cttaatggaa gagttgcaaa aatacacttg tgggagaaat gggagagtat 180
+ ttgtttctaa aatagggatt cctgtaacaa caagtcaggt tgcgcataat tttaggcttg 240
+ cagagttcca tagtgctatg aaaataaaaa ttactcccag agtacttcgt gcaagcgctt 300
+ tgattcattt aaagcaaata ggattaaaag atgaggaaat catgcgtatt tcctgtcttt 360
+ catcgagaca aagtgtgtgt tcttattgtt ctggggaaga ggtaattcct ctagtacaaa 420
+ cacccacaat attgtgatat aattaaaatt atattcatat tctgttgcca gaaaaaacac 480
+ ctttaggcta tattagagcc atcttctttg aagcgttgtc ttctcgagaa gatttatcgt 540
+ acgcaaatat catctttgcg gttgcgtgtc ctgtgacctt cattatgtcg gagtctgagc 600
+ accctaggcg tttgtactcc gtcacagcgg ttgctcgaag cacgtgcggg gttattttaa 660
+ aagggattgc agcttgtagt cctgcttgag agaacgtgcg ggcgatttgc cttaacccca 720
+ ccatttttcc ggagcgagtt acgaagacaa aacctcttcg ttgaccgatg tactcttgta 780
+ gaaagtgcat aaacttctga ggataagtta taataatcct cttttctgtc tgacggttct 840
+ taagctggga gaaagaaatg gtagcttgtt ggaaacaaat ctgactaatc tccaagctta 900
+ agacttcaga ggagcgttta cctccttgga gcattgtctg ggcgatcaac caatcccggg 960
+ cattgatttt ttttagctct tttaggaagg atgctgtttg caaactgttc atcgcatccg 1020
+ tttttactat ttccctggtt ttaaaaaatg ttcgactatt ttcttgttta gaaggttgcg 1080
+ ctatagcgac tattccttga gtcatcctgt ttaggaatct tgttaaggaa atatagcttg 1140
+ ctgctcgaac ttgtttagta ccttcggtcc aagaagtctt ggcagaggaa acttttttaa 1200
+ tcgcatctag gattagatta tgatttaaaa gggaaaactc ttgcagattc atatccaagg 1260
+ acaatagacc aatcttttct aaagacaaaa aagatcctcg atatgatcta caagtatgtt 1320
+ tgttgagtga tgcggtccaa tgcataataa cttcgaataa ggagaagctt ttcatgcgtt 1380
+ tccaatagga ttcttggcga atttttaaaa cttcctgata agacttttca ctatattcta 1440
+ acgacatttc ttgctgcaaa gataaaatcc ctttacccat gaaatccctc gtgatataac 1500
+ ctatccgtaa aatgtcctga ttagtgaaat aatcaggttg ttaacaggat agcacgctcg 1560
+ gtattttttt atataaacat gaaaactcgt tccgaaatag aaaatcgcat gcaagatatc 1620
+ gagtatgcgt tgttaggtaa agctctgata tttgaagact ctactgagta tattctgagg 1680
+ cagcttgcta attatgagtt taagtgttct catcataaaa acatattcat agtatttaaa 1740
+ cacttaaaag acaatggatt acctataact gtagactcgg cttgggaaga gcttttgcgg 1800
+ cgtcgtatca aagatatgga caaatcgtat ctcgggttaa tgttgcatga tgctttatca 1860
+ aatgacaagc ttagatccgt ttctcatacg gttttcctcg atgatttgag cgtgtgtagc 1920
+ gctgaagaaa atttgagtaa tttcattttc cgctcgttta atgagtacaa tgaaaatcca 1980
+ ttgcgtagat ctccgtttct attgcttgag cgtataaagg gaaggcttga tagtgctata 2040
+ gcaaagactt tttctattcg cagcgctaga ggccggtcta tttatgatat attctcacag 2100
+ tcagaaattg gagtgctggc tcgtataaaa aaaagacgag tagcgttctc tgagaatcaa 2160
+ aattctttct ttgatggctt cccaacagga tacaaggata ttgatgataa aggagttatc 2220
+ ttagctaaag gtaatttcgt gattatagca gctagaccat ctatagggaa aacagcttta 2280
+ gctatagaca tggcgataaa tcttgcggtt actcaacagc gtagagttgg tttcctatct 2340
+ ctagaaatga gcgcaggtca aattgttgag cggattattg ctaatttaac aggaatatct 2400
+ ggtgaaaaat tacaaagagg ggatctctct aaagaagaat tattccgagt agaagaagct 2460
+ ggagaaacgg ttagagaatc acatttttat atctgcagtg atagtcagta taagcttaac 2520
+ ttaatcgcga atcagatccg gttgctgaga aaagaagatc gagtagacgt aatatttatc 2580
+ gattacttgc agttgatcaa ctcatcggtt ggagaaaatc gtcaaaatga aatagcagat 2640
+ atatctagaa ccttaagagg tttagcctca gagctaaaca ttcctatagt ttgtttatcc 2700
+ caactatcta gaaaagttga ggatagagca aataaagttc ccatgctttc agatttgcga 2760
+ gacagcggtc aaatagagca agacgcagat gtgattttgt ttatcaatag gaaggaatcg 2820
+ tcttctaatt gtgagataac tgttgggaaa aatagacatg gatcggtttt ctcttcggta 2880
+ ttacatttcg atccaaaaat tagtaaattc tccgctatta aaaaagtatg gtaaattata 2940
+ gtaactgcca cttcatcaaa agtcctatcc accttgaaaa tcagaagttt ggaagaagac 3000
+ ctggtcaatc tattaagata tctcccaaat tggctcaaaa tgggatggta gaagttatag 3060
+ gtcttgattt tctttcatct cattaccatg cattagcagc tatccaaaga ttactgaccg 3120
+ caacgaatta caaggggaac acaaaagggg ttgttttatc cagagaatca aatagttttc 3180
+ aatttgaagg atggatacca agaatccgtt ttacaaaaac tgaattctta gaggcttatg 3240
+ gagttaagcg gtataaaaca tccagaaata agtatgagtt tagtggaaaa gaagctgaaa 3300
+ ctgctttaga agccttatac catttaggac atcaaccgtt tttaatagtg gcaactagaa 3360
+ ctcgatggac taatggaaca caaatagtag accgttacca aactctttct ccgatcatta 3420
+ ggatttacga aggatgggaa ggtttaactg acgaagaaaa tatagatata gacttaacac 3480
+ cttttaattc accacctaca cggaaacata aagggttcgt tgtagagcca tgtcctatct 3540
+ tggtagatca aatagaatcc tactttgtaa tcaagcctgc aaatgtatac caagaaataa 3600
+ aaatgcgttt cccaaatgca tcaaagtatg cttacacatt tatcgactgg gtgattacag 3660
+ cagctgcgaa aaagagacga aaattaacta aggataattc ttggccagaa aacttgttat 3720
+ taaacgttaa cgttaaaagt cttgcatata ttttaaggat gaatcggtac atctgtacaa 3780
+ ggaactggaa aaaaatcgag ttagctatcg ataaatgtat agaaatcgcc attcagcttg 3840
+ gctggttatc tagaagaaaa cgcattgaat ttctggattc ttctaaactc tctaaaaaag 3900
+ aaattctata tctaaataaa gagcgctttg aagaaataac taagaaatct aaagaacaaa 3960
+ tggaacaatt agaacaagaa tctattaatt aatagcaagc ttgaaactaa aaacctaatt 4020
+ tatttaaagc tcaaaataaa aaagagtttt aaaatgggaa attctggttt ttatttgtat 4080
+ aacactgaaa actgcgtctt tgctgataat atcaaagttg ggcaaatgac agagccgctc 4140
+ aaggaccagc aaataatcct tgggacaaca tcaacacctg tcgcagccaa aatgacagct 4200
+ tctgatggaa tatctttaac agtctccaat aattcatcaa ccaatgcttc tattacaatt 4260
+ ggtttggatg cggaaaaagc ttaccagctt attctagaaa agttgggaga tcaaattctt 4320
+ gatggaattg ctgatactat tgttgatagt acagtccaag atattttaga caaaatcaaa 4380
+ acagaccctt ctctaggttt gttgaaagct tttaacaact ttccaatcac taataaaatt 4440
+ caatgcaacg ggttattcac tcccagtaac attgaaactt tattaggagg aactgaaata 4500
+ ggaaaattca cagtcacacc caaaagctct gggagcatgt tcttagtctc agcagatatt 4560
+ attgcatcaa gaatggaagg cggcgttgtt ctagctttgg tacgagaagg tgattctaag 4620
+ ccctgcgcga ttagttatgg atactcatca ggcattccta atttatgtag tctaagaacc 4680
+ agtattacta atacaggatt gactccgaca acgtattcat tacgtgtagg cggtttagaa 4740
+ agcggtgtgg tatgggttaa tgccctttct aatggcaatg atattttagg aataacaaat 4800
+ acttctaatg tatctttttt agaggtaata cctcaaacaa acgcttaaac aatttttatt 4860
+ ggatttttct tataggtttt atatttagag aaaacagttc gaattacggg gtttgttatg 4920
+ caaaataaaa gaaaagtgag ggacgatttt attaaaattg ttaaagatgt gaaaaaagat 4980
+ ttccccgaat tagacctaaa aatacgagta aacaaggaaa aagtaacttt cttaaattct 5040
+ cccttagaac tctaccataa aagtgtctca ctaattctag gactgcttca acaaatagaa 5100
+ aactctttag gattattccc agactctcct gttcttgaaa aattagagga taacagttta 5160
+ aagctaaaaa aggctttgat tatgcttatc ttgtctagaa aagacatgtt ttccaaggct 5220
+ gaatagacaa cttactctaa cgttggagtt gatttgcaca ccttagtttt ttgctctttt 5280
+ aagggaggaa ctggaaaaac aacactttct ctaaacgtgg gatgcaactt ggcccaattt 5340
+ ttagggaaaa aagtgttact tgctgaccta gacccgcaat ccaatttatc ttctggattg 5400
+ ggggctagtg tcagaagtga ccaaaaaggc ttgcacgaca tagtatacac atcaaacgat 5460
+ ttaaaatcaa tcatttgcga aacaaaaaaa gatagtgtgg acctaattcc tgcatcattt 5520
+ tcatccgaac agtttagaga attggatatt catagaggac ctagtaacaa cttaaagtta 5580
+ tttctgaatg agtactgcgc tcctttttat gacatctgca taatagacac tccacctagc 5640
+ ctaggagggt taacgaaaga agcttttgtt gcaggagaca aattaattgc ttgtttaact 5700
+ ccagaacctt tttctattct agggttacaa aagatacgtg aattcttaag ttcggtcgga 5760
+ aaacctgaag aagaacacat tcttggaata gctttgtctt tttgggatga tcgtaactcg 5820
+ actaaccaaa tgtatataga cattatcgag tctatttaca aaaacaagct tttttcaaca 5880
+ aaaattcgtc gagatatttc tctcagccgt tctcttctta aagaagattc tgtagctaat 5940
+ gtctatccaa attctagggc cgcagaagat attctgaagt taacgcatga aatagcaaat 6000
+ attttgcata tcgaatatga acgagattac tctcagagga caacgtgaac aaactaaaaa 6060
+ aagaagcgga tgtctttttt aaaaaaaatc aaactgccgc ttctctagat tttaagaaga 6120
+ cgcttccctc cattgaacta ttctcagcaa ctttgaattc tgaggaaagt cagagtttgg 6180
+ atcgattatt tttatcagag tcccaaaact attcggatga agaattttat caagaagaca 6240
+ tcctagcggt aaaactgctt actggtcaga taaaatccat acagaagcaa cacgtacttc 6300
+ ttttaggaga aaaaatctat aatgctagaa aaatcctgag taaggatcac ttctcctcaa 6360
+ caactttttc atcttggata gagttagttt ttagaactaa gtcttctgct tacaatgctc 6420
+ ttgcatatta cgagcttttt ataaacctcc ccaaccaaac tctacaaaaa gagtttcaat 6480
+ cgatccccta taaatccgca tatattttgg ccgctagaaa aggcgattta aaaaccaagg 6540
+ tcgatgtgat agggaaagta tgtggaatgt cgaactcatc ggcgataagg gtgttggatc 6600
+ aatttcttcc ttcatctaga aacaaagacg ttagagaaac gatagataag tctgattcag 6660
+ agaagaatcg ccaattatct gatttcttaa tagagatact tcgcatcatg tgttccggag 6720
+ tttctttgtc ctcctataac gaaaatcttc tacaacagct ttttgaactt tttaagcaaa 6780
+ agagctgatc ctccgtcagc tcatatatat atatctatta tatatatata tttagggatt 6840
+ tgatttcacg agagagattt gcaactcttg gtggtagact ttgcaactct tggtggtaga 6900
+ ctttgcaact cttggtggta gactttgcaa ctcttggtgg tagacttggt cataatggac 6960
+ ttttgttaaa aaatttatta aaatcttaga gctccgattt tgaatagctt tggttaagaa 7020
+ aatgggctcg atggctttcc ataaaagtag attgttttta acttttgggg acgcgtcgga 7080
+ aatttggtta tctactttat cttatctaac tagaaaaaat tatgcgtctg ggattaactt 7140
+ tcttgtttct ttagagattc tggatttatc ggaaaccttg ataaaggcta tttctcttga 7200
+ ccacagcgaa tctttgttta aaatcaagtc tctagatgtt tttaatggaa aagttgtttc 7260
+ agaggcatct aaacaggcta gagcggcatg ctacatatct ttcacaaagt ttttgtatag 7320
+ attgaccaag ggatatatta aacccgctat tccattgaaa gattttggaa acactacatt 7380
+ ttttaaaatc cgagacaaaa tcaaaacaga atcgatttct aagcaggaat ggacagtttt 7440
+ ttttgaagcg ctccggatag tgaattatag agactattta atcggtaaat tgattgtaca 7500
+ ag 7502
+//
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.StandardCopyOption;
+
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.datamodel.AlignmentI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+
+/**
+ * WindowsFileSaveTest simply opens an alignment file and then tries to save it.
+ * This failed in Windows from 2.11.0 to 2.11.1.6 due to a combination of the
+ * opening file handle being left open ad infinitum, causing the BackupFiles
+ * operation of moving the saved (temp) file onto the original filename to fail,
+ * but only in Windows. See: https://issues.jalview.org/browse/JAL-3628
+ * https://issues.jalview.org/browse/JAL-3703
+ * https://issues.jalview.org/browse/JAL-3935 These issues are really all fixed
+ * by JAL-3703 This test is to ensure it doesn't start again, but note that this
+ * test will only fail in Windows.
+ */
+public class WindowsFileLoadAndSaveTest
+{
+
+ private final static String fileName = "examples" + File.separator
+ + "uniref50.fa";
+
+ private final static String testFileName = fileName + "-TEST";
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ /**
+ * Test saving and re-reading in a specified format
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void loadAndSaveAlignment() throws IOException
+ {
+ File file = new File(fileName);
+ File testFile = new File(testFileName);
+ Files.copy(file.toPath(), testFile.toPath(),
+ StandardCopyOption.REPLACE_EXISTING);
+ FormatAdapter fa = new FormatAdapter();
+ AlignmentI a = fa.readFile(testFile, DataSourceType.FILE,
+ FileFormat.Fasta);
+
+ AlignFrame af = new AlignFrame(a, 500, 500);
+ af.saveAlignment(testFileName, FileFormat.Fasta);
+
+ Assert.assertTrue(af.isSaveAlignmentSuccessful());
+ }
+
+ @AfterClass(alwaysRun = true)
+ private void cleanupTmpFiles()
+ {
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+ .getSavedBackupEntry();
+ BackupFilesTest.cleanupTmpFiles(testFileName, bfpe.suffix, bfpe.digits);
+ }
+
+}
import static org.testng.Assert.assertTrue;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
Cache.setProperty("VCF_FIELDS", ".*");
Cache.setProperty("VEP_FIELDS", ".*");
Cache.setProperty("VCF_ASSEMBLY", "GRCh38=GRCh38");
- Cache.initLogger();
+ Console.initLogger();
}
@BeforeTest(alwaysRun = true)
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import javax.swing.JInternalFrame;
"Mismatch PDBEntry 'Type'");
Assert.assertNotNull(recov.getFile(),
"Recovered PDBEntry should have a non-null file entry");
+ Assert.assertEquals(recov.getFile().toLowerCase(Locale.ENGLISH).lastIndexOf("pdb"),recov.getFile().length()-3, "Recovered PDBEntry file should have PDB suffix");
}
}
import jalview.structure.AtomSpec;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import junit.extensions.PA;
Color mColor = new Color(0x82827d);
AtomSpecModel atomSpec = colours.get(mColor);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#0:21.A|#1:21.B");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#0:21.A|#1:21.B");
/*
* H colour is #60609f, seq1.2 mapped to structure 0 residue 22
Color hColor = new Color(0x60609f);
atomSpec = colours.get(hColor);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#0:22.A");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#0:22.A");
/*
* V colour is #ffff00, seq2.2 mapped to structure 1 residue 22
Color vColor = new Color(0xffff00);
atomSpec = colours.get(vColor);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#1:22.B");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#1:22.B");
/*
* hidden columns are Gray (128, 128, 128)
Color gray = new Color(128, 128, 128);
atomSpec = colours.get(gray);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#0:23-25.A|#1:23-25.B");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#0:23-25.A|#1:23-25.B");
/*
* S and G are both coloured #4949b6, structure residues 26-30
Color sgColour = new Color(0x4949b6);
atomSpec = colours.get(sgColour);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false),
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
"#0:26-30.A|#1:26-30.B");
}
}
\ No newline at end of file
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+import static org.testng.Assert.assertNotNull;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.concurrent.TimeUnit;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+import io.github.classgraph.ClassGraph;
+import io.github.classgraph.ScanResult;
+import jalview.bin.Console;
+
+public class Log4jTest
+{
+ private static final int TIMEOUT = 10;
+
+ private static class Worker extends Thread
+ {
+ private final Process process;
+
+ private BufferedReader outputReader;
+
+ private BufferedReader errorReader;
+
+ private boolean exited;
+
+ private Worker(Process process)
+ {
+ this.process = process;
+ }
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ exited = process.waitFor(TIMEOUT, TimeUnit.SECONDS);
+ } catch (InterruptedException ignore)
+ {
+ return;
+ }
+ this.interrupt();
+ this.process.destroy();
+ }
+
+ public BufferedReader getOutputReader()
+ {
+ return outputReader;
+ }
+
+ public void setOutputReader(BufferedReader outputReader)
+ {
+ this.outputReader = outputReader;
+ }
+
+ public BufferedReader getErrorReader()
+ {
+ return errorReader;
+ }
+
+ public void setErrorReader(BufferedReader errorReader)
+ {
+ this.errorReader = errorReader;
+ }
+ }
+
+ private static ClassGraph scanner = null;
+
+ private static String classpath = null;
+
+ private static String java_exe = null;
+
+ public synchronized static String getClassPath()
+ {
+ if (scanner == null)
+ {
+ scanner = new ClassGraph();
+ ScanResult scan = scanner.scan();
+ classpath = scan.getClasspath();
+ java_exe = System.getProperty("java.home") + File.separator + "bin"
+ + File.separator + "java";
+
+ }
+ while (classpath == null)
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException x)
+ {
+
+ }
+ }
+ return classpath;
+ }
+
+ private Worker getJalviewDesktopRunner(String appArgs)
+ {
+ String classpath = getClassPath();
+ String cmd = java_exe + " " + " -classpath " + classpath + " "
+ + " jalview.bin.Jalview " + " "
+ + "-props test/jalview/util/log4jTestProps.jvprops " + appArgs;
+ Process proc = null;
+ Worker worker = null;
+ try
+ {
+ proc = Runtime.getRuntime().exec(cmd);
+ } catch (Throwable e)
+ {
+ e.printStackTrace();
+ }
+ if (proc != null)
+ {
+ BufferedReader outputReader = new BufferedReader(
+ new InputStreamReader(proc.getInputStream()));
+ BufferedReader errorReader = new BufferedReader(
+ new InputStreamReader(proc.getErrorStream()));
+ worker = new Worker(proc);
+ worker.start();
+ worker.setOutputReader(outputReader);
+ worker.setErrorReader(errorReader);
+ }
+ return worker;
+ }
+
+ @BeforeTest(alwaysRun = true)
+ public void initialize()
+ {
+ new Log4jTest();
+ }
+
+ @Test(groups = { "Functional" })
+ public void testLog4j()
+ {
+ String appArgs = " -open examples/uniref50.fa -nosplash -nonews -noquestionnaire -nousagestats -nowebservicediscovery";
+
+ Worker worker = getJalviewDesktopRunner(appArgs);
+ assertNotNull(worker, "worker is null");
+
+ String ln = null;
+ int count = 0;
+ boolean logTestFound = false;
+ try
+ {
+ while ((ln = worker.getErrorReader().readLine()) != null)
+ {
+ if (++count > 500)
+ {
+ break;
+ }
+ if (ln.contains(Console.LOGGING_TEST_MESSAGE))
+ {
+ logTestFound = true;
+ break;
+ }
+ }
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ if (worker != null && worker.exited == false)
+ {
+ worker.interrupt();
+ worker.process.destroy();
+ }
+ if (!logTestFound)
+ {
+ Assert.fail("Did not find Log4j Test message line '"
+ + Console.LOGGING_TEST_MESSAGE + "'");
+ }
+ }
+
+}
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
-import jalview.gui.JvOptionPane;
-
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.BitSet;
import java.util.List;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.bin.Console;
+import jalview.gui.JvOptionPane;
+
public class MapListTest
{
-
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Console.initLogger();
+ }
+
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Functional" }, enabled = false)
public void testSomething()
{
- MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 }, new int[] {
- 51, 1 }, 1, 3);
+ MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 },
+ new int[]
+ { 51, 1 }, 1, 3);
MapList ml1 = new MapList(new int[] { 1, 3, 17, 4 },
- new int[] { 51, 1 }, 1, 3);
+ new int[]
+ { 51, 1 }, 1, 3);
MapList ml2 = new MapList(new int[] { 1, 60 }, new int[] { 1, 20 }, 3,
1);
// test internal consistency
int to[] = new int[51];
testMap(ml, 1, 60);
- MapList mldna = new MapList(new int[] { 2, 2, 6, 8, 12, 16 }, new int[]
- { 1, 3 }, 3, 1);
+ MapList mldna = new MapList(new int[] { 2, 2, 6, 8, 12, 16 },
+ new int[]
+ { 1, 3 }, 3, 1);
int[] frm = mldna.locateInFrom(1, 1);
testLocateFrom(mldna, 1, 1, new int[] { 2, 2, 6, 7 });
testMap(mldna, 1, 3);
assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
assertEquals("[1, 6]", Arrays.toString(ml.locateInFrom(1, 2)));
assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(1, 3)));
+ // reversed range treated as if forwards:
+ assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(3, 1)));
assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 4)));
assertEquals("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3)));
assertEquals("[4, 12]", Arrays.toString(ml.locateInFrom(2, 4)));
assertEquals("[7, 12]", Arrays.toString(ml.locateInFrom(3, 4)));
assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
+ /*
+ * partial overlap
+ */
+ assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 5)));
+ assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(-1, 1)));
+
+ /*
+ * no overlap
+ */
assertNull(ml.locateInFrom(0, 0));
- assertNull(ml.locateInFrom(1, 5));
- assertNull(ml.locateInFrom(-1, 1));
+
}
/**
assertEquals("[10, 10, 12, 12, 14, 14]",
Arrays.toString(ml.locateInFrom(3, 3)));
assertEquals("[16, 18]", Arrays.toString(ml.locateInFrom(4, 4)));
+
+ /*
+ * codons at 11-16, 21-26, 31-36 mapped to peptide positions 1, 3-4, 6-8
+ */
+ ml = new MapList(new int[] { 11, 16, 21, 26, 31, 36 },
+ new int[]
+ { 1, 1, 3, 4, 6, 8 }, 3, 1);
+ assertArrayEquals(new int[] { 11, 13 }, ml.locateInFrom(1, 1));
+ assertArrayEquals(new int[] { 11, 16 }, ml.locateInFrom(1, 3));
+ assertArrayEquals(new int[] { 11, 16, 21, 23 }, ml.locateInFrom(1, 4));
+ assertArrayEquals(new int[] { 14, 16, 21, 23 }, ml.locateInFrom(3, 4));
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void testLocateInFrom_reverseStrand()
+ {
+ int[] codons = new int[] { 12, 1 };
+ int[] protein = new int[] { 1, 4 };
+ MapList ml = new MapList(codons, protein, 3, 1);
+ assertEquals("[12, 10]", Arrays.toString(ml.locateInFrom(1, 1)));
+ assertEquals("[9, 4]", Arrays.toString(ml.locateInFrom(2, 3)));
+ }
+
+ /**
+ * Tests for method that locates the overlap of the ranges in the 'from' map
+ * for given range in the 'to' map
+ */
+ @Test(groups = { "Functional" })
+ public void testGetOverlapsInFrom_withIntrons()
+ {
+ /*
+ * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
+ * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
+ */
+ int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+ int[] protein = { 11, 14 };
+ MapList ml = new MapList(codons, protein, 3, 1);
+
+ assertEquals("[2, 3, 5, 5]",
+ Arrays.toString(ml.getOverlapsInFrom(11, 11)));
+ assertEquals("[2, 3, 5, 7, 9, 9]",
+ Arrays.toString(ml.getOverlapsInFrom(11, 12)));
+ // out of range 5' :
+ assertEquals("[2, 3, 5, 7, 9, 9]",
+ Arrays.toString(ml.getOverlapsInFrom(8, 12)));
+ // out of range 3' :
+ assertEquals("[10, 10, 12, 12, 14, 14, 16, 18]",
+ Arrays.toString(ml.getOverlapsInFrom(13, 16)));
+ // out of range both :
+ assertEquals("[2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18]",
+ Arrays.toString(ml.getOverlapsInFrom(1, 16)));
+ // no overlap:
+ assertNull(ml.getOverlapsInFrom(20, 25));
+ }
+
+ /**
+ * Tests for method that locates the overlap of the ranges in the 'to' map for
+ * given range in the 'from' map
+ */
+ @Test(groups = { "Functional" })
+ public void testGetOverlapsInTo_withIntrons()
+ {
+ /*
+ * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [17, 18, 19] i.e.
+ * 2-3, 5-7, 9-10, 12-12, 14-14, 17-19
+ */
+ int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 17, 19 };
+ /*
+ * Mapped proteins at positions 1, 3, 4, 6 in the sequence
+ */
+ int[] protein = { 1, 1, 3, 4, 6, 6 };
+ MapList ml = new MapList(codons, protein, 3, 1);
+
+ /*
+ * Can't map from an unmapped position
+ */
+ assertNull(ml.getOverlapsInTo(1, 1));
+ assertNull(ml.getOverlapsInTo(4, 4));
+ assertNull(ml.getOverlapsInTo(15, 16));
+
+ /*
+ * nor from a range that includes no mapped position (exon)
+ */
+ assertNull(ml.getOverlapsInTo(15, 16));
+
+ // end of codon 1 maps to first peptide
+ assertEquals("[1, 1]", Arrays.toString(ml.getOverlapsInTo(2, 2)));
+ // end of codon 1 and start of codon 2 maps to first 2 peptides
+ assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.getOverlapsInTo(3, 7)));
+
+ // range overlaps 5' end of dna:
+ assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.getOverlapsInTo(1, 6)));
+ assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.getOverlapsInTo(1, 8)));
+
+ // range overlaps 3' end of dna:
+ assertEquals("[6, 6]", Arrays.toString(ml.getOverlapsInTo(17, 24)));
+ assertEquals("[6, 6]", Arrays.toString(ml.getOverlapsInTo(16, 24)));
+
+ // dna positions 8, 11 are intron but include end of exon 2 and start of
+ // exon 3
+ assertEquals("[3, 4]", Arrays.toString(ml.getOverlapsInTo(8, 11)));
}
/**
assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(1, 12)));
assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(4, 12)));
+ // reverse range treated as if forwards:
+ assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(12, 4)));
/*
* A part codon is treated as if a whole one.
assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(3, 11)));
assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(5, 11)));
+ /*
+ * partial overlap
+ */
+ assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(1, 13)));
+ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(-1, 2)));
+
+ /*
+ * no overlap
+ */
assertNull(ml.locateInTo(0, 0));
- assertNull(ml.locateInTo(1, 13));
- assertNull(ml.locateInTo(-1, 1));
}
/**
MapList ml = new MapList(codons, protein, 3, 1);
/*
- * Can't map from an unmapped position
- */
- assertNull(ml.locateInTo(1, 2));
- assertNull(ml.locateInTo(2, 4));
- assertNull(ml.locateInTo(4, 4));
-
- /*
- * Valid range or subrange of codon1 maps to protein1.
+ * Valid range or subrange of codon1 maps to protein1
*/
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 2)));
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(3, 3)));
// codon positions 7 to 17 (part) cover proteins 2/3/4 at positions 3/4/6
assertEquals("[3, 4, 6, 6]", Arrays.toString(ml.locateInTo(7, 17)));
+ /*
+ * partial overlap
+ */
+ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 2)));
+ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 4)));
+ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 4)));
+
+ /*
+ * no overlap
+ */
+ assertNull(ml.locateInTo(4, 4));
}
/**
List<int[]> ranges = new ArrayList<>();
ranges.add(new int[] { 2, 3 });
ranges.add(new int[] { 5, 6 });
- assertEquals("[2, 3, 5, 6]", Arrays.toString(MapList.getRanges(ranges)));
+ assertEquals("[2, 3, 5, 6]",
+ Arrays.toString(MapList.getRanges(ranges)));
}
/**
assertEquals(6, ml2.getToHighest());
assertEquals("{[2, 3], [5, 7], [9, 10], [12, 12], [14, 14], [16, 18]}",
prettyPrint(ml2.getFromRanges()));
- assertEquals("{[1, 1], [3, 4], [6, 6]}", prettyPrint(ml2.getToRanges()));
+ assertEquals("{[1, 1], [3, 4], [6, 6]}",
+ prettyPrint(ml2.getToRanges()));
/*
* reverse direction
}
/**
- * Test constructor can merge consecutive ranges
+ * Test constructor used to merge consecutive ranges but now just leaves them
+ * as supplied (JAL-3751)
*/
@Test(groups = { "Functional" })
public void testConstructor_mergeRanges()
{
- int[] codons = { 2, 3, 3, 7, 9, 10, 12, 12, 14, 14, 16, 17 };
- int[] protein = { 1, 1, 1, 3, 6, 6 };
+ int[] codons = { 2, 3, 3, 7, 9, 10, 12, 12, 13, 14, 16, 17 };
+ int[] protein = { 1, 1, 2, 3, 6, 6 };
MapList ml = new MapList(codons, protein, 3, 1);
assertEquals(3, ml.getFromRatio());
assertEquals(2, ml.getFromLowest());
assertEquals(17, ml.getFromHighest());
assertEquals(1, ml.getToLowest());
assertEquals(6, ml.getToHighest());
- assertEquals("{[2, 7], [9, 10], [12, 12], [14, 14], [16, 17]}",
+ assertEquals("{[2, 3], [3, 7], [9, 10], [12, 12], [13, 14], [16, 17]}",
prettyPrint(ml.getFromRanges()));
- assertEquals("{[1, 3], [6, 6]}", prettyPrint(ml.getToRanges()));
+ assertEquals("{[1, 1], [2, 3], [6, 6]}", prettyPrint(ml.getToRanges()));
}
/**
@Test(groups = { "Functional" })
public void testToString()
{
- MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 }, new int[] {
- 51, 1 }, 1, 3);
+ MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 },
+ new int[]
+ { 51, 1 }, 1, 3);
String s = ml.toString();
assertEquals("[ [1, 5] [10, 15] [25, 20] ] 1:3 to [ [51, 1] ]", s);
}
public void testAddMapList()
{
MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
- new int[] { 72, 22 }, 1, 3);
+ new int[]
+ { 72, 22 }, 1, 3);
assertEquals(11, ml.getFromLowest());
assertEquals(35, ml.getFromHighest());
assertEquals(22, ml.getToLowest());
assertEquals(72, ml.getToHighest());
- MapList ml2 = new MapList(new int[] { 2, 4, 37, 40 }, new int[] { 12,
- 17, 78, 83, 88, 96 }, 1, 3);
+ MapList ml2 = new MapList(new int[] { 2, 4, 37, 40 },
+ new int[]
+ { 12, 17, 78, 83, 88, 96 }, 1, 3);
ml.addMapList(ml2);
assertEquals(2, ml.getFromLowest());
assertEquals(40, ml.getFromHighest());
public void testAddMapList_sameMap()
{
MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
- new int[] { 72, 22 }, 1, 3);
+ new int[]
+ { 72, 22 }, 1, 3);
String before = ml.toString();
ml.addMapList(ml);
assertEquals(before, ml.toString());
MapList ml = new MapList(new int[] { 11, 15 }, new int[] { 72, 58 }, 1,
3);
- MapList ml2 = new MapList(new int[] { 15, 16 }, new int[] { 58, 53 },
- 1, 3);
+ MapList ml2 = new MapList(new int[] { 15, 16 }, new int[] { 58, 53 }, 1,
+ 3);
ml.addMapList(ml2);
assertEquals("[ [11, 16] ] 1:3 to [ [72, 53] ]", ml.toString());
}
public void testIsFromForwardStrand()
{
// [3-9] declares forward strand
- MapList ml = new MapList(new int[] { 2, 2, 3, 9, 12, 11 }, new int[] {
- 20, 11 }, 1, 1);
+ MapList ml = new MapList(new int[] { 2, 2, 3, 9, 12, 11 },
+ new int[]
+ { 20, 11 }, 1, 1);
assertTrue(ml.isFromForwardStrand());
// [11-5] declares reverse strand ([13-14] is ignored)
ml = new MapList(new int[] { 2, 2, 11, 5, 13, 14 },
- new int[] { 20, 11 }, 1, 1);
+ new int[]
+ { 20, 11 }, 1, 1);
assertFalse(ml.isFromForwardStrand());
// all single position ranges - defaults to forward strand
}
/**
- * Test the method that merges a list of ranges where possible
+ * Test the method that merges contiguous ranges
*/
@Test(groups = { "Functional" })
public void testCoalesceRanges()
// merging in forward direction:
ranges.clear();
ranges.add(new int[] { 1, 3 });
- ranges.add(new int[] { 4, 5 });
- ranges.add(new int[] { 5, 5 });
- ranges.add(new int[] { 5, 7 });
+ ranges.add(new int[] { 4, 5 }); // contiguous
+ ranges.add(new int[] { 5, 5 }); // overlap!
+ ranges.add(new int[] { 6, 7 }); // contiguous
List<int[]> merged = MapList.coalesceRanges(ranges);
- assertEquals(1, merged.size());
- assertArrayEquals(new int[] { 1, 7 }, merged.get(0));
+ assertEquals(2, merged.size());
+ assertArrayEquals(new int[] { 1, 5 }, merged.get(0));
+ assertArrayEquals(new int[] { 5, 7 }, merged.get(1));
// verify input list is unchanged
assertEquals(4, ranges.size());
assertArrayEquals(new int[] { 1, 3 }, ranges.get(0));
assertArrayEquals(new int[] { 4, 5 }, ranges.get(1));
assertArrayEquals(new int[] { 5, 5 }, ranges.get(2));
- assertArrayEquals(new int[] { 5, 7 }, ranges.get(3));
+ assertArrayEquals(new int[] { 6, 7 }, ranges.get(3));
// merging in reverse direction:
ranges.clear();
ranges.add(new int[] { 7, 5 });
- ranges.add(new int[] { 5, 4 });
- ranges.add(new int[] { 4, 4 });
- ranges.add(new int[] { 3, 1 });
+ ranges.add(new int[] { 5, 4 }); // overlap
+ ranges.add(new int[] { 4, 4 }); // overlap
+ ranges.add(new int[] { 3, 1 }); // contiguous
merged = MapList.coalesceRanges(ranges);
- assertEquals(1, merged.size());
- assertArrayEquals(new int[] { 7, 1 }, merged.get(0));
+ assertEquals(3, merged.size());
+ assertArrayEquals(new int[] { 7, 5 }, merged.get(0));
+ assertArrayEquals(new int[] { 5, 4 }, merged.get(1));
+ assertArrayEquals(new int[] { 4, 1 }, merged.get(2));
// merging with switches of direction:
ranges.clear();
ranges.add(new int[] { 1, 3 });
- ranges.add(new int[] { 4, 5 });
- ranges.add(new int[] { 5, 5 });
- ranges.add(new int[] { 6, 6 });
+ ranges.add(new int[] { 4, 5 }); // contiguous
+ ranges.add(new int[] { 5, 5 }); // overlap
+ ranges.add(new int[] { 6, 6 }); // contiguous
ranges.add(new int[] { 12, 10 });
- ranges.add(new int[] { 9, 8 });
- ranges.add(new int[] { 8, 8 });
- ranges.add(new int[] { 7, 7 });
+ ranges.add(new int[] { 9, 8 }); // contiguous
+ ranges.add(new int[] { 8, 8 }); // overlap
+ ranges.add(new int[] { 7, 7 }); // contiguous
merged = MapList.coalesceRanges(ranges);
- assertEquals(2, merged.size());
- assertArrayEquals(new int[] { 1, 6 }, merged.get(0));
- assertArrayEquals(new int[] { 12, 7 }, merged.get(1));
- }
-
- /**
- * Test the method that merges a list of ranges where possible
- */
- @Test(groups = { "Functional" })
- public void testCoalesceRanges_withOverlap()
- {
- List<int[]> ranges = new ArrayList<>();
- ranges.add(new int[] { 1, 3 });
- ranges.add(new int[] { 2, 5 });
-
- /*
- * [2, 5] should extend [1, 3]
- */
- List<int[]> merged = MapList.coalesceRanges(ranges);
- assertEquals(1, merged.size());
+ assertEquals(4, merged.size());
assertArrayEquals(new int[] { 1, 5 }, merged.get(0));
-
- /*
- * a subsumed interval should be dropped
- */
- ranges.clear();
- ranges.add(new int[] { 1, 6 });
- ranges.add(new int[] { 2, 4 });
- merged = MapList.coalesceRanges(ranges);
- assertEquals(1, merged.size());
- assertArrayEquals(new int[] { 1, 6 }, merged.get(0));
-
- ranges.clear();
- ranges.add(new int[] { 1, 5 });
- ranges.add(new int[] { 1, 6 });
- merged = MapList.coalesceRanges(ranges);
- assertEquals(1, merged.size());
- assertArrayEquals(new int[] { 1, 6 }, merged.get(0));
-
- /*
- * merge duplicate ranges
- */
+ assertArrayEquals(new int[] { 5, 6 }, merged.get(1));
+ assertArrayEquals(new int[] { 12, 8 }, merged.get(2));
+ assertArrayEquals(new int[] { 8, 7 }, merged.get(3));
+
+ // 'subsumed' ranges are preserved
ranges.clear();
- ranges.add(new int[] { 1, 3 });
- ranges.add(new int[] { 1, 3 });
- merged = MapList.coalesceRanges(ranges);
- assertEquals(1, merged.size());
- assertArrayEquals(new int[] { 1, 3 }, merged.get(0));
+ ranges.add(new int[] { 10, 30 });
+ ranges.add(new int[] { 15, 25 });
- /*
- * reverse direction
- */
- ranges.clear();
- ranges.add(new int[] { 9, 5 });
- ranges.add(new int[] { 9, 4 });
- ranges.add(new int[] { 8, 3 });
- ranges.add(new int[] { 3, 2 });
- ranges.add(new int[] { 1, 0 });
merged = MapList.coalesceRanges(ranges);
- assertEquals(1, merged.size());
- assertArrayEquals(new int[] { 9, 0 }, merged.get(0));
+ assertEquals(2, merged.size());
+ assertArrayEquals(new int[] { 10, 30 }, merged.get(0));
+ assertArrayEquals(new int[] { 15, 25 }, merged.get(1));
}
/**
/*
* simple 1:1 plus 1:1 forwards
*/
- MapList ml1 = new MapList(new int[] { 3, 4, 8, 12 }, new int[] { 5, 8,
- 11, 13 }, 1, 1);
+ MapList ml1 = new MapList(new int[] { 3, 4, 8, 12 },
+ new int[]
+ { 5, 8, 11, 13 }, 1, 1);
assertEquals("{[3, 4], [8, 12]}", prettyPrint(ml1.getFromRanges()));
assertEquals("{[5, 8], [11, 13]}", prettyPrint(ml1.getToRanges()));
- MapList ml2 = new MapList(new int[] { 1, 50 }, new int[] { 40, 45, 70,
- 75, 90, 127 }, 1, 1);
+ MapList ml2 = new MapList(new int[] { 1, 50 },
+ new int[]
+ { 40, 45, 70, 75, 90, 127 }, 1, 1);
assertEquals("{[1, 50]}", prettyPrint(ml2.getFromRanges()));
assertEquals("{[40, 45], [70, 75], [90, 127]}",
prettyPrint(ml2.getToRanges()));
*/
ml1 = new MapList(new int[] { 1, 50 }, new int[] { 70, 119 }, 1, 1);
ml2 = new MapList(new int[] { 1, 500 },
- new int[] { 1000, 901, 600, 201 }, 1, 1);
+ new int[]
+ { 1000, 901, 600, 201 }, 1, 1);
compound = ml1.traverse(ml2);
assertEquals(1, compound.getFromRatio());
* 1:1 plus 1:3 should result in 1:3
*/
ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 40 }, 1, 1);
- ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 50, 91, 340 },
- 1, 3);
+ ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 50, 91, 340 }, 1,
+ 3);
compound = ml1.traverse(ml2);
assertEquals(1, compound.getFromRatio());
* 3:1 plus 1:1 should result in 3:1
*/
ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 20 }, 3, 1);
- ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 15, 91, 175 },
- 1, 1);
+ ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 15, 91, 175 }, 1,
+ 1);
compound = ml1.traverse(ml2);
assertEquals(3, compound.getFromRatio());
assertArrayEquals(new int[] { 71, 126 }, toRanges.get(1));
/*
- * method returns null if not all regions are mapped through
+ * if not all regions are mapped through, returns what is
*/
ml1 = new MapList(new int[] { 1, 50 }, new int[] { 101, 150 }, 1, 1);
- ml2 = new MapList(new int[] { 131, 180 }, new int[] { 201, 250 }, 1, 3);
+ ml2 = new MapList(new int[] { 131, 180 }, new int[] { 201, 250 }, 1, 1);
compound = ml1.traverse(ml2);
assertNull(compound);
}
/**
- * Test that method that inspects for the (first) forward or reverse 'to' range.
- * Single position ranges are ignored.
+ * Test that method that inspects for the (first) forward or reverse 'to'
+ * range. Single position ranges are ignored.
*/
@Test(groups = { "Functional" })
public void testIsToForwardsStrand()
1);
assertTrue(ml.isToForwardStrand());
}
+
+ /**
+ * Test for mapping with overlapping ranges
+ */
+ @Test(groups = { "Functional" })
+ public void testLocateInFrom_withOverlap()
+ {
+ /*
+ * gene to protein...
+ */
+ int[] codons = new int[] { 1, 12, 12, 17 };
+ int[] protein = new int[] { 1, 6 };
+ MapList ml = new MapList(codons, protein, 3, 1);
+ assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(1, 1)));
+ assertEquals("[4, 6]", Arrays.toString(ml.locateInFrom(2, 2)));
+ assertEquals("[7, 9]", Arrays.toString(ml.locateInFrom(3, 3)));
+ assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
+ assertEquals("[12, 14]", Arrays.toString(ml.locateInFrom(5, 5)));
+ assertEquals("[15, 17]", Arrays.toString(ml.locateInFrom(6, 6)));
+ assertEquals("[1, 6]", Arrays.toString(ml.locateInFrom(1, 2)));
+ assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(1, 3)));
+ assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 4)));
+ assertEquals("[1, 12, 12, 14]", Arrays.toString(ml.locateInFrom(1, 5)));
+ assertEquals("[1, 12, 12, 17]", Arrays.toString(ml.locateInFrom(1, 6)));
+ assertEquals("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3)));
+ assertEquals("[7, 12, 12, 17]", Arrays.toString(ml.locateInFrom(3, 6)));
+
+ /*
+ * partial overlap of range
+ */
+ assertEquals("[4, 12, 12, 17]", Arrays.toString(ml.locateInFrom(2, 7)));
+ assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(-1, 1)));
+
+ /*
+ * no overlap in range
+ */
+ assertNull(ml.locateInFrom(0, 0));
+
+ /*
+ * gene to CDS...from EMBL:MN908947
+ */
+ int[] gene = new int[] { 266, 13468, 13468, 21555 };
+ int[] cds = new int[] { 1, 21291 };
+ ml = new MapList(gene, cds, 1, 1);
+ assertEquals("[13468, 13468]",
+ Arrays.toString(ml.locateInFrom(13203, 13203)));
+ assertEquals("[13468, 13468]",
+ Arrays.toString(ml.locateInFrom(13204, 13204)));
+ assertEquals("[13468, 13468, 13468, 13468]",
+ Arrays.toString(ml.locateInFrom(13203, 13204)));
+ }
+
+ /**
+ * Test for mapping with overlapping ranges
+ */
+ @Test(groups = { "Functional" })
+ public void testLocateInTo_withOverlap()
+ {
+ /*
+ * gene to protein...
+ */
+ int[] codons = new int[] { 1, 12, 12, 17 };
+ int[] protein = new int[] { 1, 6 };
+ MapList ml = new MapList(codons, protein, 3, 1);
+ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 1)));
+ assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(3, 8)));
+ assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(2, 11)));
+ assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(3, 11)));
+
+ // we want base 12 to map to both of the amino acids it codes for
+ assertEquals("[4, 5]", Arrays.toString(ml.locateInTo(12, 12)));
+ assertEquals("[4, 5]", Arrays.toString(ml.locateInTo(11, 12)));
+ assertEquals("[4, 6]", Arrays.toString(ml.locateInTo(11, 15)));
+ assertEquals("[6, 6]", Arrays.toString(ml.locateInTo(15, 17)));
+
+ /*
+ * no overlap
+ */
+ assertNull(ml.locateInTo(0, 0));
+
+ /*
+ * partial overlap
+ */
+ assertEquals("[1, 6]", Arrays.toString(ml.locateInTo(1, 18)));
+ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(-1, 1)));
+
+ /*
+ * gene to CDS...from EMBL:MN908947
+ * the base at 13468 is used twice in transcription
+ */
+ int[] gene = new int[] { 266, 13468, 13468, 21555 };
+ int[] cds = new int[] { 1, 21291 };
+ ml = new MapList(gene, cds, 1, 1);
+ assertEquals("[13203, 13204]",
+ Arrays.toString(ml.locateInTo(13468, 13468)));
+
+ /*
+ * gene to protein
+ * the base at 13468 is in the codon for 4401N and also 4402R
+ */
+ gene = new int[] { 266, 13468, 13468, 21552 }; // stop codon excluded
+ protein = new int[] { 1, 7096 };
+ ml = new MapList(gene, protein, 3, 1);
+ assertEquals("[4401, 4402]",
+ Arrays.toString(ml.locateInTo(13468, 13468)));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testTraverseToPosition()
+ {
+ List<int[]> ranges = new ArrayList<>();
+ assertNull(MapList.traverseToPosition(ranges, 0));
+
+ ranges.add(new int[] { 3, 6 });
+ assertNull(MapList.traverseToPosition(ranges, 0));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testCountPositions()
+ {
+ try
+ {
+ MapList.countPositions(null, 1);
+ fail("expected exception");
+ } catch (NullPointerException e)
+ {
+ // expected
+ }
+
+ List<int[]> intervals = new ArrayList<>();
+ assertNull(MapList.countPositions(intervals, 1));
+
+ /*
+ * forward strand
+ */
+ intervals.add(new int[] { 10, 20 });
+ assertNull(MapList.countPositions(intervals, 9));
+ assertNull(MapList.countPositions(intervals, 21));
+ assertArrayEquals(new int[] { 1, 1 },
+ MapList.countPositions(intervals, 10));
+ assertArrayEquals(new int[] { 6, 1 },
+ MapList.countPositions(intervals, 15));
+ assertArrayEquals(new int[] { 11, 1 },
+ MapList.countPositions(intervals, 20));
+
+ intervals.add(new int[] { 25, 25 });
+ assertArrayEquals(new int[] { 12, 1 },
+ MapList.countPositions(intervals, 25));
+
+ // next interval repeats position 25 - which should be counted twice if
+ // traversed
+ intervals.add(new int[] { 25, 26 });
+ assertArrayEquals(new int[] { 12, 1 },
+ MapList.countPositions(intervals, 25));
+ assertArrayEquals(new int[] { 14, 1 },
+ MapList.countPositions(intervals, 26));
+
+ /*
+ * reverse strand
+ */
+ intervals.clear();
+ intervals.add(new int[] { 5, -5 });
+ assertNull(MapList.countPositions(intervals, 6));
+ assertNull(MapList.countPositions(intervals, -6));
+ assertArrayEquals(new int[] { 1, -1 },
+ MapList.countPositions(intervals, 5));
+ assertArrayEquals(new int[] { 7, -1 },
+ MapList.countPositions(intervals, -1));
+ assertArrayEquals(new int[] { 11, -1 },
+ MapList.countPositions(intervals, -5));
+
+ /*
+ * reverse then forward
+ */
+ intervals.add(new int[] { 5, 10 });
+ assertArrayEquals(new int[] { 13, 1 },
+ MapList.countPositions(intervals, 6));
+
+ /*
+ * reverse then forward then reverse
+ */
+ intervals.add(new int[] { -10, -20 });
+ assertArrayEquals(new int[] { 20, -1 },
+ MapList.countPositions(intervals, -12));
+
+ /*
+ * an interval [x, x] is treated as forward
+ */
+ intervals.add(new int[] { 30, 30 });
+ assertArrayEquals(new int[] { 29, 1 },
+ MapList.countPositions(intervals, 30));
+
+ /*
+ * it is the first matched occurrence that is returned
+ */
+ intervals.clear();
+ intervals.add(new int[] { 1, 2 });
+ intervals.add(new int[] { 2, 3 });
+ assertArrayEquals(new int[] { 2, 1 },
+ MapList.countPositions(intervals, 2));
+ intervals.add(new int[] { -1, -2 });
+ intervals.add(new int[] { -2, -3 });
+ assertArrayEquals(new int[] { 6, -1 },
+ MapList.countPositions(intervals, -2));
+ }
+
+ /**
+ * Tests for helper method that adds any overlap (plus offset) to a set of
+ * overlaps
+ */
+ @Test(groups = { "Functional" })
+ public void testAddOffsetPositions()
+ {
+ List<int[]> mapped = new ArrayList<>();
+ int[] range = new int[] { 10, 20 };
+ BitSet offsets = new BitSet();
+
+ MapList.addOffsetPositions(mapped, 0, range, offsets);
+ assertTrue(mapped.isEmpty()); // nothing marked for overlap
+
+ offsets.set(11);
+ MapList.addOffsetPositions(mapped, 0, range, offsets);
+ assertTrue(mapped.isEmpty()); // no offset 11 in range
+
+ offsets.set(4, 6); // this sets bits 4 and 5
+ MapList.addOffsetPositions(mapped, 0, range, offsets);
+ assertEquals(1, mapped.size());
+ assertArrayEquals(new int[] { 14, 15 }, mapped.get(0));
+
+ mapped.clear();
+ offsets.set(10);
+ MapList.addOffsetPositions(mapped, 0, range, offsets);
+ assertEquals(2, mapped.size());
+ assertArrayEquals(new int[] { 14, 15 }, mapped.get(0));
+ assertArrayEquals(new int[] { 20, 20 }, mapped.get(1));
+
+ /*
+ * reverse range
+ */
+ range = new int[] { 20, 10 };
+ mapped.clear();
+ offsets.clear();
+ MapList.addOffsetPositions(mapped, 0, range, offsets);
+ assertTrue(mapped.isEmpty()); // nothing marked for overlap
+ offsets.set(11);
+ MapList.addOffsetPositions(mapped, 0, range, offsets);
+ assertTrue(mapped.isEmpty()); // no offset 11 in range
+ offsets.set(0);
+ offsets.set(10);
+ offsets.set(6, 8); // sets bits 6 and 7
+ MapList.addOffsetPositions(mapped, 0, range, offsets);
+ assertEquals(3, mapped.size());
+ assertArrayEquals(new int[] { 20, 20 }, mapped.get(0));
+ assertArrayEquals(new int[] { 14, 13 }, mapped.get(1));
+ assertArrayEquals(new int[] { 10, 10 }, mapped.get(2));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetPositionsForOffsets()
+ {
+ List<int[]> ranges = new ArrayList<>();
+ BitSet offsets = new BitSet();
+ List<int[]> mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertTrue(mapped.isEmpty()); // no ranges and no offsets!
+
+ offsets.set(5, 1000);
+ mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertTrue(mapped.isEmpty()); // no ranges
+
+ /*
+ * one range with overlap of offsets
+ */
+ ranges.add(new int[] { 15, 25 });
+ mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertEquals(1, mapped.size());
+ assertArrayEquals(new int[] { 20, 25 }, mapped.get(0));
+
+ /*
+ * two ranges
+ */
+ ranges.add(new int[] { 300, 320 });
+ mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertEquals(2, mapped.size());
+ assertArrayEquals(new int[] { 20, 25 }, mapped.get(0));
+ assertArrayEquals(new int[] { 300, 320 }, mapped.get(1));
+
+ /*
+ * boundary case - right end of first range overlaps
+ */
+ offsets.clear();
+ offsets.set(10);
+ mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertEquals(1, mapped.size());
+ assertArrayEquals(new int[] { 25, 25 }, mapped.get(0));
+
+ /*
+ * boundary case - left end of second range overlaps
+ */
+ offsets.set(11);
+ mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertEquals(2, mapped.size());
+ assertArrayEquals(new int[] { 25, 25 }, mapped.get(0));
+ assertArrayEquals(new int[] { 300, 300 }, mapped.get(1));
+
+ /*
+ * offsets into a circular range are reported in
+ * the order in which they are traversed
+ */
+ ranges.clear();
+ ranges.add(new int[] { 100, 150 });
+ ranges.add(new int[] { 60, 80 });
+ offsets.clear();
+ offsets.set(45, 55); // sets bits 45 to 54
+ mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertEquals(2, mapped.size());
+ assertArrayEquals(new int[] { 145, 150 }, mapped.get(0)); // offsets 45-50
+ assertArrayEquals(new int[] { 60, 63 }, mapped.get(1)); // offsets 51-54
+
+ /*
+ * reverse range overlap is reported with start < end
+ */
+ ranges.clear();
+ ranges.add(new int[] { 4321, 4000 });
+ offsets.clear();
+ offsets.set(20, 22); // sets bits 20 and 21
+ offsets.set(30);
+ mapped = MapList.getPositionsForOffsets(ranges, offsets);
+ assertEquals(2, mapped.size());
+ assertArrayEquals(new int[] { 4301, 4300 }, mapped.get(0));
+ assertArrayEquals(new int[] { 4291, 4291 }, mapped.get(1));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetMappedOffsetsForPositions()
+ {
+ /*
+ * start by verifying the examples in the method's Javadoc!
+ */
+ List<int[]> ranges = new ArrayList<>();
+ ranges.add(new int[] { 10, 20 });
+ ranges.add(new int[] { 31, 40 });
+ BitSet overlaps = MapList.getMappedOffsetsForPositions(1, 9, ranges, 1,
+ 1);
+ assertTrue(overlaps.isEmpty());
+ overlaps = MapList.getMappedOffsetsForPositions(1, 11, ranges, 1, 1);
+ assertEquals(2, overlaps.cardinality());
+ assertTrue(overlaps.get(0));
+ assertTrue(overlaps.get(1));
+ overlaps = MapList.getMappedOffsetsForPositions(15, 35, ranges, 1, 1);
+ assertEquals(11, overlaps.cardinality());
+ for (int i = 5; i <= 11; i++)
+ {
+ assertTrue(overlaps.get(i));
+ }
+
+ ranges.clear();
+ ranges.add(new int[] { 1, 200 });
+ overlaps = MapList.getMappedOffsetsForPositions(9, 9, ranges, 1, 3);
+ assertEquals(3, overlaps.cardinality());
+ assertTrue(overlaps.get(24));
+ assertTrue(overlaps.get(25));
+ assertTrue(overlaps.get(26));
+
+ ranges.clear();
+ ranges.add(new int[] { 101, 150 });
+ ranges.add(new int[] { 171, 180 });
+ overlaps = MapList.getMappedOffsetsForPositions(101, 102, ranges, 3, 1);
+ assertEquals(1, overlaps.cardinality());
+ assertTrue(overlaps.get(0));
+ overlaps = MapList.getMappedOffsetsForPositions(150, 171, ranges, 3, 1);
+ assertEquals(1, overlaps.cardinality());
+ assertTrue(overlaps.get(16));
+
+ ranges.clear();
+ ranges.add(new int[] { 101, 150 });
+ ranges.add(new int[] { 21, 30 });
+ overlaps = MapList.getMappedOffsetsForPositions(24, 40, ranges, 3, 1);
+ assertEquals(3, overlaps.cardinality());
+ assertTrue(overlaps.get(17));
+ assertTrue(overlaps.get(18));
+ assertTrue(overlaps.get(19));
+
+ /*
+ * reverse range 1:1 (e.g. reverse strand gene to transcript)
+ */
+ ranges.clear();
+ ranges.add(new int[] { 20, 10 });
+ overlaps = MapList.getMappedOffsetsForPositions(12, 13, ranges, 1, 1);
+ assertEquals(2, overlaps.cardinality());
+ assertTrue(overlaps.get(7));
+ assertTrue(overlaps.get(8));
+
+ /*
+ * reverse range 3:1 (e.g. reverse strand gene to peptide)
+ * from EMBL:J03321 to P0CE20
+ */
+ ranges.clear();
+ ranges.add(new int[] { 1480, 488 });
+ overlaps = MapList.getMappedOffsetsForPositions(1460, 1460, ranges, 3,
+ 1);
+ // 1460 is the end of the 7th codon
+ assertEquals(1, overlaps.cardinality());
+ assertTrue(overlaps.get(6));
+ // add one base (part codon)
+ overlaps = MapList.getMappedOffsetsForPositions(1459, 1460, ranges, 3,
+ 1);
+ assertEquals(2, overlaps.cardinality());
+ assertTrue(overlaps.get(6));
+ assertTrue(overlaps.get(7));
+ // add second base (part codon)
+ overlaps = MapList.getMappedOffsetsForPositions(1458, 1460, ranges, 3,
+ 1);
+ assertEquals(2, overlaps.cardinality());
+ assertTrue(overlaps.get(6));
+ assertTrue(overlaps.get(7));
+ // add third base (whole codon)
+ overlaps = MapList.getMappedOffsetsForPositions(1457, 1460, ranges, 3,
+ 1);
+ assertEquals(2, overlaps.cardinality());
+ assertTrue(overlaps.get(6));
+ assertTrue(overlaps.get(7));
+ // add one more base (part codon)
+ overlaps = MapList.getMappedOffsetsForPositions(1456, 1460, ranges, 3,
+ 1);
+ assertEquals(3, overlaps.cardinality());
+ assertTrue(overlaps.get(6));
+ assertTrue(overlaps.get(7));
+ assertTrue(overlaps.get(8));
+ }
}
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
import jalview.api.AlignViewportI;
+import jalview.bin.Console;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
-import java.awt.Color;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Iterator;
-import java.util.List;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
public class MappingUtilsTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Console.initLogger();
+ }
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
MapList map = new MapList(new int[] { 5, 10 }, new int[] { 12, 13 }, 3,
1);
acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
- { acf });
+ List<AlignedCodonFrame> acfList = Arrays
+ .asList(new AlignedCodonFrame[]
+ { acf });
/*
* Check protein residue 12 maps to codon 5-7, 13 to codon 8-10
* Map dna bases [6, 8, 9], [11, 13, 115] to protein residues 8 and 9
*/
AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList map = new MapList(new int[] { 6, 6, 8, 9, 11, 11, 13, 13, 15,
- 15 }, new int[] { 8, 9 }, 3, 1);
+ MapList map = new MapList(
+ new int[]
+ { 6, 6, 8, 9, 11, 11, 13, 13, 15, 15 }, new int[] { 8, 9 }, 3,
+ 1);
acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
- { acf });
+ List<AlignedCodonFrame> acfList = Arrays
+ .asList(new AlignedCodonFrame[]
+ { acf });
/*
* Check protein residue 8 maps to [6, 8, 9]
for (int i = 5; i < 18; i++)
{
sr = MappingUtils.buildSearchResults(seq1, i, acfList);
- int residue = (i == 6 || i == 8 || i == 9) ? 8 : (i == 11 || i == 13
- || i == 15 ? 9 : 0);
+ int residue = (i == 6 || i == 8 || i == 9) ? 8
+ : (i == 11 || i == 13 || i == 15 ? 9 : 0);
if (residue == 0)
{
assertEquals(0, sr.getResults().size());
MapList map = new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 3, 1);
for (int seq = 0; seq < 3; seq++)
{
- acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
- .getSequenceAt(seq).getDatasetSequence(), map);
+ acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(),
+ protein.getSequenceAt(seq).getDatasetSequence(), map);
}
- List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
- { acf });
+ List<AlignedCodonFrame> acfList = Arrays
+ .asList(new AlignedCodonFrame[]
+ { acf });
AlignViewportI dnaView = new AlignViewport(cdna);
AlignViewportI proteinView = new AlignViewport(protein);
protein.setCodonFrames(acfList);
/*
- * Select Seq1 and Seq3 in the protein (startRes=endRes=0)
+ * Select Seq1 and Seq3 in the protein
*/
SequenceGroup sg = new SequenceGroup();
sg.setColourText(true);
sg.setOutlineColour(Color.LIGHT_GRAY);
sg.addSequence(protein.getSequenceAt(0), false);
sg.addSequence(protein.getSequenceAt(2), false);
+ sg.setEndRes(protein.getWidth() - 1);
/*
* Verify the mapped sequence group in dna
assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0));
assertSame(cdna.getSequenceAt(2), mappedGroup.getSequences().get(1));
assertEquals(0, mappedGroup.getStartRes());
- assertEquals(2, mappedGroup.getEndRes());
+ assertEquals(2, mappedGroup.getEndRes()); // 3 columns (1 codon)
/*
* Verify mapping sequence group from dna to protein
protected AlignmentI loadAlignment(final String data, FileFormatI format)
throws IOException
{
- AlignmentI a = new FormatAdapter().readFile(data,
- DataSourceType.PASTE, format);
+ AlignmentI a = new FormatAdapter().readFile(data, DataSourceType.PASTE,
+ format);
a.setDataset(null);
return a;
}
cs.clear();
colsel.clear();
colsel.addElement(2);
- MappingUtils.mapColumnSelection(colsel, hidden, proteinView,
- dnaView, cs, hs);
+ MappingUtils.mapColumnSelection(colsel, hidden, proteinView, dnaView,
+ cs, hs);
assertEquals("[]", cs.getSelected().toString());
/*
cs.clear();
colsel.clear();
colsel.addElement(3);
- MappingUtils.mapColumnSelection(colsel, hidden, proteinView,
- dnaView, cs, hs);
+ MappingUtils.mapColumnSelection(colsel, hidden, proteinView, dnaView,
+ cs, hs);
assertEquals("[5, 6, 7, 8, 9, 10]", cs.getSelected().toString());
/*
colsel.clear();
colsel.addElement(1);
colsel.addElement(3);
- MappingUtils.mapColumnSelection(colsel, hidden, proteinView,
- dnaView, cs, hs);
- assertEquals("[0, 1, 2, 3, 5, 6, 7, 8, 9, 10]", cs.getSelected()
- .toString());
+ MappingUtils.mapColumnSelection(colsel, hidden, proteinView, dnaView,
+ cs, hs);
+ assertEquals("[0, 1, 2, 3, 5, 6, 7, 8, 9, 10]",
+ cs.getSelected().toString());
}
/**
// map first dna to first protein seq
AlignedCodonFrame acf = new AlignedCodonFrame();
MapList map = new MapList(new int[] { 10, 12, 15, 15, 17, 18 },
- new int[] { 40, 41 }, 3, 1);
- acf.addMap(cdna.getSequenceAt(0).getDatasetSequence(), protein
- .getSequenceAt(0).getDatasetSequence(), map);
+ new int[]
+ { 40, 41 }, 3, 1);
+ acf.addMap(cdna.getSequenceAt(0).getDatasetSequence(),
+ protein.getSequenceAt(0).getDatasetSequence(), map);
// map second dna to second protein seq
- map = new MapList(new int[] { 20, 20, 22, 23, 24, 26 }, new int[] { 50,
- 51 }, 3, 1);
- acf.addMap(cdna.getSequenceAt(1).getDatasetSequence(), protein
- .getSequenceAt(1).getDatasetSequence(), map);
+ map = new MapList(new int[] { 20, 20, 22, 23, 24, 26 },
+ new int[]
+ { 50, 51 }, 3, 1);
+ acf.addMap(cdna.getSequenceAt(1).getDatasetSequence(),
+ protein.getSequenceAt(1).getDatasetSequence(), map);
// map third dna to third protein seq
- map = new MapList(new int[] { 30, 30, 32, 34, 36, 37 }, new int[] { 60,
- 61 }, 3, 1);
- acf.addMap(cdna.getSequenceAt(2).getDatasetSequence(), protein
- .getSequenceAt(2).getDatasetSequence(), map);
- List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
- { acf });
+ map = new MapList(new int[] { 30, 30, 32, 34, 36, 37 },
+ new int[]
+ { 60, 61 }, 3, 1);
+ acf.addMap(cdna.getSequenceAt(2).getDatasetSequence(),
+ protein.getSequenceAt(2).getDatasetSequence(), map);
+ List<AlignedCodonFrame> acfList = Arrays
+ .asList(new AlignedCodonFrame[]
+ { acf });
dnaView = new AlignViewport(cdna);
proteinView = new AlignViewport(protein);
public void testFlattenRanges()
{
assertEquals("[1, 2, 3, 4]",
- Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 4 })));
- assertEquals(
- "[1, 2, 3, 4]",
- Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 2, 3,
- 4 })));
- assertEquals(
- "[1, 2, 3, 4]",
- Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 1, 2,
- 2, 3, 3, 4, 4 })));
- assertEquals(
- "[1, 2, 3, 4, 7, 8, 9, 12]",
- Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 4, 7,
- 9, 12, 12 })));
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 1, 4 })));
+ assertEquals("[1, 2, 3, 4]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 1, 2, 3, 4 })));
+ assertEquals("[1, 2, 3, 4]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 1, 1, 2, 2, 3, 3, 4, 4 })));
+ assertEquals("[1, 2, 3, 4, 7, 8, 9, 12]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 1, 4, 7, 9, 12, 12 })));
// trailing unpaired start position is ignored:
- assertEquals(
- "[1, 2, 3, 4, 7, 8, 9, 12]",
- Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 4, 7,
- 9, 12, 12, 15 })));
+ assertEquals("[1, 2, 3, 4, 7, 8, 9, 12]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 1, 4, 7, 9, 12, 12, 15 })));
}
/**
MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
for (int seq = 0; seq < 3; seq++)
{
- acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
- .getSequenceAt(seq).getDatasetSequence(), map);
+ acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(),
+ protein.getSequenceAt(seq).getDatasetSequence(), map);
}
- List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
- { acf });
+ List<AlignedCodonFrame> acfList = Arrays
+ .asList(new AlignedCodonFrame[]
+ { acf });
AlignViewportI dnaView = new AlignViewport(cdna);
AlignViewportI proteinView = new AlignViewport(protein);
FileFormat.Fasta);
cdna.setDataset(null);
AlignmentI protein = loadAlignment(
- ">Seq1\n-KA-S\n>Seq2\n--L-QY\n>Seq3\nQ-V-M\n", FileFormat.Fasta);
+ ">Seq1\n-KA-S\n>Seq2\n--L-QY\n>Seq3\nQ-V-M\n",
+ FileFormat.Fasta);
protein.setDataset(null);
AlignedCodonFrame acf = new AlignedCodonFrame();
MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1);
for (int seq = 0; seq < 3; seq++)
{
- acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
- .getSequenceAt(seq).getDatasetSequence(), map);
+ acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(),
+ protein.getSequenceAt(seq).getDatasetSequence(), map);
}
- List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
- { acf });
+ List<AlignedCodonFrame> acfList = Arrays
+ .asList(new AlignedCodonFrame[]
+ { acf });
AlignViewportI dnaView = new AlignViewport(cdna);
AlignViewportI proteinView = new AlignViewport(protein);
/*
* Seq1 has three mappings
*/
- List<AlignedCodonFrame> result = MappingUtils.findMappingsForSequence(
- seq1, mappings);
+ List<AlignedCodonFrame> result = MappingUtils
+ .findMappingsForSequence(seq1, mappings);
assertEquals(3, result.size());
assertTrue(result.contains(acf1));
assertTrue(result.contains(acf2));
*/
List<AlignedCodonFrame> result = MappingUtils
.findMappingsForSequenceAndOthers(null, mappings,
- Arrays.asList(new SequenceI[] { seq1, seq2 }));
+ Arrays.asList(new SequenceI[]
+ { seq1, seq2 }));
assertTrue(result.isEmpty());
result = MappingUtils.findMappingsForSequenceAndOthers(seq1, null,
- Arrays.asList(new SequenceI[] { seq1, seq2 }));
+ Arrays.asList(new SequenceI[]
+ { seq1, seq2 }));
assertTrue(result.isEmpty());
/*
* Seq1 has three mappings, but filter argument will only accept
* those to seq2
*/
- result = MappingUtils.findMappingsForSequenceAndOthers(
- seq1,
- mappings,
- Arrays.asList(new SequenceI[] { seq1, seq2,
- seq1.getDatasetSequence() }));
+ result = MappingUtils.findMappingsForSequenceAndOthers(seq1, mappings,
+ Arrays.asList(new SequenceI[]
+ { seq1, seq2, seq1.getDatasetSequence() }));
assertEquals(2, result.size());
assertTrue(result.contains(acf1));
assertTrue(result.contains(acf2));
dna.createDatasetSequence();
protein.createDatasetSequence();
AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList map = new MapList(new int[] { 8, 16 }, new int[] { 5, 7 }, 3, 1);
+ MapList map = new MapList(new int[] { 8, 16 }, new int[] { 5, 7 }, 3,
+ 1);
acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
List<AlignedCodonFrame> mappings = new ArrayList<>();
mappings.add(acf);
*/
EditCommand ec = new EditCommand();
final Edit edit = ec.new Edit(Action.INSERT_GAP,
- new SequenceI[] { protein }, 4, 2, '-');
+ new SequenceI[]
+ { protein }, 4, 2, '-');
ec.appendEdit(edit, prot, true, null);
/*
public void testFlattenRanges_reverseStrand()
{
assertEquals("[4, 3, 2, 1]",
- Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 1 })));
- assertEquals(
- "[4, 3, 2, 1]",
- Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 3, 2,
- 1 })));
- assertEquals(
- "[4, 3, 2, 1]",
- Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 4, 3,
- 3, 2, 2, 1, 1 })));
- assertEquals(
- "[12, 9, 8, 7, 4, 3, 2, 1]",
- Arrays.toString(MappingUtils.flattenRanges(new int[] { 12, 12,
- 9, 7, 4, 1 })));
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 4, 1 })));
+ assertEquals("[4, 3, 2, 1]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 4, 3, 2, 1 })));
+ assertEquals("[4, 3, 2, 1]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 4, 4, 3, 3, 2, 2, 1, 1 })));
+ assertEquals("[12, 9, 8, 7, 4, 3, 2, 1]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 12, 12, 9, 7, 4, 1 })));
// forwards and backwards anyone?
- assertEquals(
- "[4, 5, 6, 3, 2, 1]",
- Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 6, 3,
- 1 })));
+ assertEquals("[4, 5, 6, 3, 2, 1]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 4, 6, 3, 1 })));
// backwards and forwards
- assertEquals(
- "[3, 2, 1, 4, 5, 6]",
- Arrays.toString(MappingUtils.flattenRanges(new int[] { 3, 1, 4,
- 6 })));
+ assertEquals("[3, 2, 1, 4, 5, 6]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 3, 1, 4, 6 })));
// trailing unpaired start position is ignored:
- assertEquals(
- "[12, 9, 8, 7, 4, 3, 2]",
- Arrays.toString(MappingUtils.flattenRanges(new int[] { 12, 12,
- 9, 7, 4, 2, 1 })));
+ assertEquals("[12, 9, 8, 7, 4, 3, 2]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 12, 12, 9, 7, 4, 2, 1 })));
}
/**
/*
* both forward ranges
*/
- assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
- 1, 10 }));
- assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
- 2, 10 }));
- assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
- 1, 9 }));
- assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
- 4, 5 }));
- assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
- 0, 9 }));
- assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
- -10, -9 }));
- assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
- 1, 11 }));
- assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
- 11, 12 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10 }, new int[] { 1, 10 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10 }, new int[] { 2, 10 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10 }, new int[] { 1, 9 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10 }, new int[] { 4, 5 }));
+ assertFalse(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10 }, new int[] { 0, 9 }));
+ assertFalse(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10 }, new int[] { -10, -9 }));
+ assertFalse(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10 }, new int[] { 1, 11 }));
+ assertFalse(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10 }, new int[] { 11, 12 }));
/*
* forward range, reverse query
*/
- assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
- 10, 1 }));
- assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
- 9, 1 }));
- assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
- 10, 2 }));
- assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
- 5, 5 }));
- assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
- 11, 1 }));
- assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
- 10, 0 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10 }, new int[] { 10, 1 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10 }, new int[] { 9, 1 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10 }, new int[] { 10, 2 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10 }, new int[] { 5, 5 }));
+ assertFalse(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10 }, new int[] { 11, 1 }));
+ assertFalse(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10 }, new int[] { 10, 0 }));
/*
* reverse range, forward query
*/
- assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
- 1, 10 }));
- assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
- 1, 9 }));
- assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
- 2, 10 }));
- assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
- 6, 6 }));
- assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
- 6, 11 }));
- assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
- 11, 20 }));
- assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
- -3, -2 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 10, 1 }, new int[] { 1, 10 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 10, 1 }, new int[] { 1, 9 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 10, 1 }, new int[] { 2, 10 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 10, 1 }, new int[] { 6, 6 }));
+ assertFalse(
+ MappingUtils.rangeContains(new int[]
+ { 10, 1 }, new int[] { 6, 11 }));
+ assertFalse(
+ MappingUtils.rangeContains(new int[]
+ { 10, 1 }, new int[] { 11, 20 }));
+ assertFalse(
+ MappingUtils.rangeContains(new int[]
+ { 10, 1 }, new int[] { -3, -2 }));
/*
* both reverse
*/
- assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
- 10, 1 }));
- assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
- 9, 1 }));
- assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
- 10, 2 }));
- assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
- 3, 3 }));
- assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
- 11, 1 }));
- assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
- 10, 0 }));
- assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
- 12, 11 }));
- assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
- -5, -8 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 10, 1 }, new int[] { 10, 1 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 10, 1 }, new int[] { 9, 1 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 10, 1 }, new int[] { 10, 2 }));
+ assertTrue(
+ MappingUtils.rangeContains(new int[]
+ { 10, 1 }, new int[] { 3, 3 }));
+ assertFalse(
+ MappingUtils.rangeContains(new int[]
+ { 10, 1 }, new int[] { 11, 1 }));
+ assertFalse(
+ MappingUtils.rangeContains(new int[]
+ { 10, 1 }, new int[] { 10, 0 }));
+ assertFalse(
+ MappingUtils.rangeContains(new int[]
+ { 10, 1 }, new int[] { 12, 11 }));
+ assertFalse(
+ MappingUtils.rangeContains(new int[]
+ { 10, 1 }, new int[] { -5, -8 }));
/*
* bad arguments
*/
- assertFalse(MappingUtils.rangeContains(new int[] { 1, 10, 12 },
- new int[] {
- 1, 10 }));
- assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 },
- new int[] { 1 }));
+ assertFalse(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10, 12 }, new int[] { 1, 10 }));
+ assertFalse(
+ MappingUtils.rangeContains(new int[]
+ { 1, 10 }, new int[] { 1 }));
assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, null));
assertFalse(MappingUtils.rangeContains(null, new int[] { 1, 10 }));
}
assertEquals(1, ranges.size());
assertEquals(9, ranges.get(0)[1]);
}
+
+ @Test(groups = "Functional")
+ public void testFindOverlap()
+ {
+ List<int[]> ranges = new ArrayList<>();
+ ranges.add(new int[] { 4, 8 });
+ ranges.add(new int[] { 10, 12 });
+ ranges.add(new int[] { 16, 19 });
+
+ int[] overlap = MappingUtils.findOverlap(ranges, 5, 13);
+ assertArrayEquals(overlap, new int[] { 5, 12 });
+ overlap = MappingUtils.findOverlap(ranges, -100, 100);
+ assertArrayEquals(overlap, new int[] { 4, 19 });
+ overlap = MappingUtils.findOverlap(ranges, 7, 17);
+ assertArrayEquals(overlap, new int[] { 7, 17 });
+ overlap = MappingUtils.findOverlap(ranges, 13, 15);
+ assertNull(overlap);
+ }
+
+ /**
+ * Test mapping a sequence group where sequences in and outside the group
+ * share a dataset sequence (e.g. alternative CDS for the same gene)
+ * <p>
+ * This scenario doesn't arise after JAL-3763 changes, but test left as still valid
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testMapSequenceGroup_sharedDataset() throws IOException
+ {
+ /*
+ * Set up dna and protein Seq1/2/3 with mappings (held on the protein
+ * viewport). CDS sequences share the same 'gene' dataset sequence.
+ */
+ SequenceI dna = new Sequence("dna", "aaatttgggcccaaatttgggccc");
+ SequenceI cds1 = new Sequence("cds1/1-6", "aaattt");
+ SequenceI cds2 = new Sequence("cds1/4-9", "tttggg");
+ SequenceI cds3 = new Sequence("cds1/19-24", "gggccc");
+
+ cds1.setDatasetSequence(dna);
+ cds2.setDatasetSequence(dna);
+ cds3.setDatasetSequence(dna);
+
+ SequenceI pep1 = new Sequence("pep1", "KF");
+ SequenceI pep2 = new Sequence("pep2", "FG");
+ SequenceI pep3 = new Sequence("pep3", "GP");
+ pep1.createDatasetSequence();
+ pep2.createDatasetSequence();
+ pep3.createDatasetSequence();
+
+ /*
+ * add mappings from coding positions of dna to respective peptides
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(dna, pep1,
+ new MapList(new int[]
+ { 1, 6 }, new int[] { 1, 2 }, 3, 1));
+ acf.addMap(dna, pep2,
+ new MapList(new int[]
+ { 4, 9 }, new int[] { 1, 2 }, 3, 1));
+ acf.addMap(dna, pep3,
+ new MapList(new int[]
+ { 19, 24 }, new int[] { 1, 2 }, 3, 1));
+
+ List<AlignedCodonFrame> acfList = Arrays
+ .asList(new AlignedCodonFrame[]
+ { acf });
+
+ AlignmentI cdna = new Alignment(new SequenceI[] { cds1, cds2, cds3 });
+ AlignmentI protein = new Alignment(
+ new SequenceI[]
+ { pep1, pep2, pep3 });
+ AlignViewportI cdnaView = new AlignViewport(cdna);
+ AlignViewportI peptideView = new AlignViewport(protein);
+ protein.setCodonFrames(acfList);
+
+ /*
+ * Select pep1 and pep3 in the protein alignment
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setColourText(true);
+ sg.setIdColour(Color.GREEN);
+ sg.setOutlineColour(Color.LIGHT_GRAY);
+ sg.addSequence(pep1, false);
+ sg.addSequence(pep3, false);
+ sg.setEndRes(protein.getWidth() - 1);
+
+ /*
+ * Verify the mapped sequence group in dna is cds1 and cds3
+ */
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
+ peptideView, cdnaView);
+ assertTrue(mappedGroup.getColourText());
+ assertSame(sg.getIdColour(), mappedGroup.getIdColour());
+ assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
+ assertEquals(2, mappedGroup.getSequences().size());
+ assertSame(cds1, mappedGroup.getSequences().get(0));
+ assertSame(cds3, mappedGroup.getSequences().get(1));
+ // columns 1-6 selected (0-5 base zero)
+ assertEquals(0, mappedGroup.getStartRes());
+ assertEquals(5, mappedGroup.getEndRes());
+
+ /*
+ * Select mapping sequence group from dna to protein
+ */
+ sg.clear();
+ sg.addSequence(cds2, false);
+ sg.addSequence(cds1, false);
+ sg.setStartRes(0);
+ sg.setEndRes(cdna.getWidth() - 1);
+ mappedGroup = MappingUtils.mapSequenceGroup(sg, cdnaView, peptideView);
+ assertTrue(mappedGroup.getColourText());
+ assertSame(sg.getIdColour(), mappedGroup.getIdColour());
+ assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
+ assertEquals(2, mappedGroup.getSequences().size());
+ assertSame(protein.getSequenceAt(1), mappedGroup.getSequences().get(0));
+ assertSame(protein.getSequenceAt(0), mappedGroup.getSequences().get(1));
+ assertEquals(0, mappedGroup.getStartRes());
+ assertEquals(1, mappedGroup.getEndRes()); // two columns
+ }
}
--- /dev/null
+#---JalviewX Properties File---
+# HiDPI screen
+SCREENGEOMETRY_WIDTH=3840
+SCREENGEOMETRY_HEIGHT=2160
+SCREEN_WIDTH=3000
+SCREEN_HEIGHT=2000
+USAGESTATS=false
+STARTUP_FILE=examples/uniref50.fa
+SHOW_STARTUP_FILE=false
+FONT_STYLE=plain
+FONT_SIZE=10
+ANTI_ALIAS=false
+SHOW_JAVA_CONSOLE=false
+DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
+logs.Jalview.level=DEBUG
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import java.io.ByteArrayInputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
import jalview.xml.binding.embl.XrefType;
-import java.io.ByteArrayInputStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.testng.annotations.Test;
-
-public class EmblSourceTest
+public class EmblXmlSourceTest
{
// adapted from http://www.ebi.ac.uk/ena/data/view/X07547&display=xml
+ "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT"
+ "</sequence></entry></ROOT>";
+ private EmblXmlSource testee;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ testee = new EmblXmlSource()
+ {
+
+ @Override
+ public String getDbSource()
+ {
+ return null;
+ }
+
+ @Override
+ public String getDbName()
+ {
+ return null;
+ }
+
+ @Override
+ public String getTestQuery()
+ {
+ return null;
+ }
+
+ @Override
+ public AlignmentI getSequenceRecords(String queries) throws Exception
+ {
+ return null;
+ }
+ };
+ }
+
@Test(groups = "Functional")
public void testGetCdsRanges()
{
- EmblSource testee = new EmblSource();
-
/*
* Make a (CDS) Feature with 5 locations
*/
Feature cds = new Feature();
- cds.setLocation("join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
+ cds.setLocation(
+ "join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
int[] exons = testee.getCdsRanges("EMBL", cds);
assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110]",
{
// not the whole sequence but enough for this test...
List<SequenceI> peptides = new ArrayList<>();
- List<EntryType> entries = EmblSourceTest.getEmblEntries();
+ List<EntryType> entries = getEmblEntries();
assertEquals(1, entries.size());
EntryType entry = entries.get(0);
- EmblSource testee = new EmblSource();
String sourceDb = "EMBL";
SequenceI dna = testee.getSequence(sourceDb, entry, peptides);
3, 1);
MapList cds2Map = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 },
3, 1);
- MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 }, new int[] {
- 1, 3 }, 3, 1);
+ MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 },
+ new int[]
+ { 1, 3 }, 3, 1);
List<DBRefEntry> dbrefs = dna.getDBRefs();
assertEquals(7, dbrefs.size());
* - to EMBLCDS (with 1:3 mapping)
* - direct (no mapping) to other protein accessions
*/
- MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 }, new int[] {
- 1, 12 }, 1, 3);
- MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 }, new int[] {
- 1, 9 }, 1, 3);
+ MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 },
+ new int[]
+ { 1, 12 }, 1, 3);
+ MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 },
+ new int[]
+ { 1, 9 }, 1, 3);
// dbrefs for first CDS EMBL product CAA30420.1
dbrefs = peptides.get(0).getDBRefs();
// exact length match:
assertSame(exons, EmblXmlSource.adjustForProteinLength(6, exons));
- // match if we assume exons include stop codon not in protein:
- assertSame(exons, EmblXmlSource.adjustForProteinLength(5, exons));
+ // truncate last exon by 3bp (e.g. stop codon)
+ int[] truncated = EmblXmlSource.adjustForProteinLength(5, exons);
+ assertEquals("[11, 15, 21, 25, 31, 35]", Arrays.toString(truncated));
// truncate last exon by 6bp
- int[] truncated = EmblXmlSource.adjustForProteinLength(4, exons);
+ truncated = EmblXmlSource.adjustForProteinLength(4, exons);
assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
// remove last exon and truncate preceding by 1bp
@Test(groups = { "Functional" })
public void testGetEmblEntries()
{
- List<EntryType> entries = EmblSourceTest.getEmblEntries();
+ List<EntryType> entries = getEmblEntries();
assertEquals(1, entries.size());
EntryType entry = entries.get(0);
-
+
assertEquals("X07547", entry.getAccession());
assertEquals("C. trachomatis plasmid", entry.getDescription());
assertEquals("STD", entry.getDataClass());
assertEquals(2, entry.getKeyword().size());
assertEquals("plasmid", entry.getKeyword().get(0));
assertEquals("unidentified reading frame", entry.getKeyword().get(1));
-
+
/*
* dbrefs
*/
assertEquals("MD5", dbref.getDb());
assertEquals("ac73317", dbref.getId());
assertNull(dbref.getSecondaryId());
-
+
/*
* three sequence features for CDS
*/
q = ef.getQualifier().get(2);
assertEquals("translation", q.getName());
assertEquals("MLCF", q.getValue());
-
+
/*
* second CDS
*/
q = ef.getQualifier().get(1);
assertEquals("translation", q.getName());
assertEquals("MSSS", q.getValue());
-
+
/*
* third CDS
*/
q = ef.getQualifier().get(1);
assertEquals("translation", q.getName());
assertEquals("MSS", q.getValue());
-
+
/*
* Sequence - raw data before removal of newlines
*/
String seq = entry.getSequence();
- assertEquals(
- "GGTATGTCCTCTAGTACAAAC\n"
- + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
- seq);
-
+ assertEquals("GGTATGTCCTCTAGTACAAAC\n"
+ + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT", seq);
+
/*
* getSequence() converts empty DBRefEntry.version to "0"
*/
assertNull(entry.getFeature().get(0).getXref().get(1).getSecondaryId());
}
- static List<EntryType> getEmblEntries()
+ List<EntryType> getEmblEntries()
{
- return new EmblSource()
+ return testee
.getEmblEntries(new ByteArrayInputStream(TESTDATA.getBytes()));
}
}
*/
package jalview.ws.dbsources;
+import static org.testng.Assert.assertFalse;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
+import jalview.util.DBRefUtils;
import jalview.xml.binding.uniprot.DbReferenceType;
import jalview.xml.binding.uniprot.Entry;
import jalview.xml.binding.uniprot.FeatureType;
assertEquals(6, seq.getDBRefs().size()); // 2*Uniprot, PDB, PDBsum, 2*EMBL
assertEquals(seq.getSequenceAsString(),
seq.createDatasetSequence().getSequenceAsString());
+ assertEquals(2,seq.getPrimaryDBRefs().size());
+ List<DBRefEntry> res = DBRefUtils.searchRefs(seq.getPrimaryDBRefs(), "A9CKP4");
+ assertEquals(1,res.size());
+ assertTrue(res.get(0).isCanonical());
+ res = DBRefUtils.searchRefsForSource(seq.getDBRefs(), DBRefSource.UNIPROT);
+ assertEquals(2,res.size());
+ /*
+ * NB this test fragile - relies on ordering being preserved
+ */
+ assertTrue(res.get(0).isCanonical());
+ assertFalse(res.get(1).isCanonical());
}
/**
/*
* EMBL
*/
- assertEquals("https://www.ebi.ac.uk/ena/data/view/x53838&display=xml",
+ assertEquals("https://www.ebi.ac.uk/ena/browser/api/embl/x53838?download=true&gzip=true",
EBIFetchClient.buildUrl("X53838", "EMBL", "display=xml"));
/*
* EMBLCDS
*/
- assertEquals("https://www.ebi.ac.uk/ena/data/view/caa37824&display=xml",
+ assertEquals("https://www.ebi.ac.uk/ena/browser/api/embl/caa37824?download=true&gzip=true",
EBIFetchClient.buildUrl("CAA37824", "EMBL", "display=xml"));
/*
*/
package jalview.ws.gui;
+import java.util.Locale;
+
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.JvOptionPane;
import jalview.gui.WsJobParameters;
import jalview.util.MessageManager;
public static List<String> presetTests = new ArrayList<String>();
static
{
- serviceTests.add("AAConWS".toLowerCase());
+ serviceTests.add("AAConWS".toLowerCase(Locale.ROOT));
}
public static Jws2Discoverer disc = null;
public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.initLogger();
+ Console.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
}
for (Jws2Instance service : disc.getServices())
{
if (serviceTests.size() == 0
- || serviceTests.contains(service.serviceType.toLowerCase()))
+ || serviceTests.contains(service.serviceType.toLowerCase(Locale.ROOT)))
{
List<Preset> prl = null;
Preset pr = null;
*/
package jalview.ws.jabaws;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.JvOptionPane;
public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.initLogger();
+ Console.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
while (disc.isRunning())
iupreds = new ArrayList<Jws2Instance>();
for (Jws2Instance svc : disc.getServices())
{
- if (svc.getServiceTypeURI().toLowerCase().contains("iupredws"))
+ if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT).contains("iupredws"))
{
iupreds.add(svc);
}
*/
package jalview.ws.jabaws;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.JvOptionPane;
public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.initLogger();
+ Console.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
while (disc.isRunning())
for (Jws2Instance svc : disc.getServices())
{
- if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
+ if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT).contains("rnaalifoldws"))
{
rnaalifoldws = svc;
}
*/
package jalview.ws.jws2;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.JvOptionPane;
import jalview.ws.jabaws.JalviewJabawsTestUtils;
import jalview.ws.jws2.jabaws2.Jws2Instance;
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- serviceTests.add("AAConWS".toLowerCase());
+ serviceTests.add("AAConWS".toLowerCase(Locale.ROOT));
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.initLogger();
+ Console.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
}
public boolean isForTesting(Jws2Instance service)
{
return serviceTests.size() == 0
- || serviceTests.contains(service.serviceType.toLowerCase());
+ || serviceTests.contains(service.serviceType.toLowerCase(Locale.ROOT));
}
@Test(groups = { "Network" })
RestClient rc = new RestClient(_rc.service, alf, true);
assertNotNull("Couldn't creat RestClient job.", rc);
- jalview.bin.Cache.initLogger();
+ jalview.bin.Console.initLogger();
RestJob rjb = new RestJob(0, new RestJobThread(rc),
rc.av.getAlignment(), null);
rjb.setAlignmentForInputs(rc.service.getInputParams().values(),
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
import jalview.util.DBRefUtils;
+import jalview.ws.DBRefFetcher;
import jalview.ws.SequenceFetcher;
import jalview.ws.dbsources.EBIAlfaFold;
import jalview.ws.dbsources.Pdb;
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- jalview.bin.Cache.initLogger();
+ jalview.bin.Console.initLogger();
}
/**
{
}
+ @Test(groups= {"Network"})
+ public void checkUniprotCanonicalFlagSet()
+ {
+ // TODO - mock this - for moment it is a live request.
+ SequenceI uniprotSeq = new Sequence("FER1_SPIOL",
+ "MAATTTTMMGMATTFVPKPQAPPMMAALPSNTGRSLFGLKTGSRGGRMTMAAYKVTLVTPTGNVEFQCPDDV"
+ + "YILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEE"
+ + "LTA");
+ DBRefFetcher dbr = new DBRefFetcher(new SequenceI[] { uniprotSeq });
+ dbr.fetchDBRefs(true);
+ List<DBRefEntry> primRefs = uniprotSeq.getPrimaryDBRefs();
+ assertNotNull(primRefs);
+ assertTrue(primRefs.size()>0);
+ boolean canonicalUp=false;
+ for (DBRefEntry ref:primRefs) {
+ assertEquals(DBRefSource.UNIPROT, ref.getCanonicalSourceName());
+ canonicalUp |= ref.isCanonical();
+ }
+ assertTrue("No Canonical Uniprot reference detected", canonicalUp);
+ }
/**
* Tests that standard protein database sources include Uniprot (as the first)
* and also PDB. (Additional sources are dependent on availability of DAS
*/
package junit.extensions;
+import java.util.Locale;
+
import java.lang.reflect.Array;
import java.lang.reflect.Constructor;
import java.lang.reflect.Field;
{
return false;
}
- if (className.startsWith(className.substring(0, 1).toUpperCase()))
+ if (className.startsWith(className.substring(0, 1).toUpperCase(Locale.ROOT)))
{
return true;
}
uod_banner.30=/images/UoD_banner-30.png
uod_banner.32=/images/UoD_banner-32.png
default_appbase=https://www.jalview.org/getdown/release/1.8
-preferences.filename=.jalview_properties
+preferences.filename=.jalview_nonrelease_properties
xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
- width="210mm"
- height="297mm"
- viewBox="0 0 210 297"
+ width="132.29233mm"
+ height="132.29326mm"
+ viewBox="0 0 132.29233 132.29326"
version="1.1"
id="svg8"
- inkscape:version="1.0.1 (0767f8302a, 2020-10-17)"
- sodipodi:docname="JalviewDevelopLogo2.svg">
+ inkscape:version="0.92.5 (2060ec1f9f, 2020-04-08)"
+ sodipodi:docname="jalview_develop_logo.svg">
<defs
id="defs2">
<linearGradient
clipPathUnits="userSpaceOnUse"
id="clipPath1000">
<path
- style="fill:none;stroke:#000000;stroke-width:0.264583px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ style="fill:none;stroke:#000000;stroke-width:0.26458299px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
d="M 87.312506,136.26042 162.71876,190.5 133.61459,206.375 H 107.15626 L 84.666668,186.53125 80.697918,158.75 Z"
- id="path1002" />
+ id="path1002"
+ inkscape:connector-curvature="0" />
</clipPath>
<clipPath
clipPathUnits="userSpaceOnUse"
id="clipPath1093-1">
<rect
- style="fill:#256c7a;fill-opacity:1;stroke:#000000;stroke-width:0.850394;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="fill:#256c7a;fill-opacity:1;stroke:#000000;stroke-width:0.85039401;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="rect1095-8"
width="105"
height="229.99998"
clipPathUnits="userSpaceOnUse"
id="clipPath1281">
<rect
- style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.256539;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.25653899;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="rect1283"
width="34.395832"
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clipPathUnits="userSpaceOnUse"
id="clipPath1285">
<rect
- style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.256539;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
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width="34.395832"
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id="clipPath1333">
<rect
- style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.225;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
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id="rect1335"
width="62.177082"
height="54.239582"
clipPathUnits="userSpaceOnUse"
id="clipPath1375">
<rect
- style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.225;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.22499999;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="rect1377"
width="64.822914"
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clipPathUnits="userSpaceOnUse"
id="clipPath1675">
<rect
- style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.204471;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
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id="rect1677"
width="33.037834"
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id="clipPath1680">
<rect
- style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.515557;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.51555699;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="rect1682"
width="68.626167"
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clipPathUnits="userSpaceOnUse"
id="clipPath1692">
<path
- style="fill:none;stroke:#000000;stroke-width:0.989976px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ style="fill:none;stroke:#000000;stroke-width:0.98997599px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
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- id="path1694" />
+ id="path1694"
+ inkscape:connector-curvature="0" />
</clipPath>
<clipPath
clipPathUnits="userSpaceOnUse"
<path
id="mask-powermask-path-effect945_box"
style="fill:#ffffff;fill-opacity:1"
- d="M 43.979163,54.562507 H 167.06656 V 178.27083 H 43.979163 Z" />
+ d="M 43.979163,54.562507 H 167.06656 V 178.27083 H 43.979163 Z"
+ inkscape:connector-curvature="0" />
<g
id="g943"
style="fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.5;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
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+
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\ No newline at end of file
getdown_instant_background_image = jalview_test-release_getdown_background_initialising.png
getdown_error_background = jalview_test-release_getdown_background_error.png
getdown_progress_image = jalview_getdown_progress_bar.png
-getdown_mac_dock_icon = jalview_logo.icns
-getdown_icon = jalview_logo.png
+getdown_mac_dock_icon = jalview_test-release_logo.icns
+getdown_icon = jalview_test-release_logo.png
getdown_txt_allow_offline = true
getdown_txt_max_concurrent_downloads = 10
getdown_txt_ui.install_error = https://www.jalview.org/faq/getdownerror
getdown_txt_ui.hide_decorations = true
install4j_images_dir = utils/channels/test-release/images
-install4j_mac_icons_file = jalview_logo.icns
-install4j_windows_icons_file = jalview_logo.ico
-install4j_png_icon_file = jalview_logo.png
+install4j_mac_icons_file = jalview_test-release_logo.icns
+install4j_windows_icons_file = jalview_test-release_logo.ico
+install4j_png_icon_file = jalview_test-release_logo.png
install4j_background = jalview_logo_background_fade-640x480.png
install4j_dmg_background = jalview_test-release_dmg_background-72dpi.png
install4j_dmg_ds_store = jalview_test-release_dmg_DS_Store
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app_name=Jalview Test
banner=/images/jalview_test-release_banner.png
-logo.16=/images/jalview_logo-16.png
-logo.32=/images/jalview_logo-32.png
-logo.38=/images/jalview_logo-38.png
-logo.48=/images/jalview_logo-48.png
-logo.64=/images/jalview_logo-64.png
-logo.128=/images/jalview_logo-128.png
-logo.256=/images/jalview_logo-256.png
-logo.512=/images/jalview_logo-512.png
-rotatable_logo.48=/images/rotatable_jalview_logo-38.png
+logo.16=/images/jalview_test-release_logo-16.png
+logo.32=/images/jalview_test-release_logo-32.png
+logo.38=/images/jalview_test-release_logo-38.png
+logo.48=/images/jalview_test-release_logo-48.png
+logo.64=/images/jalview_test-release_logo-64.png
+logo.128=/images/jalview_test-release_logo-128.png
+logo.256=/images/jalview_test-release_logo-256.png
+logo.512=/images/jalview_test-release_logo-512.png
+rotatable_logo.48=/images/rotatable_jalview_test-release_logo-38.png
bg_logo.28=/images/barton_group-28.png
bg_logo.30=/images/barton_group-30.png
bg_logo.32=/images/barton_group-32.png
uod_banner.28=/images/UoD_banner-28.png
uod_banner.30=/images/UoD_banner-30.png
uod_banner.32=/images/UoD_banner-32.png
-default_appbase=https://www.jalview.org/getdown/release/1.8
-preferences.filename=.jalview_properties
+default_appbase=https://www.jalview.org/getdown/test-release/1.8
+preferences.filename=.jalview_test_properties
+++ /dev/null
-#!/usr/bin/env bash
-
-# given a list of differently sized png files with the size in the filename like this:
-# myiconfile-16.png myiconfile-32.png myiconfile-48.png myiconfile-64.png myiconfile-128.png myiconfile-256.png myiconfile-512.png
-# run
-# create_iconfiles.sh myiconfile-*.png
-# to create an ICO file (for Windows) myiconfile.ico and an ICNS file (for macOS) myiconfile.icns
-
-BASENAME=${1%-*}
-if [ x$BASENAME = x ]; then
- echo "Could not calculate basename from '${1}'"
- exit 1
-fi
-
-ICOFILE=${BASENAME}.ico
-echo "Creating ${ICOFILE}"
-convert $* ${ICOFILE}
-
-ICNSFILE=${BASENAME}.icns
-echo "Creating ${ICNSFILE}"
-# dont' include 64x64 icon (for some reason they're not allowed in icns file)
-ICNSARGS=""
-for ARG in $*; do
- NUM=${ARG##*-}
- NUM=${NUM%px*}
- NUM=${NUM%x*}
- NUM=${NUM%.*}
- if [ x$NUM != x64 -a x$NUM != x38 ]; then
- ICNSARGS="${ICNSARGS} $ARG"
- fi
-done
-png2icns ${ICNSFILE} ${ICNSARGS}
--- /dev/null
+--- a/build.gradle 2021-09-21 09:52:04.653972716 +0100
++++ b/build.gradle 2021-09-21 09:52:18.117985307 +0100
+@@ -2,56 +2,12 @@
+ * For properties set within build.gradle, use camelCaseNoSpace.
+ */
+ import org.apache.tools.ant.filters.ReplaceTokens
+-import org.gradle.internal.os.OperatingSystem
+-import org.gradle.plugins.ide.internal.generator.PropertiesPersistableConfigurationObject
+-import org.gradle.api.internal.PropertiesTransformer
+-import org.gradle.util.ConfigureUtil
+-import org.gradle.plugins.ide.eclipse.model.Output
+-import org.gradle.plugins.ide.eclipse.model.Library
+-import java.security.MessageDigest
+-import groovy.transform.ExternalizeMethods
+-import groovy.util.XmlParser
+-import groovy.xml.XmlUtil
+-import com.vladsch.flexmark.util.ast.Node
+-import com.vladsch.flexmark.html.HtmlRenderer
+-import com.vladsch.flexmark.parser.Parser
+-import com.vladsch.flexmark.util.data.MutableDataSet
+-import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
+-import com.vladsch.flexmark.ext.tables.TablesExtension
+-import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
+-import com.vladsch.flexmark.ext.autolink.AutolinkExtension
+-import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
+-import com.vladsch.flexmark.ext.toc.TocExtension
+-
+-buildscript {
+- repositories {
+- mavenCentral()
+- mavenLocal()
+- }
+- dependencies {
+- classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
+- }
+-}
+-
+
+ plugins {
+ id 'java'
+ id 'application'
+- id 'eclipse'
+- id "com.diffplug.gradle.spotless" version "3.28.0"
+- id 'com.github.johnrengelman.shadow' version '4.0.3'
+- id 'com.install4j.gradle' version '8.0.10'
+- id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
+- id 'com.palantir.git-version' version '0.12.3'
+-}
+-
+-repositories {
+- jcenter()
+- mavenCentral()
+- mavenLocal()
+ }
+
+-
+ // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
+ def string(Object o) {
+ return o == null ? "" : o.toString()
+@@ -92,23 +48,15 @@
+ }
+ }
+
+-ext {
++project.ext {
+ jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+ jalviewDirRelativePath = jalviewDir
+
+- getdownChannelName = CHANNEL.toLowerCase()
+- // default to "default". Currently only has different cosmetics for "develop", "release", "default"
+- propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
+- // Import channel_properties
++ propertiesChannelName = "release"
+ channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
+ channelGradleProperties = string("${channelDir}/channel_gradle.properties")
+ overrideProperties(channelGradleProperties, false)
+- // local build environment properties
+- // can be "projectDir/local.properties"
+- overrideProperties("${projectDir}/local.properties", true)
+- // or "../projectDir_local.properties"
+- overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
+-
++
+ ////
+ // Import releaseProps from the RELEASE file
+ // or a file specified via JALVIEW_RELEASE_FILE if defined
+@@ -128,41 +76,6 @@
+ if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
+ JALVIEW_VERSION = releaseProps.get("jalview.version")
+ }
+-
+- // this property set when running Eclipse headlessly
+- j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
+- // this property set by Eclipse
+- eclipseApplicationProperty = string("eclipse.application")
+- // CHECK IF RUNNING FROM WITHIN ECLIPSE
+- def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
+- IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
+- // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
+- if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
+- println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
+- IN_ECLIPSE = false
+- }
+- if (IN_ECLIPSE) {
+- println("WITHIN ECLIPSE IDE")
+- } else {
+- println("HEADLESS BUILD")
+- }
+-
+- J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
+- if (J2S_ENABLED) {
+- println("J2S ENABLED")
+- }
+- /* *-/
+- System.properties.sort { it.key }.each {
+- key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
+- }
+- /-* *-/
+- if (false && IN_ECLIPSE) {
+- jalviewDir = jalviewDirAbsolutePath
+- }
+- */
+-
+- // datestamp
+- buildDate = new Date().format("yyyyMMdd")
+
+ // essentials
+ bareSourceDir = string(source_dir)
+@@ -173,218 +86,18 @@
+
+ classesDir = string("${jalviewDir}/${classes_dir}")
+
+- // clover
+- useClover = clover.equals("true")
+- cloverBuildDir = "${buildDir}/clover"
+- cloverInstrDir = file("${cloverBuildDir}/clover-instr")
+- cloverClassesDir = file("${cloverBuildDir}/clover-classes")
+- cloverReportDir = file("${buildDir}/reports/clover")
+- cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
+- cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
+- //cloverTestClassesDir = cloverClassesDir
+- cloverDb = string("${cloverBuildDir}/clover.db")
+-
+- testSourceDir = useClover ? cloverTestInstrDir : testDir
+- testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
+-
+- getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
+- buildDist = true
+- buildProperties = null
+-
+- // the following values might be overridden by the CHANNEL switch
+- getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+- getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
+- getdownAppDistDir = getdown_app_dir_alt
+- getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
+- getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
+- reportRsyncCommand = false
+- jvlChannelName = CHANNEL.toLowerCase()
+- install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
+- install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
+- install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}"
+- install4jInstallerName = "${jalview_name} Non-Release Installer"
+- install4jExecutableName = install4j_executable_name
+- install4jExtraScheme = "jalviewx"
+- install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
+- install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
+- install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
+- install4jBackground = string("${install4j_images_dir}/${install4j_background}")
+- switch (CHANNEL) {
+-
+- case "BUILD":
+- // TODO: get bamboo build artifact URL for getdown artifacts
+- getdown_channel_base = bamboo_channelbase
+- getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
+- getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
+- jvlChannelName += "_${getdownChannelName}"
+- // automatically add the test group Not-bamboo for exclusion
+- if ("".equals(testng_excluded_groups)) {
+- testng_excluded_groups = "Not-bamboo"
+- }
+- install4jExtraScheme = "jalviewb"
+- break
++ useClover = false
+
+- case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
+- getdownAppDistDir = getdown_app_dir_release
+- reportRsyncCommand = true
+- install4jSuffix = ""
+- install4jInstallerName = "${jalview_name} Installer"
+- break
+-
+- case "ARCHIVE":
+- getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
+- getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+- getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+- if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
+- throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
+- } else {
+- package_dir = string("${ARCHIVEDIR}/${package_dir}")
+- buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
+- buildDist = false
+- }
+- reportRsyncCommand = true
+- install4jExtraScheme = "jalviewa"
+- break
+-
+- case "ARCHIVELOCAL":
+- getdownChannelName = string("archive/${JALVIEW_VERSION}")
+- getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+- getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+- if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
+- throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
+- } else {
+- package_dir = string("${ARCHIVEDIR}/${package_dir}")
+- buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
+- buildDist = false
+- }
+- reportRsyncCommand = true
+- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+- install4jSuffix = "Archive"
+- install4jExtraScheme = "jalviewa"
+- break
+-
+- case "DEVELOP":
+- reportRsyncCommand = true
+- getdownSetAppBaseProperty = true
+- // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
+- JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
+-
+- install4jSuffix = "Develop"
+- install4jExtraScheme = "jalviewd"
+- install4jInstallerName = "${jalview_name} Develop Installer"
+- break
+-
+- case "TEST-RELEASE":
+- reportRsyncCommand = true
+- // Don't ignore transpile errors for release build
+- if (jalviewjs_ignore_transpile_errors.equals("true")) {
+- jalviewjs_ignore_transpile_errors = "false"
+- println("Setting jalviewjs_ignore_transpile_errors to 'false'")
+- }
+- JALVIEW_VERSION = JALVIEW_VERSION+"-test"
+- install4jSuffix = "Test"
+- install4jExtraScheme = "jalviewt"
+- install4jInstallerName = "${jalview_name} Test Installer"
+- break
+-
+- case ~/^SCRATCH(|-[-\w]*)$/:
+- getdownChannelName = CHANNEL
+- JALVIEW_VERSION = JALVIEW_VERSION+"-"+CHANNEL
+-
+- getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
+- getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+- reportRsyncCommand = true
+- install4jSuffix = "Scratch"
+- break
+-
+- case "TEST-LOCAL":
+- if (!file("${LOCALDIR}").exists()) {
+- throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
+- } else {
+- getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
+- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+- }
+- JALVIEW_VERSION = "TEST"
+- install4jSuffix = "Test-Local"
+- install4jExtraScheme = "jalviewt"
+- install4jInstallerName = "${jalview_name} Test Installer"
+- break
+-
+- case [ "LOCAL", "JALVIEWJS" ]:
+- JALVIEW_VERSION = "TEST"
+- getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+- install4jExtraScheme = "jalviewl"
+- break
+-
+- default: // something wrong specified
+- throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
+- break
+-
+- }
+- // override getdownAppBase if requested
+- if (findProperty("getdown_appbase_override") != null) {
+- // revert to LOCAL if empty string
+- if (string(getdown_appbase_override) == "") {
+- getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+- } else if (string(getdown_appbase_override).startsWith("file://")) {
+- getdownAppBase = string(getdown_appbase_override)
+- getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+- } else {
+- getdownAppBase = string(getdown_appbase_override)
+- }
+- println("Overriding getdown appbase with '${getdownAppBase}'")
+- }
+- // sanitise file name for jalview launcher file for this channel
+- jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
+- // install4j application and folder names
+- if (install4jSuffix == "") {
+- install4jApplicationName = "${jalview_name}"
+- install4jBundleId = "${install4j_bundle_id}"
+- install4jWinApplicationId = install4j_release_win_application_id
+- } else {
+- install4jApplicationName = "${jalview_name} ${install4jSuffix}"
+- install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
+- // add int hash of install4jSuffix to the last part of the application_id
+- def id = install4j_release_win_application_id
+- def idsplitreverse = id.split("-").reverse()
+- idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
+- install4jWinApplicationId = idsplitreverse.reverse().join("-")
+- }
+- // sanitise folder and id names
+- // install4jApplicationFolder = e.g. "Jalview Build"
+- install4jApplicationFolder = install4jApplicationName
+- .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
+- .replaceAll("_+", "_") // collapse __
+- install4jInternalId = install4jApplicationName
+- .replaceAll(" ","_")
+- .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
+- .replaceAll("_+", "") // collapse __
+- //.replaceAll("_*-_*", "-") // collapse _-_
+- install4jUnixApplicationFolder = install4jApplicationName
+- .replaceAll(" ","_")
+- .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
+- .replaceAll("_+", "_") // collapse __
+- .replaceAll("_*-_*", "-") // collapse _-_
+- .toLowerCase()
+-
+- getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
+- getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
+- //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
+- getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
+- getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}")
+- getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
+- getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
+- /* compile without modules -- using classpath libraries
+- modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
+- modules_runtimeClasspath = modules_compileClasspath
+- */
+- def details = versionDetails()
+- gitHash = details.gitHash
+- gitBranch = details.branchName
++ resourceClassesDir = classesDir
++
++ testSourceDir = testDir
++ testClassesDir = "${jalviewDir}/${test_output_dir}"
+
++ buildProperties = string("${classesDir}/${build_properties_file}")
++ getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
++
++ install4jApplicationName = "${jalview_name}"
++
+ println("Using a ${CHANNEL} profile.")
+
+ additional_compiler_args = []
+@@ -396,71 +109,16 @@
+ libDistDir = j8libDir
+ compile_source_compatibility = 1.8
+ compile_target_compatibility = 1.8
+- // these are getdown.txt properties defined dependent on the JAVA_VERSION
+- getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
+- getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
+- // this property is assigned below and expanded to multiple lines in the getdown task
+- getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
+- // this property is for the Java library used in eclipse
+- eclipseJavaRuntimeName = string("JavaSE-1.8")
+ } else if (JAVA_VERSION.equals("11")) {
+ JAVA_INTEGER_VERSION = string("11")
+ libDir = j11libDir
+ libDistDir = j11libDir
+ compile_source_compatibility = 11
+ compile_target_compatibility = 11
+- getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
+- getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
+- getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
+- eclipseJavaRuntimeName = string("JavaSE-11")
+- /* compile without modules -- using classpath libraries
+- additional_compiler_args += [
+- '--module-path', modules_compileClasspath.asPath,
+- '--add-modules', j11modules
+- ]
+- */
+- } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
+- JAVA_INTEGER_VERSION = JAVA_VERSION
+- libDir = j11libDir
+- libDistDir = j11libDir
+- compile_source_compatibility = JAVA_VERSION
+- compile_target_compatibility = JAVA_VERSION
+- getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
+- getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
+- getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
+- eclipseJavaRuntimeName = string("JavaSE-11")
+- /* compile without modules -- using classpath libraries
+- additional_compiler_args += [
+- '--module-path', modules_compileClasspath.asPath,
+- '--add-modules', j11modules
+- ]
+- */
+ } else {
+ throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
+ }
+
+-
+- // for install4j
+- JAVA_MIN_VERSION = JAVA_VERSION
+- JAVA_MAX_VERSION = JAVA_VERSION
+- def jreInstallsDir = string(jre_installs_dir)
+- if (jreInstallsDir.startsWith("~/")) {
+- jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
+- }
+- macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
+- macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz")
+- windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
+- windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz")
+- linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
+- linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz")
+- install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
+- install4jConfFileName = string("jalview-install4j-conf.install4j")
+- install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
+- install4jHomeDir = install4j_home_dir
+- if (install4jHomeDir.startsWith("~/")) {
+- install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
+- }
+-
+ resourceBuildDir = string("${buildDir}/resources")
+ resourcesBuildDir = string("${resourceBuildDir}/resources_build")
+ helpBuildDir = string("${resourceBuildDir}/help_build")
+@@ -474,31 +132,6 @@
+ helpSourceDir = string("${helpParentDir}/${help_dir}")
+ helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
+
+-
+- relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
+- jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
+- jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
+- if (IN_ECLIPSE) {
+- jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
+- } else {
+- jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
+- }
+- jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
+- jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
+- jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
+- jalviewjsJalviewCoreHtmlFile = string("")
+- jalviewjsJalviewCoreName = string(jalviewjs_core_name)
+- jalviewjsCoreClasslists = []
+- jalviewjsJalviewTemplateName = string(jalviewjs_name)
+- jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
+- jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
+- jalviewjsJ2sProps = null
+- jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
+-
+- eclipseWorkspace = null
+- eclipseBinary = string("")
+- eclipseVersion = string("")
+- eclipseDebug = false
+ // ENDEXT
+ }
+
+@@ -517,27 +150,12 @@
+ compileClasspath = files(sourceSets.main.java.outputDir)
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+
+- runtimeClasspath = compileClasspath
+- runtimeClasspath += files(sourceSets.main.resources.srcDirs)
+- }
+-
+- clover {
+- java {
+- srcDirs cloverInstrDir
+- outputDir = cloverClassesDir
+- }
+-
+- resources {
+- srcDirs = sourceSets.main.resources.srcDirs
+- }
+
+- compileClasspath = files( sourceSets.clover.java.outputDir )
+- //compileClasspath += files( testClassesDir )
++ compileClasspath = files(sourceSets.main.java.outputDir)
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+- compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+- compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
+
+ runtimeClasspath = compileClasspath
++ runtimeClasspath += files(sourceSets.main.resources.srcDirs)
+ }
+
+ test {
+@@ -557,453 +175,41 @@
+ runtimeClasspath = compileClasspath
+ runtimeClasspath += files(sourceSets.test.resources.srcDirs)
+ }
+-
+-}
+-
+-
+-// eclipse project and settings files creation, also used by buildship
+-eclipse {
+- project {
+- name = eclipse_project_name
+-
+- natures 'org.eclipse.jdt.core.javanature',
+- 'org.eclipse.jdt.groovy.core.groovyNature',
+- 'org.eclipse.buildship.core.gradleprojectnature'
+-
+- buildCommand 'org.eclipse.jdt.core.javabuilder'
+- buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
+- }
+-
+- classpath {
+- //defaultOutputDir = sourceSets.main.java.outputDir
+- configurations.each{ c->
+- if (c.isCanBeResolved()) {
+- minusConfigurations += [c]
+- }
+- }
+-
+- plusConfigurations = [ ]
+- file {
+-
+- whenMerged { cp ->
+- def removeTheseToo = []
+- HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
+- cp.entries.each { entry ->
+- // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
+- // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
+- // we add the resources and help/help dirs in as libs afterwards (see below)
+- if (entry.kind == 'src') {
+- if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
+- removeTheseToo += entry
+- } else {
+- alreadyAddedSrcPath.putAt(entry.path, true)
+- }
+- }
+-
+- }
+- cp.entries.removeAll(removeTheseToo)
+-
+- //cp.entries += new Output("${eclipse_bin_dir}/main")
+- if (file(helpParentDir).isDirectory()) {
+- cp.entries += new Library(fileReference(helpParentDir))
+- }
+- if (file(resourceDir).isDirectory()) {
+- cp.entries += new Library(fileReference(resourceDir))
+- }
+-
+- HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
+-
+- sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
+- //don't want to add outputDir as eclipse is using its own output dir in bin/main
+- if (it.isDirectory() || ! it.exists()) {
+- // don't add dirs to classpath, especially if they don't exist
+- return false // groovy "continue" in .any closure
+- }
+- def itPath = it.toString()
+- if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
+- // make relative path
+- itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+- }
+- if (alreadyAddedLibPath.get(itPath)) {
+- //println("Not adding duplicate entry "+itPath)
+- } else {
+- //println("Adding entry "+itPath)
+- cp.entries += new Library(fileReference(itPath))
+- alreadyAddedLibPath.put(itPath, true)
+- }
+- }
+-
+- sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
+- //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+- if (it.isDirectory() || ! it.exists()) {
+- // don't add dirs to classpath
+- return false // groovy "continue" in .any closure
+- }
+-
+- def itPath = it.toString()
+- if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
+- itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+- }
+- if (alreadyAddedLibPath.get(itPath)) {
+- // don't duplicate
+- } else {
+- def lib = new Library(fileReference(itPath))
+- lib.entryAttributes["test"] = "true"
+- cp.entries += lib
+- alreadyAddedLibPath.put(itPath, true)
+- }
+- }
+-
+- } // whenMerged
+-
+- } // file
+-
+- containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
+-
+- } // classpath
+-
+- jdt {
+- // for the IDE, use java 11 compatibility
+- sourceCompatibility = compile_source_compatibility
+- targetCompatibility = compile_target_compatibility
+- javaRuntimeName = eclipseJavaRuntimeName
+-
+- // add in jalview project specific properties/preferences into eclipse core preferences
+- file {
+- withProperties { props ->
+- def jalview_prefs = new Properties()
+- def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
+- jalview_prefs.load(ins)
+- ins.close()
+- jalview_prefs.forEach { t, v ->
+- if (props.getAt(t) == null) {
+- props.putAt(t, v)
+- }
+- }
+- // codestyle file -- overrides previous formatter prefs
+- def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
+- if (csFile.exists()) {
+- XmlParser parser = new XmlParser()
+- def profiles = parser.parse(csFile)
+- def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
+- if (profile != null) {
+- profile.'setting'.each { s ->
+- def id = s.'@id'
+- def value = s.'@value'
+- if (id != null && value != null) {
+- props.putAt(id, value)
+- }
+- }
+- }
+- }
+- }
+- }
+-
+- } // jdt
+-
+- if (IN_ECLIPSE) {
+- // Don't want these to be activated if in headless build
+- synchronizationTasks "eclipseSynchronizationTask"
+- //autoBuildTasks "eclipseAutoBuildTask"
+-
+- }
+-}
+-
+-
+-/* hack to change eclipse prefs in .settings files other than org.eclipse.jdt.core.prefs */
+-// Class to allow updating arbitrary properties files
+-class PropertiesFile extends PropertiesPersistableConfigurationObject {
+- public PropertiesFile(PropertiesTransformer t) { super(t); }
+- @Override protected void load(Properties properties) { }
+- @Override protected void store(Properties properties) { }
+- @Override protected String getDefaultResourceName() { return ""; }
+- // This is necessary, because PropertiesPersistableConfigurationObject fails
+- // if no default properties file exists.
+- @Override public void loadDefaults() { load(new StringBufferInputStream("")); }
+-}
+-
+-// Task to update arbitrary properties files (set outputFile)
+-class PropertiesFileTask extends PropertiesGeneratorTask<PropertiesFile> {
+- private final PropertiesFileContentMerger file;
+- public PropertiesFileTask() { file = new PropertiesFileContentMerger(getTransformer()); }
+- protected PropertiesFile create() { return new PropertiesFile(getTransformer()); }
+- protected void configure(PropertiesFile props) {
+- file.getBeforeMerged().execute(props); file.getWhenMerged().execute(props);
+- }
+- public void file(Closure closure) { ConfigureUtil.configure(closure, file); }
+-}
+-
+-task eclipseUIPreferences(type: PropertiesFileTask) {
+- description = "Generate Eclipse additional settings"
+- def filename = "org.eclipse.jdt.ui.prefs"
+- outputFile = "$projectDir/.settings/${filename}" as File
+- file {
+- withProperties {
+- it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
++ /* test {
++ java {
++ srcDirs testSourceDir
++ outputDir = file(testClassesDir)
+ }
+- }
+-}
+
+-task eclipseGroovyCorePreferences(type: PropertiesFileTask) {
+- description = "Generate Eclipse additional settings"
+- def filename = "org.eclipse.jdt.groovy.core.prefs"
+- outputFile = "$projectDir/.settings/${filename}" as File
+- file {
+- withProperties {
+- it.load new FileInputStream("$projectDir/utils/eclipse/${filename}" as String)
++ resources {
++ srcDirs = sourceSets.main.resources.srcDirs
+ }
+- }
+-}
+-
+-task eclipseAllPreferences {
+- dependsOn eclipseJdt
+- dependsOn eclipseUIPreferences
+- dependsOn eclipseGroovyCorePreferences
+-}
+-
+-eclipseUIPreferences.mustRunAfter eclipseJdt
+-eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
+-
+-/* end of eclipse preferences hack */
+-
+-
+-// clover bits
+-
+-
+-task cleanClover {
+- doFirst {
+- delete cloverBuildDir
+- delete cloverReportDir
+- }
+-}
+-
+-
+-task cloverInstrJava(type: JavaExec) {
+- group = "Verification"
+- description = "Create clover instrumented source java files"
+-
+- dependsOn cleanClover
+-
+- inputs.files(sourceSets.main.allJava)
+- outputs.dir(cloverInstrDir)
+-
+- //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+- classpath = sourceSets.clover.compileClasspath
+- main = "com.atlassian.clover.CloverInstr"
+-
+- def argsList = [
+- "--encoding",
+- "UTF-8",
+- "--initstring",
+- cloverDb,
+- "--destdir",
+- cloverInstrDir.getPath(),
+- ]
+- def srcFiles = sourceSets.main.allJava.files
+- argsList.addAll(
+- srcFiles.collect(
+- { file -> file.absolutePath }
+- )
+- )
+- args argsList.toArray()
+-
+- doFirst {
+- delete cloverInstrDir
+- println("Clover: About to instrument "+srcFiles.size() +" files")
+- }
+-}
+-
+-
+-task cloverInstrTests(type: JavaExec) {
+- group = "Verification"
+- description = "Create clover instrumented source test files"
+-
+- dependsOn cleanClover
+-
+- inputs.files(testDir)
+- outputs.dir(cloverTestInstrDir)
+-
+- classpath = sourceSets.clover.compileClasspath
+- main = "com.atlassian.clover.CloverInstr"
+-
+- def argsList = [
+- "--encoding",
+- "UTF-8",
+- "--initstring",
+- cloverDb,
+- "--srcdir",
+- testDir,
+- "--destdir",
+- cloverTestInstrDir.getPath(),
+- ]
+- args argsList.toArray()
+-
+- doFirst {
+- delete cloverTestInstrDir
+- println("Clover: About to instrument test files")
+- }
+-}
+-
+-
+-task cloverInstr {
+- group = "Verification"
+- description = "Create clover instrumented all source files"
+-
+- dependsOn cloverInstrJava
+- dependsOn cloverInstrTests
+-}
+-
+-
+-cloverClasses.dependsOn cloverInstr
+-
+-
+-task cloverConsoleReport(type: JavaExec) {
+- group = "Verification"
+- description = "Creates clover console report"
+-
+- onlyIf {
+- file(cloverDb).exists()
+- }
+-
+- inputs.dir cloverClassesDir
+-
+- classpath = sourceSets.clover.runtimeClasspath
+- main = "com.atlassian.clover.reporters.console.ConsoleReporter"
+-
+- if (cloverreport_mem.length() > 0) {
+- maxHeapSize = cloverreport_mem
+- }
+- if (cloverreport_jvmargs.length() > 0) {
+- jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+- }
+-
+- def argsList = [
+- "--alwaysreport",
+- "--initstring",
+- cloverDb,
+- "--unittests"
+- ]
+-
+- args argsList.toArray()
+-}
+-
+-
+-task cloverHtmlReport(type: JavaExec) {
+- group = "Verification"
+- description = "Creates clover HTML report"
+-
+- onlyIf {
+- file(cloverDb).exists()
+- }
+-
+- def cloverHtmlDir = cloverReportDir
+- inputs.dir cloverClassesDir
+- outputs.dir cloverHtmlDir
+-
+- classpath = sourceSets.clover.runtimeClasspath
+- main = "com.atlassian.clover.reporters.html.HtmlReporter"
+-
+- if (cloverreport_mem.length() > 0) {
+- maxHeapSize = cloverreport_mem
+- }
+- if (cloverreport_jvmargs.length() > 0) {
+- jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+- }
+-
+- def argsList = [
+- "--alwaysreport",
+- "--initstring",
+- cloverDb,
+- "--outputdir",
+- cloverHtmlDir
+- ]
+-
+- if (cloverreport_html_options.length() > 0) {
+- argsList += cloverreport_html_options.split(" ")
+- }
+-
+- args argsList.toArray()
+-}
+-
+-
+-task cloverXmlReport(type: JavaExec) {
+- group = "Verification"
+- description = "Creates clover XML report"
+-
+- onlyIf {
+- file(cloverDb).exists()
+- }
+-
+- def cloverXmlFile = "${cloverReportDir}/clover.xml"
+- inputs.dir cloverClassesDir
+- outputs.file cloverXmlFile
+-
+- classpath = sourceSets.clover.runtimeClasspath
+- main = "com.atlassian.clover.reporters.xml.XMLReporter"
+-
+- if (cloverreport_mem.length() > 0) {
+- maxHeapSize = cloverreport_mem
+- }
+- if (cloverreport_jvmargs.length() > 0) {
+- jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+- }
+-
+- def argsList = [
+- "--alwaysreport",
+- "--initstring",
+- cloverDb,
+- "--outfile",
+- cloverXmlFile
+- ]
+-
+- if (cloverreport_xml_options.length() > 0) {
+- argsList += cloverreport_xml_options.split(" ")
+- }
+-
+- args argsList.toArray()
+-}
+
++ compileClasspath = files( sourceSets.test.java.outputDir )
++ compileClasspath += sourceSets.main.compileClasspath
++ compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["** REMOVE_THIS_GAP /*.jar"])
+
+-task cloverReport {
+- group = "Verification"
+- description = "Creates clover reports"
+-
+- dependsOn cloverXmlReport
+- dependsOn cloverHtmlReport
+-}
+-
+-
+-compileCloverJava {
+-
+- doFirst {
+- sourceCompatibility = compile_source_compatibility
+- targetCompatibility = compile_target_compatibility
+- options.compilerArgs += additional_compiler_args
+- print ("Setting target compatibility to "+targetCompatibility+"\n")
++ runtimeClasspath = compileClasspath
+ }
+- //classpath += configurations.cloverRuntime
++*/
+ }
+-// end clover bits
+
+
+ compileJava {
+- // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ?
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+- options.encoding = "UTF-8"
+ doFirst {
+ print ("Setting target compatibility to "+compile_target_compatibility+"\n")
+ }
+-
+ }
+
+
+ compileTestJava {
+- sourceCompatibility = compile_source_compatibility
+- targetCompatibility = compile_target_compatibility
+- options.compilerArgs = additional_compiler_args
+ doFirst {
++ sourceCompatibility = compile_source_compatibility
++ targetCompatibility = compile_target_compatibility
++ options.compilerArgs = additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+ }
+@@ -1017,7 +223,6 @@
+
+
+ cleanTest {
+- dependsOn cleanClover
+ doFirst {
+ delete sourceSets.test.java.outputDir
+ }
+@@ -1031,85 +236,6 @@
+ }
+
+
+-def convertMdToHtml (FileTree mdFiles, File cssFile) {
+- MutableDataSet options = new MutableDataSet()
+-
+- def extensions = new ArrayList<>()
+- extensions.add(AnchorLinkExtension.create())
+- extensions.add(AutolinkExtension.create())
+- extensions.add(StrikethroughExtension.create())
+- extensions.add(TaskListExtension.create())
+- extensions.add(TablesExtension.create())
+- extensions.add(TocExtension.create())
+-
+- options.set(Parser.EXTENSIONS, extensions)
+-
+- // set GFM table parsing options
+- options.set(TablesExtension.WITH_CAPTION, false)
+- options.set(TablesExtension.COLUMN_SPANS, false)
+- options.set(TablesExtension.MIN_HEADER_ROWS, 1)
+- options.set(TablesExtension.MAX_HEADER_ROWS, 1)
+- options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
+- options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
+- options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
+- // GFM anchor links
+- options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
+- options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
+- options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
+- options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
+-
+- Parser parser = Parser.builder(options).build()
+- HtmlRenderer renderer = HtmlRenderer.builder(options).build()
+-
+- mdFiles.each { mdFile ->
+- // add table of contents
+- def mdText = "[TOC]\n"+mdFile.text
+-
+- // grab the first top-level title
+- def title = null
+- def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
+- def matcher = mdText =~ titleRegex
+- if (matcher.size() > 0) {
+- // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
+- title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
+- }
+- // or use the filename if none found
+- if (title == null) {
+- title = mdFile.getName()
+- }
+-
+- Node document = parser.parse(mdText)
+- String htmlBody = renderer.render(document)
+- def htmlText = '''<html>
+-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+-<html xmlns="http://www.w3.org/1999/xhtml">
+- <head>
+- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+- <meta http-equiv="Content-Style-Type" content="text/css" />
+- <meta name="generator" content="flexmark" />
+-'''
+- htmlText += ((title != null) ? " <title>${title}</title>" : '' )
+- htmlText += '''
+- <style type="text/css">code{white-space: pre;}</style>
+-'''
+- htmlText += ((cssFile != null) ? cssFile.text : '')
+- htmlText += '''</head>
+- <body>
+-'''
+- htmlText += htmlBody
+- htmlText += '''
+- </body>
+-</html>
+-'''
+-
+- def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
+- def htmlFile = file(htmlFilePath)
+- println("Creating ${htmlFilePath}")
+- htmlFile.text = htmlText
+- }
+-}
+-
+-
+ task copyDocs(type: Copy) {
+ def inputDir = "${jalviewDir}/${doc_dir}"
+ def outputDir = "${docBuildDir}/${doc_dir}"
+@@ -1140,27 +266,6 @@
+ }
+
+
+-task convertMdFiles {
+- dependsOn copyDocs
+- def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
+- def cssFile = file("${jalviewDir}/${flexmark_css}")
+-
+- doLast {
+- convertMdToHtml(mdFiles, cssFile)
+- }
+-
+- inputs.files(mdFiles)
+- inputs.file(cssFile)
+-
+- def htmlFiles = []
+- mdFiles.each { mdFile ->
+- def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
+- htmlFiles.add(file(htmlFilePath))
+- }
+- outputs.files(htmlFiles)
+-}
+-
+-
+ task copyHelp(type: Copy) {
+ def inputDir = helpSourceDir
+ def outputDir = "${helpBuildDir}/${help_dir}"
+@@ -1242,24 +347,15 @@
+ outputs.dir(outputDir)
+ }
+
+-task createBuildProperties(type: WriteProperties) {
+- dependsOn copyResources
+- group = "build"
+- description = "Create the ${buildProperties} file"
+-
+- inputs.dir(sourceDir)
+- inputs.dir(resourcesBuildDir)
+- outputFile (buildProperties)
+- // taking time specific comment out to allow better incremental builds
+- comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
+- //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
+- property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
+- property "VERSION", JALVIEW_VERSION
+- property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
+- if (getdownSetAppBaseProperty) {
+- property "GETDOWNAPPBASE", getdownAppBase
+- property "GETDOWNAPPDISTDIR", getdownAppDistDir
+- }
++task createBuildProperties(type: Copy) {
++ // using the build_properties already included in the source tarball
++ def inputFile = "build_properties"
++ def outputFile = buildProperties
++ from inputFile
++ into file(outputFile).getParent()
++ rename(file(inputFile).getName(), file(outputFile).getName())
++
++ inputs.file(inputFile)
+ outputs.file(outputFile)
+ }
+
+@@ -1293,7 +389,6 @@
+ dependsOn buildResources
+ dependsOn copyDocs
+ dependsOn copyHelp
+- dependsOn convertMdFiles
+ dependsOn buildIndices
+ }
+
+@@ -1306,12 +401,7 @@
+ //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
+ test {
+ dependsOn prepare
+-
+- if (useClover) {
+- dependsOn cloverClasses
+- } else { //?
+- dependsOn compileJava //?
+- }
++ dependsOn compileJava //?
+
+ useTestNG() {
+ includeGroups testng_groups
+@@ -1323,6 +413,7 @@
+ maxHeapSize = "1024m"
+
+ workingDir = jalviewDir
++ //systemProperties 'clover.jar' System.properties.clover.jar
+ def testLaf = project.findProperty("test_laf")
+ if (testLaf != null) {
+ println("Setting Test LaF to '${testLaf}'")
+@@ -1338,9 +429,6 @@
+ jvmArgs += additional_compiler_args
+
+ doFirst {
+- if (useClover) {
+- println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
+- }
+ }
+ }
+
+@@ -1420,1752 +508,7 @@
+ sourceSets.main.resources.srcDirs.each{ dir ->
+ inputs.dir(dir)
+ }
+- outputs.file("${outputDir}/${archiveFileName}")
+-}
+-
+-
+-task copyJars(type: Copy) {
+- from fileTree(dir: classesDir, include: "**/*.jar").files
+- into "${jalviewDir}/${package_dir}"
+-}
+-
+-
+-// doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
+-task syncJars(type: Sync) {
+- dependsOn jar
+- from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
+- into "${jalviewDir}/${package_dir}"
+- preserve {
+- include jar.archiveFileName.getOrNull()
+- }
+-}
+-
+-
+-task makeDist {
+- group = "build"
+- description = "Put all required libraries in dist"
+- // order of "cleanPackageDir", "copyJars", "jar" important!
+- jar.mustRunAfter cleanPackageDir
+- syncJars.mustRunAfter cleanPackageDir
+- dependsOn cleanPackageDir
+- dependsOn syncJars
+- dependsOn jar
+- outputs.dir("${jalviewDir}/${package_dir}")
+-}
+-
+-
+-task cleanDist {
+- dependsOn cleanPackageDir
+- dependsOn cleanTest
+- dependsOn clean
+-}
+-
+-
+-shadowJar {
+- group = "distribution"
+- description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
+- if (buildDist) {
+- dependsOn makeDist
+- }
+- from ("${jalviewDir}/${libDistDir}") {
+- include("*.jar")
+- }
+- manifest {
+- attributes "Implementation-Version": JALVIEW_VERSION,
+- "Application-Name": install4jApplicationName
+- }
+- mainClassName = shadow_jar_main_class
+- mergeServiceFiles()
+- classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
+- minimize()
+-}
+-
+-
+-task getdownWebsite() {
+- group = "distribution"
+- description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
+- if (buildDist) {
+- dependsOn makeDist
+- }
+-
+- def getdownWebsiteResourceFilenames = []
+- def getdownTextString = ""
+- def getdownResourceDir = getdownResourceDir
+- def getdownResourceFilenames = []
+-
+- doFirst {
+- // clean the getdown website and files dir before creating getdown folders
+- delete getdownWebsiteDir
+- delete getdownFilesDir
+-
+- copy {
+- from buildProperties
+- rename(file(buildProperties).getName(), getdown_build_properties)
+- into getdownAppDir
+- }
+- getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
+-
+- // set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
+- def props = project.properties.sort { it.key }
+- if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
+- props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
+- }
+- if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
+- props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
+- }
+- if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
+- props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
+- }
+- if (getdownImagesDir != null && file(getdownImagesDir).exists()) {
+- props.put("getdown_txt_ui.background_image", "${getdownImagesDir}/${getdown_background_image}")
+- props.put("getdown_txt_ui.instant_background_image", "${getdownImagesDir}/${getdown_instant_background_image}")
+- props.put("getdown_txt_ui.error_background", "${getdownImagesDir}/${getdown_error_background}")
+- props.put("getdown_txt_ui.progress_image", "${getdownImagesDir}/${getdown_progress_image}")
+- props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
+- props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
+- }
+-
+- props.put("getdown_txt_title", jalview_name)
+- props.put("getdown_txt_ui.name", install4jApplicationName)
+-
+- // start with appbase
+- getdownTextString += "appbase = ${getdownAppBase}\n"
+- props.each{ prop, val ->
+- if (prop.startsWith("getdown_txt_") && val != null) {
+- if (prop.startsWith("getdown_txt_multi_")) {
+- def key = prop.substring(18)
+- val.split(",").each{ v ->
+- def line = "${key} = ${v}\n"
+- getdownTextString += line
+- }
+- } else {
+- // file values rationalised
+- if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
+- def r = null
+- if (val.indexOf('/') == 0) {
+- // absolute path
+- r = file(val)
+- } else if (val.indexOf('/') > 0) {
+- // relative path (relative to jalviewDir)
+- r = file( "${jalviewDir}/${val}" )
+- }
+- if (r.exists()) {
+- val = "${getdown_resource_dir}/" + r.getName()
+- getdownWebsiteResourceFilenames += val
+- getdownResourceFilenames += r.getPath()
+- }
+- }
+- if (! prop.startsWith("getdown_txt_resource")) {
+- def line = prop.substring(12) + " = ${val}\n"
+- getdownTextString += line
+- }
+- }
+- }
+- }
+-
+- getdownWebsiteResourceFilenames.each{ filename ->
+- getdownTextString += "resource = ${filename}\n"
+- }
+- getdownResourceFilenames.each{ filename ->
+- copy {
+- from filename
+- into getdownResourceDir
+- }
+- }
+-
+- def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
+- getdownWrapperScripts.each{ script ->
+- def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
+- if (s.exists()) {
+- copy {
+- from s
+- into "${getdownWebsiteDir}/${getdown_wrapper_script_dir}"
+- }
+- getdownTextString += "resource = ${getdown_wrapper_script_dir}/${script}\n"
+- }
+- }
+-
+- def codeFiles = []
+- fileTree(file(package_dir)).each{ f ->
+- if (f.isDirectory()) {
+- def files = fileTree(dir: f, include: ["*"]).getFiles()
+- codeFiles += files
+- } else if (f.exists()) {
+- codeFiles += f
+- }
+- }
+- codeFiles.sort().each{f ->
+- def name = f.getName()
+- def line = "code = ${getdownAppDistDir}/${name}\n"
+- getdownTextString += line
+- copy {
+- from f.getPath()
+- into getdownAppDir
+- }
+- }
+-
+- // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
+- /*
+- if (JAVA_VERSION.equals("11")) {
+- def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
+- j11libFiles.sort().each{f ->
+- def name = f.getName()
+- def line = "code = ${getdown_j11lib_dir}/${name}\n"
+- getdownTextString += line
+- copy {
+- from f.getPath()
+- into getdownJ11libDir
+- }
+- }
+- }
+- */
+-
+- // getdown-launcher.jar should not be in main application class path so the main application can move it when updated. Listed as a resource so it gets updated.
+- //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
+- getdownTextString += "resource = ${getdown_launcher_new}\n"
+- getdownTextString += "class = ${main_class}\n"
+- // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
+- if (getdownSetAppBaseProperty) {
+- getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n"
+- getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n"
+- }
+-
+- def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
+- getdown_txt.write(getdownTextString)
+-
+- def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
+- def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
+- launchJvl.write("appbase=${getdownAppBase}")
+-
+- // files going into the getdown website dir: getdown-launcher.jar
+- copy {
+- from getdownLauncher
+- rename(file(getdownLauncher).getName(), getdown_launcher_new)
+- into getdownWebsiteDir
+- }
+-
+- // files going into the getdown website dir: getdown-launcher(-local).jar
+- copy {
+- from getdownLauncher
+- if (file(getdownLauncher).getName() != getdown_launcher) {
+- rename(file(getdownLauncher).getName(), getdown_launcher)
+- }
+- into getdownWebsiteDir
+- }
+-
+- // files going into the getdown website dir: ./install dir and files
+- if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
+- copy {
+- from getdown_txt
+- from getdownLauncher
+- from "${getdownAppDir}/${getdown_build_properties}"
+- if (file(getdownLauncher).getName() != getdown_launcher) {
+- rename(file(getdownLauncher).getName(), getdown_launcher)
+- }
+- into getdownInstallDir
+- }
+-
+- // and make a copy in the getdown files dir (these are not downloaded by getdown)
+- copy {
+- from getdownInstallDir
+- into getdownFilesInstallDir
+- }
+- }
+-
+- // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
+- copy {
+- from getdown_txt
+- from launchJvl
+- from getdownLauncher
+- from "${getdownWebsiteDir}/${getdown_build_properties}"
+- if (file(getdownLauncher).getName() != getdown_launcher) {
+- rename(file(getdownLauncher).getName(), getdown_launcher)
+- }
+- into getdownFilesDir
+- }
+-
+- // and ./resources (not all downloaded by getdown)
+- copy {
+- from getdownResourceDir
+- into "${getdownFilesDir}/${getdown_resource_dir}"
+- }
+- }
+-
+- if (buildDist) {
+- inputs.dir("${jalviewDir}/${package_dir}")
+- }
+- outputs.dir(getdownWebsiteDir)
+- outputs.dir(getdownFilesDir)
+-}
+-
+-
+-// a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
+-task getdownDigestDir(type: JavaExec) {
+- group "Help"
+- description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
+-
+- def digestDirPropertyName = "DIGESTDIR"
+- doFirst {
+- classpath = files(getdownLauncher)
+- def digestDir = findProperty(digestDirPropertyName)
+- if (digestDir == null) {
+- throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
+- }
+- args digestDir
+- }
+- main = "com.threerings.getdown.tools.Digester"
+-}
+-
+-
+-task getdownDigest(type: JavaExec) {
+- group = "distribution"
+- description = "Digest the getdown website folder"
+- dependsOn getdownWebsite
+- doFirst {
+- classpath = files(getdownLauncher)
+- }
+- main = "com.threerings.getdown.tools.Digester"
+- args getdownWebsiteDir
+- inputs.dir(getdownWebsiteDir)
+- outputs.file("${getdownWebsiteDir}/digest2.txt")
+-}
+-
+-
+-task getdown() {
+- group = "distribution"
+- description = "Create the minimal and full getdown app folder for installers and website and create digest file"
+- dependsOn getdownDigest
+- doLast {
+- if (reportRsyncCommand) {
+- def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
+- def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
+- println "LIKELY RSYNC COMMAND:"
+- println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
+- if (RUNRSYNC == "true") {
+- exec {
+- commandLine "mkdir", "-p", toDir
+- }
+- exec {
+- commandLine "rsync", "-avh", "--delete", fromDir, toDir
+- }
+- }
+- }
+- }
+-}
+-
+-
+-tasks.withType(JavaCompile) {
+- options.encoding = 'UTF-8'
+-}
+-
+-
+-clean {
+- doFirst {
+- delete getdownWebsiteDir
+- delete getdownFilesDir
+- }
+-}
+-
+-
+-install4j {
+- if (file(install4jHomeDir).exists()) {
+- // good to go!
+- } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
+- install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
+- } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
+- install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
+- }
+- installDir(file(install4jHomeDir))
+-
+- mediaTypes = Arrays.asList(install4j_media_types.split(","))
+-}
+-
+-
+-task copyInstall4jTemplate {
+- def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
+- def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
+- inputs.file(install4jTemplateFile)
+- inputs.file(install4jFileAssociationsFile)
+- inputs.property("CHANNEL", { CHANNEL })
+- outputs.file(install4jConfFile)
+-
+- doLast {
+- def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
+-
+- // turn off code signing if no OSX_KEYPASS
+- if (OSX_KEYPASS == "") {
+- install4jConfigXml.'**'.codeSigning.each { codeSigning ->
+- codeSigning.'@macEnabled' = "false"
+- }
+- install4jConfigXml.'**'.windows.each { windows ->
+- windows.'@runPostProcessor' = "false"
+- }
+- }
+-
+- // turn off checksum creation for LOCAL channel
+- def e = install4jConfigXml.application[0]
+- if (CHANNEL == "LOCAL") {
+- e.'@createChecksums' = "false"
+- } else {
+- e.'@createChecksums' = "true"
+- }
+-
+- // put file association actions where placeholder action is
+- def install4jFileAssociationsText = install4jFileAssociationsFile.text
+- def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
+- install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
+- if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
+- def parent = a.parent()
+- parent.remove(a)
+- fileAssociationActions.each { faa ->
+- parent.append(faa)
+- }
+- // don't need to continue in .any loop once replacements have been made
+- return true
+- }
+- }
+-
+- // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
+- // NB we're deleting the /other/ one!
+- // Also remove the examples subdir from non-release versions
+- def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
+- // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
+- if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
+- customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
+- } else {
+- // remove the examples subdir from Full File Set
+- def files = install4jConfigXml.files[0]
+- def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
+- def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
+- def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
+- def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
+- dirEntry.parent().remove(dirEntry)
+- }
+- install4jConfigXml.'**'.action.any { a ->
+- if (a.'@customizedId' == customizedIdToDelete) {
+- def parent = a.parent()
+- parent.remove(a)
+- return true
+- }
+- }
+-
+- // write install4j file
+- install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
+- }
+-}
+-
+-
+-clean {
+- doFirst {
+- delete install4jConfFile
+- }
+-}
+-
+-
+-task installers(type: com.install4j.gradle.Install4jTask) {
+- group = "distribution"
+- description = "Create the install4j installers"
+- dependsOn getdown
+- dependsOn copyInstall4jTemplate
+-
+- projectFile = install4jConfFile
+-
+- // create an md5 for the input files to use as version for install4j conf file
+- def digest = MessageDigest.getInstance("MD5")
+- digest.update(
+- (file("${install4jDir}/${install4j_template}").text +
+- file("${install4jDir}/${install4j_info_plist_file_associations}").text +
+- file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
+- def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
+- if (filesMd5.length() >= 8) {
+- filesMd5 = filesMd5.substring(0,8)
+- }
+- def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
+- // make install4jBuildDir relative to jalviewDir
+- def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
+-
+- variables = [
+- 'JALVIEW_NAME': jalview_name,
+- 'JALVIEW_APPLICATION_NAME': install4jApplicationName,
+- 'JALVIEW_DIR': "../..",
+- 'OSX_KEYSTORE': OSX_KEYSTORE,
+- 'OSX_APPLEID': OSX_APPLEID,
+- 'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
+- 'JSIGN_SH': JSIGN_SH,
+- 'JRE_DIR': getdown_app_dir_java,
+- 'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
+- 'JALVIEW_VERSION': JALVIEW_VERSION,
+- 'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
+- 'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
+- 'JAVA_VERSION': JAVA_VERSION,
+- 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
+- 'VERSION': JALVIEW_VERSION,
+- 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
+- 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
+- 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
+- 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
+- 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
+- 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
+- 'COPYRIGHT_MESSAGE': install4j_copyright_message,
+- 'BUNDLE_ID': install4jBundleId,
+- 'INTERNAL_ID': install4jInternalId,
+- 'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
+- 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
+- 'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
+- 'WRAPPER_LINK': getdownWrapperLink,
+- 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
+- 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
+- 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
+- 'INSTALLER_NAME': install4jInstallerName,
+- 'INSTALL4J_UTILS_DIR': install4j_utils_dir,
+- 'GETDOWN_WEBSITE_DIR': getdown_website_dir,
+- 'GETDOWN_FILES_DIR': getdown_files_dir,
+- 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
+- 'GETDOWN_DIST_DIR': getdownAppDistDir,
+- 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
+- 'GETDOWN_INSTALL_DIR': getdown_install_dir,
+- 'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
+- 'BUILD_DIR': install4jBuildDir,
+- 'APPLICATION_CATEGORIES': install4j_application_categories,
+- 'APPLICATION_FOLDER': install4jApplicationFolder,
+- 'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
+- 'EXECUTABLE_NAME': install4jExecutableName,
+- 'EXTRA_SCHEME': install4jExtraScheme,
+- 'MAC_ICONS_FILE': install4jMacIconsFile,
+- 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
+- 'PNG_ICON_FILE': install4jPngIconFile,
+- 'BACKGROUND': install4jBackground,
+-
+- ]
+-
+- //println("INSTALL4J VARIABLES:")
+- //variables.each{k,v->println("${k}=${v}")}
+-
+- destination = "${jalviewDir}/${install4jBuildDir}"
+- buildSelected = true
+-
+- if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
+- faster = true
+- disableSigning = true
+- disableNotarization = true
+- }
+-
+- if (OSX_KEYPASS) {
+- macKeystorePassword = OSX_KEYPASS
+- }
+-
+- if (OSX_ALTOOLPASS) {
+- appleIdPassword = OSX_ALTOOLPASS
+- disableNotarization = false
+- } else {
+- disableNotarization = true
+- }
+-
+- doFirst {
+- println("Using projectFile "+projectFile)
+- if (!disableNotarization) { println("Will notarize OSX App DMG") }
+- }
+- //verbose=true
+-
+- inputs.dir(getdownWebsiteDir)
+- inputs.file(install4jConfFile)
+- inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
+- inputs.dir(macosJavaVMDir)
+- inputs.dir(windowsJavaVMDir)
+- outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
+-}
+-
+-
+-spotless {
+- java {
+- eclipse().configFile(eclipse_codestyle_file)
+- }
+-}
+-
+-
+-task sourceDist(type: Tar) {
+- group "distribution"
+- description "Create a source .tar.gz file for distribution"
+-
+- dependsOn createBuildProperties
+- dependsOn convertMdFiles
+-
+- def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
+- def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
+- archiveFileName = outputFileName
+-
+- compression Compression.GZIP
+-
+- into project.name
+-
+- def EXCLUDE_FILES=[
+- "build/*",
+- "bin/*",
+- "test-output/",
+- "test-reports",
+- "tests",
+- "clover*/*",
+- ".*",
+- "benchmarking/*",
+- "**/.*",
+- "*.class",
+- "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
+- "*locales/**",
+- "utils/InstallAnywhere",
+- "**/*.log",
+- ]
+- def PROCESS_FILES=[
+- "AUTHORS",
+- "CITATION",
+- "FEATURETODO",
+- "JAVA-11-README",
+- "FEATURETODO",
+- "LICENSE",
+- "**/README",
+- "RELEASE",
+- "THIRDPARTYLIBS",
+- "TESTNG",
+- "build.gradle",
+- "gradle.properties",
+- "**/*.java",
+- "**/*.html",
+- "**/*.xml",
+- "**/*.gradle",
+- "**/*.groovy",
+- "**/*.properties",
+- "**/*.perl",
+- "**/*.sh",
+- ]
+- def INCLUDE_FILES=[
+- ".settings/org.eclipse.jdt.core.jalview.prefs",
+- ]
+-
+- from(jalviewDir) {
+- exclude (EXCLUDE_FILES)
+- include (PROCESS_FILES)
+- filter(ReplaceTokens,
+- beginToken: '$$',
+- endToken: '$$',
+- tokens: [
+- 'Version-Rel': JALVIEW_VERSION,
+- 'Year-Rel': getDate("yyyy")
+- ]
+- )
+- }
+- from(jalviewDir) {
+- exclude (EXCLUDE_FILES)
+- exclude (PROCESS_FILES)
+- exclude ("appletlib")
+- exclude ("**/*locales")
+- exclude ("*locales/**")
+- exclude ("utils/InstallAnywhere")
+-
+- exclude (getdown_files_dir)
+- exclude (getdown_website_dir)
+-
+- // exluding these as not using jars as modules yet
+- exclude ("${j11modDir}/**/*.jar")
+- }
+- from(jalviewDir) {
+- include(INCLUDE_FILES)
+- }
+-// from (jalviewDir) {
+-// // explicit includes for stuff that seemed to not get included
+-// include(fileTree("test/**/*."))
+-// exclude(EXCLUDE_FILES)
+-// exclude(PROCESS_FILES)
+-// }
+-
+- from(file(buildProperties).getParent()) {
+- include(file(buildProperties).getName())
+- rename(file(buildProperties).getName(), "build_properties")
+- filter({ line ->
+- line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
+- })
+- }
+-
+-}
+-
+-
+-task helppages {
+- dependsOn copyHelp
+- dependsOn pubhtmlhelp
+-
+- inputs.dir("${helpBuildDir}/${help_dir}")
+- outputs.dir("${buildDir}/distributions/${help_dir}")
+-}
+-
+-
+-task j2sSetHeadlessBuild {
+- doFirst {
+- IN_ECLIPSE = false
+- }
+-}
+-
+-
+-task jalviewjsEnableAltFileProperty(type: WriteProperties) {
+- group "jalviewjs"
+- description "Enable the alternative J2S Config file for headless build"
+-
+- outputFile = jalviewjsJ2sSettingsFileName
+- def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
+- def j2sProps = new Properties()
+- if (j2sPropsFile.exists()) {
+- try {
+- def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
+- j2sProps.load(j2sPropsFileFIS)
+- j2sPropsFileFIS.close()
+-
+- j2sProps.each { prop, val ->
+- property(prop, val)
+- }
+- } catch (Exception e) {
+- println("Exception reading ${jalviewjsJ2sSettingsFileName}")
+- e.printStackTrace()
+- }
+- }
+- if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
+- property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
+- }
+-}
+-
+-
+-task jalviewjsSetEclipseWorkspace {
+- def propKey = "jalviewjs_eclipse_workspace"
+- def propVal = null
+- if (project.hasProperty(propKey)) {
+- propVal = project.getProperty(propKey)
+- if (propVal.startsWith("~/")) {
+- propVal = System.getProperty("user.home") + propVal.substring(1)
+- }
+- }
+- def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
+- def propsFile = file(propsFileName)
+- def eclipseWsDir = propVal
+- def props = new Properties()
+-
+- def writeProps = true
+- if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
+- def ins = new FileInputStream(propsFileName)
+- props.load(ins)
+- ins.close()
+- if (props.getProperty(propKey, null) != null) {
+- eclipseWsDir = props.getProperty(propKey)
+- writeProps = false
+- }
+- }
+-
+- if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
+- def tempDir = File.createTempDir()
+- eclipseWsDir = tempDir.getAbsolutePath()
+- writeProps = true
+- }
+- eclipseWorkspace = file(eclipseWsDir)
+-
+- doFirst {
+- // do not run a headless transpile when we claim to be in Eclipse
+- if (IN_ECLIPSE) {
+- println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+- } else {
+- println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- }
+-
+- if (writeProps) {
+- props.setProperty(propKey, eclipseWsDir)
+- propsFile.parentFile.mkdirs()
+- def bytes = new ByteArrayOutputStream()
+- props.store(bytes, null)
+- def propertiesString = bytes.toString()
+- propsFile.text = propertiesString
+- print("NEW ")
+- } else {
+- print("EXISTING ")
+- }
+-
+- println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
+- }
+-
+- //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
+- outputs.file(propsFileName)
+- outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
+-}
+-
+-
+-task jalviewjsEclipsePaths {
+- def eclipseProduct
+-
+- def eclipseRoot = jalviewjs_eclipse_root
+- if (eclipseRoot.startsWith("~/")) {
+- eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
+- }
+- if (OperatingSystem.current().isMacOsX()) {
+- eclipseRoot += "/Eclipse.app"
+- eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
+- eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
+- } else if (OperatingSystem.current().isWindows()) { // check these paths!!
+- if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
+- eclipseRoot += "/eclipse"
+- }
+- eclipseBinary = "${eclipseRoot}/eclipse.exe"
+- eclipseProduct = "${eclipseRoot}/.eclipseproduct"
+- } else { // linux or unix
+- if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
+- eclipseRoot += "/eclipse"
+-println("eclipseDir exists")
+- }
+- eclipseBinary = "${eclipseRoot}/eclipse"
+- eclipseProduct = "${eclipseRoot}/.eclipseproduct"
+- }
+-
+- eclipseVersion = "4.13" // default
+- def assumedVersion = true
+- if (file(eclipseProduct).exists()) {
+- def fis = new FileInputStream(eclipseProduct)
+- def props = new Properties()
+- props.load(fis)
+- eclipseVersion = props.getProperty("version")
+- fis.close()
+- assumedVersion = false
+- }
+-
+- def propKey = "eclipse_debug"
+- eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
+-
+- doFirst {
+- // do not run a headless transpile when we claim to be in Eclipse
+- if (IN_ECLIPSE) {
+- println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+- } else {
+- println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- }
+-
+- if (!assumedVersion) {
+- println("ECLIPSE VERSION=${eclipseVersion}")
+- }
+- }
+-}
+-
+-
+-task printProperties {
+- group "Debug"
+- description "Output to console all System.properties"
+- doFirst {
+- System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
+- }
+-}
+-
+-
+-task eclipseSetup {
+- dependsOn eclipseProject
+- dependsOn eclipseClasspath
+- dependsOn eclipseJdt
+-}
+-
+-
+-// this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
+-task jalviewjsEclipseCopyDropins(type: Copy) {
+- dependsOn jalviewjsEclipsePaths
+-
+- def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
+- inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
+- def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
+-
+- from inputFiles
+- into outputDir
+-}
+-
+-
+-// this eclipse -clean doesn't actually work
+-task jalviewjsCleanEclipse(type: Exec) {
+- dependsOn eclipseSetup
+- dependsOn jalviewjsEclipsePaths
+- dependsOn jalviewjsEclipseCopyDropins
+-
+- executable(eclipseBinary)
+- args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
+- if (eclipseDebug) {
+- args += "-debug"
+- }
+- args += "-l"
+-
+- def inputString = """exit
+-y
+-"""
+- def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
+- standardInput = inputByteStream
+-}
+-
+-/* not really working yet
+-jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
+-*/
+-
+-
+-task jalviewjsTransferUnzipSwingJs {
+- def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
+-
+- doLast {
+- copy {
+- from zipTree(file_zip)
+- into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+- }
+- }
+-
+- inputs.file file_zip
+- outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+-}
+-
+-
+-task jalviewjsTransferUnzipLib {
+- def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
+-
+- doLast {
+- zipFiles.each { file_zip ->
+- copy {
+- from zipTree(file_zip)
+- into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+- }
+- }
+- }
+-
+- inputs.files zipFiles
+- outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+-}
+-
+-
+-task jalviewjsTransferUnzipAllLibs {
+- dependsOn jalviewjsTransferUnzipSwingJs
+- dependsOn jalviewjsTransferUnzipLib
+-}
+-
+-
+-task jalviewjsCreateJ2sSettings(type: WriteProperties) {
+- group "JalviewJS"
+- description "Create the alternative j2s file from the j2s.* properties"
+-
+- jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
+- def siteDirProperty = "j2s.site.directory"
+- def setSiteDir = false
+- jalviewjsJ2sProps.each { prop, val ->
+- if (val != null) {
+- if (prop == siteDirProperty) {
+- if (!(val.startsWith('/') || val.startsWith("file://") )) {
+- val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
+- }
+- setSiteDir = true
+- }
+- property(prop,val)
+- }
+- if (!setSiteDir) { // default site location, don't override specifically set property
+- property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
+- }
+- }
+- outputFile = jalviewjsJ2sAltSettingsFileName
+-
+- if (! IN_ECLIPSE) {
+- inputs.properties(jalviewjsJ2sProps)
+- outputs.file(jalviewjsJ2sAltSettingsFileName)
+- }
+-}
+-
+-
+-task jalviewjsEclipseSetup {
+- dependsOn jalviewjsEclipseCopyDropins
+- dependsOn jalviewjsSetEclipseWorkspace
+- dependsOn jalviewjsCreateJ2sSettings
+-}
+-
+-
+-task jalviewjsSyncAllLibs (type: Sync) {
+- dependsOn jalviewjsTransferUnzipAllLibs
+- def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
+- inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
+- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+-
+- from inputFiles
+- into outputDir
+- def outputFiles = []
+- rename { filename ->
+- outputFiles += "${outputDir}/${filename}"
+- null
+- }
+- preserve {
+- include "**"
+- }
+- outputs.files outputFiles
+- inputs.files inputFiles
+-}
+-
+-
+-task jalviewjsSyncResources (type: Sync) {
+- dependsOn buildResources
+-
+- def inputFiles = fileTree(dir: resourcesBuildDir)
+- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+-
+- from inputFiles
+- into outputDir
+- def outputFiles = []
+- rename { filename ->
+- outputFiles += "${outputDir}/${filename}"
+- null
+- }
+- preserve {
+- include "**"
+- }
+- outputs.files outputFiles
+- inputs.files inputFiles
+-}
+-
+-
+-task jalviewjsSyncSiteResources (type: Sync) {
+- def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
+- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+-
+- from inputFiles
+- into outputDir
+- def outputFiles = []
+- rename { filename ->
+- outputFiles += "${outputDir}/${filename}"
+- null
+- }
+- preserve {
+- include "**"
+- }
+- outputs.files outputFiles
+- inputs.files inputFiles
+-}
+-
+-
+-task jalviewjsSyncBuildProperties (type: Sync) {
+- dependsOn createBuildProperties
+- def inputFiles = [file(buildProperties)]
+- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+-
+- from inputFiles
+- into outputDir
+- def outputFiles = []
+- rename { filename ->
+- outputFiles += "${outputDir}/${filename}"
+- null
+- }
+- preserve {
+- include "**"
+- }
+- outputs.files outputFiles
+- inputs.files inputFiles
+-}
+-
+-
+-task jalviewjsProjectImport(type: Exec) {
+- dependsOn eclipseSetup
+- dependsOn jalviewjsEclipsePaths
+- dependsOn jalviewjsEclipseSetup
+-
+- doFirst {
+- // do not run a headless import when we claim to be in Eclipse
+- if (IN_ECLIPSE) {
+- println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- throw new StopExecutionException("Not running headless import whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+- } else {
+- println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- }
+- }
+
+- //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
+- def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
+- executable(eclipseBinary)
+- args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
+- if (eclipseDebug) {
+- args += "-debug"
+- }
+- args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
+- if (!IN_ECLIPSE) {
+- args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+- args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
+- }
+-
+- inputs.file("${jalviewDir}/.project")
+- outputs.upToDateWhen {
+- file(projdir).exists()
+- }
+-}
+-
+-
+-task jalviewjsTranspile(type: Exec) {
+- dependsOn jalviewjsEclipseSetup
+- dependsOn jalviewjsProjectImport
+- dependsOn jalviewjsEclipsePaths
+- if (!IN_ECLIPSE) {
+- dependsOn jalviewjsEnableAltFileProperty
+- }
+-
+- doFirst {
+- // do not run a headless transpile when we claim to be in Eclipse
+- if (IN_ECLIPSE) {
+- println("Skipping task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- throw new StopExecutionException("Not running headless transpile whilst IN_ECLIPSE is '${IN_ECLIPSE}'")
+- } else {
+- println("Running task ${name} as IN_ECLIPSE=${IN_ECLIPSE}")
+- }
+- }
+-
+- executable(eclipseBinary)
+- args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
+- if (eclipseDebug) {
+- args += "-debug"
+- }
+- args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
+- if (!IN_ECLIPSE) {
+- args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+- args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
+- }
+-
+- def stdout
+- def stderr
+- doFirst {
+- stdout = new ByteArrayOutputStream()
+- stderr = new ByteArrayOutputStream()
+-
+- def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
+- def logOutFile = file(logOutFileName)
+- logOutFile.createNewFile()
+- logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
+-BINARY: ${eclipseBinary}
+-VERSION: ${eclipseVersion}
+-WORKSPACE: ${eclipseWorkspace}
+-DEBUG: ${eclipseDebug}
+-----
+-"""
+- def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+- // combine stdout and stderr
+- def logErrFOS = logOutFOS
+-
+- if (jalviewjs_j2s_to_console.equals("true")) {
+- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- new org.apache.tools.ant.util.TeeOutputStream(
+- logOutFOS,
+- stdout),
+- System.out)
+- errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- new org.apache.tools.ant.util.TeeOutputStream(
+- logErrFOS,
+- stderr),
+- System.err)
+- } else {
+- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- logOutFOS,
+- stdout)
+- errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- logErrFOS,
+- stderr)
+- }
+- }
+-
+- doLast {
+- if (stdout.toString().contains("Error processing ")) {
+- // j2s did not complete transpile
+- //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+- if (jalviewjs_ignore_transpile_errors.equals("true")) {
+- println("IGNORING TRANSPILE ERRORS")
+- println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+- } else {
+- throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+- }
+- }
+- }
+-
+- inputs.dir("${jalviewDir}/${sourceDir}")
+- outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
+- outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
+-}
+-
+-
+-def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
+-
+- def stdout = new ByteArrayOutputStream()
+- def stderr = new ByteArrayOutputStream()
+-
+- def coreFile = file(jsfile)
+- def msg = ""
+- msg = "Creating core for ${name}...\nGenerating ${jsfile}"
+- println(msg)
+- logOutFile.createNewFile()
+- logOutFile.append(msg+"\n")
+-
+- def coreTop = file(prefixFile)
+- def coreBottom = file(suffixFile)
+- coreFile.getParentFile().mkdirs()
+- coreFile.createNewFile()
+- coreFile.write( coreTop.getText("UTF-8") )
+- list.each {
+- f ->
+- if (f.exists()) {
+- def t = f.getText("UTF-8")
+- t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
+- coreFile.append( t )
+- } else {
+- msg = "...file '"+f.getPath()+"' does not exist, skipping"
+- println(msg)
+- logOutFile.append(msg+"\n")
+- }
+- }
+- coreFile.append( coreBottom.getText("UTF-8") )
+-
+- msg = "Generating ${zjsfile}"
+- println(msg)
+- logOutFile.append(msg+"\n")
+- def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+- def logErrFOS = logOutFOS
+-
+- javaexec {
+- classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
+- main = "com.google.javascript.jscomp.CommandLineRunner"
+- jvmArgs = [ "-Dfile.encoding=UTF-8" ]
+- args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
+- maxHeapSize = "2g"
+-
+- msg = "\nRunning '"+commandLine.join(' ')+"'\n"
+- println(msg)
+- logOutFile.append(msg+"\n")
+-
+- if (logOutConsole) {
+- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- new org.apache.tools.ant.util.TeeOutputStream(
+- logOutFOS,
+- stdout),
+- standardOutput)
+- errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- new org.apache.tools.ant.util.TeeOutputStream(
+- logErrFOS,
+- stderr),
+- errorOutput)
+- } else {
+- standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- logOutFOS,
+- stdout)
+- errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+- logErrFOS,
+- stderr)
+- }
+- }
+- msg = "--"
+- println(msg)
+- logOutFile.append(msg+"\n")
+-}
+-
+-
+-task jalviewjsBuildAllCores {
+- group "JalviewJS"
+- description "Build the core js lib closures listed in the classlists dir"
+- dependsOn jalviewjsTranspile
+- dependsOn jalviewjsTransferUnzipSwingJs
+-
+- def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
+- def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
+- def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
+- def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
+- def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
+- def prefixFile = "${jsDir}/core/coretop2.js"
+- def suffixFile = "${jsDir}/core/corebottom2.js"
+-
+- inputs.file prefixFile
+- inputs.file suffixFile
+-
+- def classlistFiles = []
+- // add the classlists found int the jalviewjs_classlists_dir
+- fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
+- file ->
+- def name = file.getName() - ".txt"
+- classlistFiles += [
+- 'file': file,
+- 'name': name
+- ]
+- }
+-
+- // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
+- //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
+- classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
+-
+- jalviewjsCoreClasslists = []
+-
+- classlistFiles.each {
+- hash ->
+-
+- def file = hash['file']
+- if (! file.exists()) {
+- //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
+- return false // this is a "continue" in groovy .each closure
+- }
+- def name = hash['name']
+- if (name == null) {
+- name = file.getName() - ".txt"
+- }
+-
+- def filelist = []
+- file.eachLine {
+- line ->
+- filelist += line
+- }
+- def list = fileTree(dir: j2sDir, includes: filelist)
+-
+- def jsfile = "${outputDir}/core${name}.js"
+- def zjsfile = "${outputDir}/core${name}.z.js"
+-
+- jalviewjsCoreClasslists += [
+- 'jsfile': jsfile,
+- 'zjsfile': zjsfile,
+- 'list': list,
+- 'name': name
+- ]
+-
+- inputs.file(file)
+- inputs.files(list)
+- outputs.file(jsfile)
+- outputs.file(zjsfile)
+- }
+-
+- // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
+- def stevesoftClasslistName = "_stevesoft"
+- def stevesoftClasslist = [
+- 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
+- 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
+- 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
+- 'name': stevesoftClasslistName
+- ]
+- jalviewjsCoreClasslists += stevesoftClasslist
+- inputs.files(stevesoftClasslist['list'])
+- outputs.file(stevesoftClasslist['jsfile'])
+- outputs.file(stevesoftClasslist['zjsfile'])
+-
+- // _all core
+- def allClasslistName = "_all"
+- def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
+- allJsFiles += fileTree(
+- dir: libJ2sDir,
+- include: "**/*.js",
+- excludes: [
+- // these exlusions are files that the closure-compiler produces errors for. Should fix them
+- "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
+- "**/org/jmol/export/JSExporter.js"
+- ]
+- )
+- allJsFiles += fileTree(
+- dir: swingJ2sDir,
+- include: "**/*.js",
+- excludes: [
+- // these exlusions are files that the closure-compiler produces errors for. Should fix them
+- "**/sun/misc/Unsafe.js",
+- "**/swingjs/jquery/jquery-editable-select.js",
+- "**/swingjs/jquery/j2sComboBox.js",
+- "**/sun/misc/FloatingDecimal.js"
+- ]
+- )
+- def allClasslist = [
+- 'jsfile': "${outputDir}/core${allClasslistName}.js",
+- 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
+- 'list': allJsFiles,
+- 'name': allClasslistName
+- ]
+- // not including this version of "all" core at the moment
+- //jalviewjsCoreClasslists += allClasslist
+- inputs.files(allClasslist['list'])
+- outputs.file(allClasslist['jsfile'])
+- outputs.file(allClasslist['zjsfile'])
+-
+- doFirst {
+- def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
+- logOutFile.getParentFile().mkdirs()
+- logOutFile.createNewFile()
+- logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
+-
+- jalviewjsCoreClasslists.each {
+- jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
+- }
+- }
+-
+-}
+-
+-
+-def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
+- copy {
+- from inputFile
+- into file(outputFile).getParentFile()
+- rename { filename ->
+- if (filename.equals(inputFile.getName())) {
+- return file(outputFile).getName()
+- }
+- return null
+- }
+- filter(ReplaceTokens,
+- beginToken: '_',
+- endToken: '_',
+- tokens: [
+- 'MAIN': '"'+main_class+'"',
+- 'CODE': "null",
+- 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
+- 'COREKEY': jalviewjs_core_key,
+- 'CORENAME': coreName
+- ]
+- )
+- }
+-}
+-
+-
+-task jalviewjsPublishCoreTemplates {
+- dependsOn jalviewjsBuildAllCores
+- def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
+- def inputFile = file(inputFileName)
+- def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+-
+- def outputFiles = []
+- jalviewjsCoreClasslists.each { cl ->
+- def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+- cl['outputfile'] = outputFile
+- outputFiles += outputFile
+- }
+-
+- doFirst {
+- jalviewjsCoreClasslists.each { cl ->
+- jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
+- }
+- }
+- inputs.file(inputFile)
+- outputs.files(outputFiles)
+-}
+-
+-
+-task jalviewjsSyncCore (type: Sync) {
+- dependsOn jalviewjsBuildAllCores
+- dependsOn jalviewjsPublishCoreTemplates
+- def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
+- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+-
+- from inputFiles
+- into outputDir
+- def outputFiles = []
+- rename { filename ->
+- outputFiles += "${outputDir}/${filename}"
+- null
+- }
+- preserve {
+- include "**"
+- }
+- outputs.files outputFiles
+- inputs.files inputFiles
+-}
+-
+-
+-// this Copy version of TransferSiteJs will delete anything else in the target dir
+-task jalviewjsCopyTransferSiteJs(type: Copy) {
+- dependsOn jalviewjsTranspile
+- from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+- into "${jalviewDir}/${jalviewjsSiteDir}"
+-}
+-
+-
+-// this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
+-task jalviewjsSyncTransferSiteJs(type: Sync) {
+- from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+- include "**/*.*"
+- into "${jalviewDir}/${jalviewjsSiteDir}"
+- preserve {
+- include "**"
+- }
+-}
+-
+-
+-jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
+-jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
+-jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
+-jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
+-
+-jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
+-jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
+-jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
+-jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
+-
+-
+-task jalviewjsPrepareSite {
+- group "JalviewJS"
+- description "Prepares the website folder including unzipping files and copying resources"
+- dependsOn jalviewjsSyncAllLibs
+- dependsOn jalviewjsSyncResources
+- dependsOn jalviewjsSyncSiteResources
+- dependsOn jalviewjsSyncBuildProperties
+- dependsOn jalviewjsSyncCore
+-}
+-
+-
+-task jalviewjsBuildSite {
+- group "JalviewJS"
+- description "Builds the whole website including transpiled code"
+- dependsOn jalviewjsCopyTransferSiteJs
+- dependsOn jalviewjsPrepareSite
+-}
+-
+-
+-task cleanJalviewjsTransferSite {
+- doFirst {
+- delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+- delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+- delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+- delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+- }
+-}
+-
+-
+-task cleanJalviewjsSite {
+- dependsOn cleanJalviewjsTransferSite
+- doFirst {
+- delete "${jalviewDir}/${jalviewjsSiteDir}"
+- }
+-}
+-
+-
+-task jalviewjsSiteTar(type: Tar) {
+- group "JalviewJS"
+- description "Creates a tar.gz file for the website"
+- dependsOn jalviewjsBuildSite
+- def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
+- archiveFileName = outputFilename
+-
+- compression Compression.GZIP
+-
+- from "${jalviewDir}/${jalviewjsSiteDir}"
+- into jalviewjs_site_dir // this is inside the tar file
+-
+- inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
+-}
+-
+-
+-task jalviewjsServer {
+- group "JalviewJS"
+- def filename = "jalviewjsTest.html"
+- description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
+- def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
+- doLast {
+-
+- def factory
+- try {
+- def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
+- factory = f.newInstance()
+- } catch (ClassNotFoundException e) {
+- throw new GradleException("Unable to create SimpleHttpFileServerFactory")
+- }
+- def port = Integer.valueOf(jalviewjs_server_port)
+- def start = port
+- def running = false
+- def url
+- def jalviewjsServer
+- while(port < start+1000 && !running) {
+- try {
+- def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
+- jalviewjsServer = factory.start(doc_root, port)
+- running = true
+- url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
+- println("SERVER STARTED with document root ${doc_root}.")
+- println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).")
+- println("For debug: "+url+"?j2sdebug")
+- println("For verbose: "+url+"?j2sverbose")
+- } catch (Exception e) {
+- port++;
+- }
+- }
+- def htmlText = """
+- <p><a href="${url}">JalviewJS Test. <${url}></a></p>
+- <p><a href="${url}?j2sdebug">JalviewJS Test with debug. <${url}?j2sdebug></a></p>
+- <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. <${url}?j2sdebug></a></p>
+- """
+- jalviewjsCoreClasslists.each { cl ->
+- def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
+- htmlText += """
+- <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. <${urlcore}></a></p>
+- """
+- println("For core ${cl.name}: "+urlcore)
+- }
+-
+- file(htmlFile).text = htmlText
+- }
+-
+- outputs.file(htmlFile)
+- outputs.upToDateWhen({false})
+-}
+-
+-
+-task cleanJalviewjsAll {
+- group "JalviewJS"
+- description "Delete all configuration and build artifacts to do with JalviewJS build"
+- dependsOn cleanJalviewjsSite
+- dependsOn jalviewjsEclipsePaths
+-
+- doFirst {
+- delete "${jalviewDir}/${jalviewjsBuildDir}"
+- delete "${jalviewDir}/${eclipse_bin_dir}"
+- if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
+- delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
+- }
+- delete jalviewjsJ2sAltSettingsFileName
+- }
+-
+- outputs.upToDateWhen( { false } )
+-}
+-
+-
+-task jalviewjsIDE_checkJ2sPlugin {
+- group "00 JalviewJS in Eclipse"
+- description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
+-
+- doFirst {
+- def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
+- def j2sPluginFile = file(j2sPlugin)
+- def eclipseHome = System.properties["eclipse.home.location"]
+- if (eclipseHome == null || ! IN_ECLIPSE) {
+- throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
+- }
+- def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
+- def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
+- if (altPluginsDir != null && file(altPluginsDir).exists()) {
+- eclipseJ2sPluginDirs += altPluginsDir
+- }
+- def foundPlugin = false
+- def j2sPluginFileName = j2sPluginFile.getName()
+- def eclipseJ2sPlugin
+- def eclipseJ2sPluginFile
+- eclipseJ2sPluginDirs.any { dir ->
+- eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
+- eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+- if (eclipseJ2sPluginFile.exists()) {
+- foundPlugin = true
+- return true
+- }
+- }
+- if (!foundPlugin) {
+- def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
+- System.err.println(msg)
+- throw new StopExecutionException(msg)
+- }
+-
+- def digest = MessageDigest.getInstance("MD5")
+-
+- digest.update(j2sPluginFile.text.bytes)
+- def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+-
+- digest.update(eclipseJ2sPluginFile.text.bytes)
+- def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+-
+- if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
+- def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
+- System.err.println(msg)
+- throw new StopExecutionException(msg)
+- } else {
+- def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
+- println(msg)
+- }
+- }
+-}
+-
+-task jalviewjsIDE_copyJ2sPlugin {
+- group "00 JalviewJS in Eclipse"
+- description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
+-
+- doFirst {
+- def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
+- def j2sPluginFile = file(j2sPlugin)
+- def eclipseHome = System.properties["eclipse.home.location"]
+- if (eclipseHome == null || ! IN_ECLIPSE) {
+- throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
+- }
+- def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
+- def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+- def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
+- System.err.println(msg)
+- copy {
+- from j2sPlugin
+- eclipseJ2sPluginFile.getParentFile().mkdirs()
+- into eclipseJ2sPluginFile.getParent()
+- }
+- }
+-}
+-
+-
+-task jalviewjsIDE_j2sFile {
+- group "00 JalviewJS in Eclipse"
+- description "Creates the .j2s file"
+- dependsOn jalviewjsCreateJ2sSettings
+-}
+-
+-
+-task jalviewjsIDE_SyncCore {
+- group "00 JalviewJS in Eclipse"
+- description "Build the core js lib closures listed in the classlists dir and publish core html from template"
+- dependsOn jalviewjsSyncCore
+-}
+-
+-
+-task jalviewjsIDE_SyncSiteAll {
+- dependsOn jalviewjsSyncAllLibs
+- dependsOn jalviewjsSyncResources
+- dependsOn jalviewjsSyncSiteResources
+- dependsOn jalviewjsSyncBuildProperties
+-}
+-
+-
+-cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
+-
+-
+-task jalviewjsIDE_PrepareSite {
+- group "00 JalviewJS in Eclipse"
+- description "Sync libs and resources to site dir, but not closure cores"
+-
+- dependsOn jalviewjsIDE_SyncSiteAll
+- //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
+-}
+-
+-
+-task jalviewjsIDE_AssembleSite {
+- group "00 JalviewJS in Eclipse"
+- description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
+- dependsOn jalviewjsPrepareSite
+-}
+-
+-
+-task jalviewjsIDE_SiteClean {
+- group "00 JalviewJS in Eclipse"
+- description "Deletes the Eclipse transpiled site"
+- dependsOn cleanJalviewjsSite
+-}
+-
+-
+-task jalviewjsIDE_Server {
+- group "00 JalviewJS in Eclipse"
+- description "Starts a webserver on localhost to test the website"
+- dependsOn jalviewjsServer
+-}
+-
+-
+-// buildship runs this at import or gradle refresh
+-task eclipseSynchronizationTask {
+- //dependsOn eclipseSetup
+- dependsOn createBuildProperties
+- if (J2S_ENABLED) {
+- dependsOn jalviewjsIDE_j2sFile
+- dependsOn jalviewjsIDE_checkJ2sPlugin
+- dependsOn jalviewjsIDE_PrepareSite
+- }
+-}
+-
+-
+-// buildship runs this at build time or project refresh
+-task eclipseAutoBuildTask {
+- //dependsOn jalviewjsIDE_checkJ2sPlugin
+- //dependsOn jalviewjsIDE_PrepareSite
++ outputs.file("${outputDir}/${archiveFileName}")
+ }
+
+-
+-task jalviewjs {
+- group "JalviewJS"
+- description "Build the site"
+- dependsOn jalviewjsBuildSite
+-}
<mime-type type="application/x-jalview+xml+zip">
<comment>Jalview File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.jvp" weight="100"/>
</mime-type>
<mime-type type="chemical/x-cif">
<comment>CIF File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.cif" weight="40"/>
</mime-type>
<mime-type type="chemical/x-mmcif">
<comment>mmCIF File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.mcif" weight="40"/>
<glob pattern="*.mmcif" weight="40"/>
</mime-type>
<mime-type type="chemical/x-pdb">
<comment>PDB File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.pdb" weight="40"/>
<glob pattern="*.ent" weight="40"/>
</mime-type>
<mime-type type="application/x-amsa+txt">
<comment>AMSA File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.amsa" weight="90"/>
</mime-type>
<mime-type type="application/x-jalview-annotations+text">
<comment>Jalview Annotations File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.annotations" weight="100"/>
<glob pattern="*.jvannotations" weight="100"/>
</mime-type>
<mime-type type="application/x-jalview-biojson+json">
<comment>BioJSON File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.biojson" weight="100"/>
</mime-type>
<mime-type type="application/x-blc+txt">
<comment>BLC File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.blc" weight="90"/>
</mime-type>
<mime-type type="application/x-clustal+txt">
<comment>Clustal File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.aln" weight="90"/>
</mime-type>
<mime-type type="application/x-fasta+txt">
<comment>Fasta File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.fa" weight="90"/>
<glob pattern="*.fasta" weight="90"/>
</mime-type>
<mime-type type="application/x-jalview-features+text">
<comment>Jalview Features File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.features" weight="100"/>
<glob pattern="*.jvfeatures" weight="100"/>
</mime-type>
<mime-type type="application/x-gff2+txt">
<comment>Generic Features Format v2 File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.gff2" weight="90"/>
</mime-type>
<mime-type type="application/x-gff3+txt">
<comment>Generic Features Format v3 File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.gff3" weight="90"/>
</mime-type>
<mime-type type="application/x-jalview-jnet+text">
<comment>JnetFile File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.concise" weight="100"/>
<glob pattern="*.jnet" weight="100"/>
</mime-type>
<mime-type type="application/x-msf+txt">
<comment>MSF File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.msf" weight="90"/>
</mime-type>
<mime-type type="application/x-pfam+txt">
<comment>PFAM File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.pfam" weight="90"/>
</mime-type>
<mime-type type="application/x-phylip+txt">
<comment>PHYLIP File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.phy" weight="90"/>
</mime-type>
<mime-type type="application/x-pileup+txt">
<comment>PileUp File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.pileup" weight="90"/>
</mime-type>
<mime-type type="application/x-pir+txt">
<comment>PIR File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.pir" weight="90"/>
</mime-type>
<mime-type type="application/rnaml+xml">
<comment>RNAML File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.rnaml" weight="90"/>
</mime-type>
<mime-type type="application/x-jalview-scorematrix+text">
<comment>Substitution Matrix File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.mat" weight="100"/>
</mime-type>
<mime-type type="application/x-stockholm+txt">
<comment>Stockholm File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.sto" weight="90"/>
<glob pattern="*.stk" weight="90"/>
</mime-type>
Icon=jalview-icon
Type=Application
TryExec=jalview
-Exec=jalview -open %u
+Exec=jalview %u
Terminal=false
Categories=Science;Biology;
Keywords=alignment;sequence;
--- /dev/null
+#!/usr/bin/env bash
+set -e
+ARG1=$1
+
+# copy the debian default settings if no user jalview settings file exist
+if [ -n "${HOME}" -a \! -e ${HOME}/.jalview_properties ]; then
+ /bin/cp /etc/jalview_properties ${HOME}/.jalview_properties
+fi
+
+# check to see if $1 is set and is not start of other cli set args
+OPEN=""
+if [ -n "$ARG1" -a "$ARG1" = "${ARG1#-}" ]; then
+ # first argument exists and does not start with a "-"
+ OPEN="-open"
+fi
+
+java -jar /usr/share/java/jalview.jar $OPEN "$@"
--- /dev/null
+/* Convention for properties. Read from gradle.properties, use lower_case_underlines for property names.
+ * For properties set within build.gradle, use camelCaseNoSpace.
+ */
+import org.apache.tools.ant.filters.ReplaceTokens
+
+plugins {
+ id 'java'
+ id 'application'
+}
+
+// in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
+def string(Object o) {
+ return o == null ? "" : o.toString()
+}
+
+def overrideProperties(String propsFileName, boolean output = false) {
+ if (propsFileName == null) {
+ return
+ }
+ def propsFile = file(propsFileName)
+ if (propsFile != null && propsFile.exists()) {
+ println("Using properties from file '${propsFileName}'")
+ try {
+ def p = new Properties()
+ def localPropsFIS = new FileInputStream(propsFile)
+ p.load(localPropsFIS)
+ localPropsFIS.close()
+ p.each {
+ key, val ->
+ def oldval
+ if (project.hasProperty(key)) {
+ oldval = project.findProperty(key)
+ project.setProperty(key, val)
+ if (output) {
+ println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
+ }
+ } else {
+ ext.setProperty(key, val)
+ if (output) {
+ println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
+ }
+ }
+ }
+ } catch (Exception e) {
+ println("Exception reading local.properties")
+ e.printStackTrace()
+ }
+ }
+}
+
+project.ext {
+ jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+ jalviewDirRelativePath = jalviewDir
+
+ propertiesChannelName = "release"
+ channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
+ channelGradleProperties = string("${channelDir}/channel_gradle.properties")
+ overrideProperties(channelGradleProperties, false)
+
+ ////
+ // Import releaseProps from the RELEASE file
+ // or a file specified via JALVIEW_RELEASE_FILE if defined
+ // Expect jalview.version and target release branch in jalview.release
+ def releaseProps = new Properties();
+ def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
+ def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
+ try {
+ (new File(releasePropFile!=null ? releasePropFile : defaultReleasePropFile)).withInputStream {
+ releaseProps.load(it)
+ }
+ } catch (Exception fileLoadError) {
+ throw new Error("Couldn't load release properties file "+(releasePropFile==null ? defaultReleasePropFile : "from custom location: releasePropFile"),fileLoadError);
+ }
+ ////
+ // Set JALVIEW_VERSION if it is not already set
+ if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
+ JALVIEW_VERSION = releaseProps.get("jalview.version")
+ }
+
+ // essentials
+ bareSourceDir = string(source_dir)
+ sourceDir = string("${jalviewDir}/${bareSourceDir}")
+ resourceDir = string("${jalviewDir}/${resource_dir}")
+ bareTestSourceDir = string(test_source_dir)
+ testDir = string("${jalviewDir}/${bareTestSourceDir}")
+
+ classesDir = string("${jalviewDir}/${classes_dir}")
+
+ useClover = false
+
+ resourceClassesDir = classesDir
+
+ testSourceDir = testDir
+ testClassesDir = "${jalviewDir}/${test_output_dir}"
+
+ buildProperties = string("${classesDir}/${build_properties_file}")
+ getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
+
+ install4jApplicationName = "${jalview_name}"
+
+ println("Using a ${CHANNEL} profile.")
+
+ additional_compiler_args = []
+ // configure classpath/args for j8/j11 compilation
+ if (JAVA_VERSION.equals("1.8")) {
+ JAVA_INTEGER_VERSION = string("8")
+ //libDir = j8libDir
+ libDir = j11libDir
+ libDistDir = j8libDir
+ compile_source_compatibility = 1.8
+ compile_target_compatibility = 1.8
+ } else if (JAVA_VERSION.equals("11")) {
+ JAVA_INTEGER_VERSION = string("11")
+ libDir = j11libDir
+ libDistDir = j11libDir
+ compile_source_compatibility = 11
+ compile_target_compatibility = 11
+ } else {
+ throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
+ }
+
+ resourceBuildDir = string("${buildDir}/resources")
+ resourcesBuildDir = string("${resourceBuildDir}/resources_build")
+ helpBuildDir = string("${resourceBuildDir}/help_build")
+ docBuildDir = string("${resourceBuildDir}/doc_build")
+
+ if (buildProperties == null) {
+ buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
+ }
+ buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
+ helpParentDir = string("${jalviewDir}/${help_parent_dir}")
+ helpSourceDir = string("${helpParentDir}/${help_dir}")
+ helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
+
+ // ENDEXT
+}
+
+
+sourceSets {
+ main {
+ java {
+ srcDirs sourceDir
+ outputDir = file(classesDir)
+ }
+
+ resources {
+ srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
+ }
+
+ compileClasspath = files(sourceSets.main.java.outputDir)
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+
+
+ compileClasspath = files(sourceSets.main.java.outputDir)
+ compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+
+ runtimeClasspath = compileClasspath
+ runtimeClasspath += files(sourceSets.main.resources.srcDirs)
+ }
+
+ test {
+ java {
+ srcDirs testSourceDir
+ outputDir = file(testClassesDir)
+ }
+
+ resources {
+ srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
+ }
+
+ compileClasspath = files( sourceSets.test.java.outputDir )
+ compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
+ compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
+
+ runtimeClasspath = compileClasspath
+ runtimeClasspath += files(sourceSets.test.resources.srcDirs)
+ }
+ /* test {
+ java {
+ srcDirs testSourceDir
+ outputDir = file(testClassesDir)
+ }
+
+ resources {
+ srcDirs = sourceSets.main.resources.srcDirs
+ }
+
+ compileClasspath = files( sourceSets.test.java.outputDir )
+ compileClasspath += sourceSets.main.compileClasspath
+ compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["** REMOVE_THIS_GAP /*.jar"])
+
+ runtimeClasspath = compileClasspath
+ }
+*/
+}
+
+
+compileJava {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+ doFirst {
+ print ("Setting target compatibility to "+compile_target_compatibility+"\n")
+ }
+}
+
+
+compileTestJava {
+ doFirst {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+}
+
+
+clean {
+ doFirst {
+ delete sourceSets.main.java.outputDir
+ }
+}
+
+
+cleanTest {
+ doFirst {
+ delete sourceSets.test.java.outputDir
+ }
+}
+
+
+// format is a string like date.format("dd MMMM yyyy")
+def getDate(format) {
+ def date = new Date()
+ return date.format(format)
+}
+
+
+task copyDocs(type: Copy) {
+ def inputDir = "${jalviewDir}/${doc_dir}"
+ def outputDir = "${docBuildDir}/${doc_dir}"
+ from(inputDir) {
+ include('**/*.txt')
+ include('**/*.md')
+ include('**/*.html')
+ include('**/*.xml')
+ filter(ReplaceTokens,
+ beginToken: '$$',
+ endToken: '$$',
+ tokens: [
+ 'Version-Rel': JALVIEW_VERSION,
+ 'Year-Rel': getDate("yyyy")
+ ]
+ )
+ }
+ from(inputDir) {
+ exclude('**/*.txt')
+ exclude('**/*.md')
+ exclude('**/*.html')
+ exclude('**/*.xml')
+ }
+ into outputDir
+
+ inputs.dir(inputDir)
+ outputs.dir(outputDir)
+}
+
+
+task copyHelp(type: Copy) {
+ def inputDir = helpSourceDir
+ def outputDir = "${helpBuildDir}/${help_dir}"
+ from(inputDir) {
+ include('**/*.txt')
+ include('**/*.md')
+ include('**/*.html')
+ include('**/*.hs')
+ include('**/*.xml')
+ include('**/*.jhm')
+ filter(ReplaceTokens,
+ beginToken: '$$',
+ endToken: '$$',
+ tokens: [
+ 'Version-Rel': JALVIEW_VERSION,
+ 'Year-Rel': getDate("yyyy")
+ ]
+ )
+ }
+ from(inputDir) {
+ exclude('**/*.txt')
+ exclude('**/*.md')
+ exclude('**/*.html')
+ exclude('**/*.hs')
+ exclude('**/*.xml')
+ exclude('**/*.jhm')
+ }
+ into outputDir
+
+ inputs.dir(inputDir)
+ outputs.files(helpFile)
+ outputs.dir(outputDir)
+}
+
+
+task copyResources(type: Copy) {
+ group = "build"
+ description = "Copy (and make text substitutions in) the resources dir to the build area"
+
+ def inputDir = resourceDir
+ def outputDir = resourcesBuildDir
+ from(inputDir) {
+ include('**/*.txt')
+ include('**/*.md')
+ include('**/*.html')
+ include('**/*.xml')
+ filter(ReplaceTokens,
+ beginToken: '$$',
+ endToken: '$$',
+ tokens: [
+ 'Version-Rel': JALVIEW_VERSION,
+ 'Year-Rel': getDate("yyyy")
+ ]
+ )
+ }
+ from(inputDir) {
+ exclude('**/*.txt')
+ exclude('**/*.md')
+ exclude('**/*.html')
+ exclude('**/*.xml')
+ }
+ into outputDir
+
+ inputs.dir(inputDir)
+ outputs.dir(outputDir)
+}
+
+task copyChannelResources(type: Copy) {
+ dependsOn copyResources
+ group = "build"
+ description = "Copy the channel resources dir to the build resources area"
+
+ def inputDir = "${channelDir}/${resource_dir}"
+ def outputDir = resourcesBuildDir
+ from inputDir
+ into outputDir
+
+ inputs.dir(inputDir)
+ outputs.dir(outputDir)
+}
+
+task createBuildProperties(type: Copy) {
+ // using the build_properties already included in the source tarball
+ def inputFile = "build_properties"
+ def outputFile = buildProperties
+ from inputFile
+ into file(outputFile).getParent()
+ rename(file(inputFile).getName(), file(outputFile).getName())
+
+ inputs.file(inputFile)
+ outputs.file(outputFile)
+}
+
+
+task buildIndices(type: JavaExec) {
+ dependsOn copyHelp
+ classpath = sourceSets.main.compileClasspath
+ main = "com.sun.java.help.search.Indexer"
+ workingDir = "${helpBuildDir}/${help_dir}"
+ def argDir = "html"
+ args = [ argDir ]
+ inputs.dir("${workingDir}/${argDir}")
+
+ outputs.dir("${classesDir}/doc")
+ outputs.dir("${classesDir}/help")
+ outputs.file("${workingDir}/JavaHelpSearch/DOCS")
+ outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
+ outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
+ outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
+ outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
+ outputs.file("${workingDir}/JavaHelpSearch/TMAP")
+}
+
+task buildResources {
+ dependsOn copyResources
+ dependsOn copyChannelResources
+ dependsOn createBuildProperties
+}
+
+task prepare {
+ dependsOn buildResources
+ dependsOn copyDocs
+ dependsOn copyHelp
+ dependsOn buildIndices
+}
+
+
+compileJava.dependsOn prepare
+run.dependsOn compileJava
+//run.dependsOn prepare
+
+
+//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
+test {
+ dependsOn prepare
+ dependsOn compileJava //?
+
+ useTestNG() {
+ includeGroups testng_groups
+ excludeGroups testng_excluded_groups
+ preserveOrder true
+ useDefaultListeners=true
+ }
+
+ maxHeapSize = "1024m"
+
+ workingDir = jalviewDir
+ //systemProperties 'clover.jar' System.properties.clover.jar
+ def testLaf = project.findProperty("test_laf")
+ if (testLaf != null) {
+ println("Setting Test LaF to '${testLaf}'")
+ systemProperty "laf", testLaf
+ }
+ def testHiDPIScale = project.findProperty("test_HiDPIScale")
+ if (testHiDPIScale != null) {
+ println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
+ systemProperty "sun.java2d.uiScale", testHiDPIScale
+ }
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ jvmArgs += additional_compiler_args
+
+ doFirst {
+ }
+}
+
+
+task compileLinkCheck(type: JavaCompile) {
+ options.fork = true
+ classpath = files("${jalviewDir}/${utils_dir}")
+ destinationDir = file("${jalviewDir}/${utils_dir}")
+ source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+
+ inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+ inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+ outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
+ outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
+}
+
+
+task linkCheck(type: JavaExec) {
+ dependsOn prepare
+ dependsOn compileLinkCheck
+
+ def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
+ classpath = files("${jalviewDir}/${utils_dir}")
+ main = "HelpLinksChecker"
+ workingDir = jalviewDir
+ args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
+
+ def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ outFOS,
+ System.out)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ outFOS,
+ System.err)
+
+ inputs.dir(helpBuildDir)
+ outputs.file(helpLinksCheckerOutFile)
+}
+
+
+// import the pubhtmlhelp target
+ant.properties.basedir = "${jalviewDir}"
+ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
+ant.importBuild "${utils_dir}/publishHelp.xml"
+
+
+task cleanPackageDir(type: Delete) {
+ doFirst {
+ delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
+ }
+}
+
+
+jar {
+ dependsOn prepare
+ dependsOn linkCheck
+
+ manifest {
+ attributes "Main-Class": main_class,
+ "Permissions": "all-permissions",
+ "Application-Name": install4jApplicationName,
+ "Codebase": application_codebase,
+ "Implementation-Version": JALVIEW_VERSION
+ }
+
+ def outputDir = "${jalviewDir}/${package_dir}"
+ destinationDirectory = file(outputDir)
+ archiveFileName = rootProject.name+".jar"
+
+ exclude "cache*/**"
+ exclude "*.jar"
+ exclude "*.jar.*"
+ exclude "**/*.jar"
+ exclude "**/*.jar.*"
+
+ inputs.dir(sourceSets.main.java.outputDir)
+ sourceSets.main.resources.srcDirs.each{ dir ->
+ inputs.dir(dir)
+ }
+
+ outputs.file("${outputDir}/${archiveFileName}")
+}
+
--- /dev/null
+# global template for ~/.jalview_properties for debian systems
+#
+# this file is copied into a user's home directory by
+# the jalview wrapper script when no .jalview_properties file
+# exists.
+#
+# changes to this file will not affect the jalview configuration
+# for existing users (at least not at the time of writing)
+
+# Configure the automatic display of the Jalview Example Project for new users
+# default is true
+# SHOW_STARTUP_FILE=false
+
+# Location of the file to be loaded in on startup if SHOW_STARTUP_FILE is true
+# default is https://www.jalview.org/examples/exampleFile_2_7.jvp
+# STARTUP_FILE=https://www.jalview.org/examples/exampleFile_2_7.jvp
+
+#
+# Disable Jalview's connections to various web services
+#
+
+# Connection: https://www.jalview.org/services/identifiers
+# uncomment to stop jalview retrieving a list of URL templates for
+# biological databases originally provided by identifiers.org
+#
+# NOIDENTIFIERSSERVICE=true
+
+# Connection: https://www.jalview.org/feeds/desktop/rss
+# uncomment to stop Jalview checking the www.jalview.org news feed
+# NONEWS=true
+
+# Connection: https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json
+# uncomment to disable download of the latest 'BioJS' HTML export template
+# NOHTMLTEMPLATES=true
+
+# Uncomment to disable pings to google analytics
+# these provide record of launch statistics for the Jalview project
+#
+# default is to prompt user on launch.
+# Allowed values are 'true', 'false' or undefined
+# USAGESTATS=false
+
+# Uncomment to disable jalview's retrieval of https://www.jalview.org/cgi-bin/questionnaire.pl
+# this service is used to make Jalview users aware
+# of any community questionnaires currently active on www.jalview.org
+# Allowed values are true/false. Default is true.
+# NOQUESTIONNAIRES=true
+
+# Uncomment to disable jalview's retrieval of https://www.jalview.org/webstart/jalview.jnlp
+# this document contains the version number of the latest release
+# and used to notify the user if they should consider upgrading their installation.
+# Allowed values are true/false. Default is true.
+# VERSION_CHECK=false
+
+# Uncomment to prevent jalview automatically contacting
+# https://www.compbio.dundee.ac.uk/jabaws/ to discover web services
+# When disabled, users can still initiate service discovery via a button
+# in the 'Web Services' menu.
+# Allowed values are true or false. Default is true.
+# SHOW_JWS2_SERVICES=false
\ No newline at end of file
<mime-type type="$$MIMETYPE$$">
<comment>$$NAME$$ File</comment>
- <icon name="$$ICONFILE$$"/>
+ <generic-icon name="$$ICONFILE$$"/>
$$ <glob pattern="*.EXTENSIONS" weight="$$PRIORITY$$0"/>
$$ </mime-type>
$MimeType .= $mimetype;
my $iconfile = $a->{iconfile};
- $iconfile = "jalview-file" unless $iconfile;
+ $iconfile = "x-jalview-file" unless $iconfile;
my $primary = (! grep($_ eq $shortname, @non_primary));
my $primarystring = $primary?"true":"false";
Icon=jalview-icon
Type=Application
TryExec=jalview
-Exec=jalview -open %u
+Exec=jalview %u
Terminal=false
Categories=Science;Biology;
Keywords=alignment;sequence;
### and
### ./tgz/jre-VERSION-OS-ARCH.tgz
### which is an archive of the _contents_ of ./jre-VERSION-OS-ARCH/jre/ and used by install4j for the installer
+### bs 2021-10-26
+### Edited to use adoptium domain to gain access to Java 17 (LTS) versions.
-BASE=https://api.adoptopenjdk.net/v3/binary/latest
+BASE=https://api.adoptium.net/v3/binary/latest
RELEASE_TYPE=ga
JVM_IMPL=hotspot
HEAP_SIZE=normal
-VENDOR=adoptopenjdk
+VENDOR=eclipse
IMAGE_TYPE=jdk
RM=/bin/rm
fi && rmdir "$temp"/* "$temp"
)
-for FEATURE_VERSION in 8 11 12 13; do
- for OS in mac; do
- #for OS in linux mac windows; do
- for ARCH in x64; do
- #for ARCH in aarch64 arm x32 x64; do
- NAME="${IMAGE_TYPE}-${FEATURE_VERSION}-${OS}-${ARCH}"
- TARFILE="${NAME}.tgz"
- echo "* Downloading ${TARFILE}"
- URL="${BASE}/${FEATURE_VERSION}/${RELEASE_TYPE}/${OS}/${ARCH}/${IMAGE_TYPE}/${JVM_IMPL}/${HEAP_SIZE}/${VENDOR}"
- wget -q -O "${TARFILE}" "${URL}"
- if [ "$?" != 0 ]; then
- echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}'"
- $RM -f "${TARFILE}"
- continue;
- fi
- echo "Unpacking ${TARFILE}"
- JREDIR="${NAME}/${IMAGE_TYPE}"
- [ x$NAME != x -a -e "${JREDIR}" ] && $RM -rf "${JREDIR}"
- mkdir -p "${JREDIR}"
- if [ x$OS = xwindows ]; then
- echo "using unzip"
- unzip-strip "${TARFILE}" "${JREDIR}"
- RET=$?
- else
- echo "using tar"
- tar --strip-components=1 -C "${JREDIR}" -zxf "${TARFILE}"
- RET=$?
- fi
- if [ "$RET" != 0 ]; then
- echo "Error unpacking ${TARFILE}"
- exit 1
- fi
- $RM "${TARFILE}"
- done
+for FEATURE_VERSION in 8 11 17; do
+ for OS_ARCH in mac:x64 mac:aarch64 windows:x64 linux:x64 linux:arm linux:aarch64; do
+ OS=${OS_ARCH%:*}
+ ARCH=${OS_ARCH#*:}
+ NAME="${IMAGE_TYPE}-${FEATURE_VERSION}-${OS}-${ARCH}"
+ TARFILE="${NAME}.tgz"
+ echo "* Downloading ${TARFILE}"
+ URL="${BASE}/${FEATURE_VERSION}/${RELEASE_TYPE}/${OS}/${ARCH}/${IMAGE_TYPE}/${JVM_IMPL}/${HEAP_SIZE}/${VENDOR}"
+ wget -q -O "${TARFILE}" "${URL}"
+ if [ "$?" != 0 ]; then
+ echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}'"
+ $RM -f "${TARFILE}"
+ continue;
+ fi
+ echo "Unpacking ${TARFILE}"
+ JREDIR="${NAME}/${IMAGE_TYPE}"
+ [ x$NAME != x -a -e "${JREDIR}" ] && $RM -rf "${JREDIR}"
+ mkdir -p "${JREDIR}"
+ if [ x$OS = xwindows ]; then
+ echo "using unzip"
+ unzip-strip "${TARFILE}" "${JREDIR}"
+ RET=$?
+ else
+ echo "using tar"
+ tar --strip-components=1 -C "${JREDIR}" -zxf "${TARFILE}"
+ RET=$?
+ fi
+ if [ "$RET" != 0 ]; then
+ echo "Error unpacking ${TARFILE}"
+ exit 1
+ fi
+ $RM "${TARFILE}"
done
done
### and
### ./tgz/jre-VERSION-OS-ARCH.tgz
### which is an archive of the _contents_ of ./jre-VERSION-OS-ARCH/jre/ and used by install4j for the installer
+### bs 2021-10-26
+### Edited to use adoptium domain to gain access to Java 17 (LTS) versions.
-BASE=https://api.adoptopenjdk.net/v3/binary/latest
+BASE=https://api.adoptium.net/v3/binary/latest
RELEASE_TYPE=ga
JVM_IMPL=hotspot
HEAP_SIZE=normal
-VENDOR=adoptopenjdk
+VENDOR=eclipse
IMAGE_TYPE=jre
TAR=tar
ZIP=zip
fi && rmdir "$temp"/* "$temp"
)
-for FEATURE_VERSION in 8 11; do
- for OS in linux mac windows; do
- for ARCH in x64 x32 arm; do
- #for ARCH in aarch64 arm x32 x64; do
- NAME="${IMAGE_TYPE}-${FEATURE_VERSION}-${OS}-${ARCH}"
- TARFILE="${NAME}.tgz"
- echo "* Downloading ${TARFILE}"
- URL="${BASE}/${FEATURE_VERSION}/${RELEASE_TYPE}/${OS}/${ARCH}/${IMAGE_TYPE}/${JVM_IMPL}/${HEAP_SIZE}/${VENDOR}"
- wget -q -O "${TARFILE}" "${URL}"
- if [ "$?" != 0 ]; then
- echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}'"
- $RM -f "${TARFILE}"
- continue;
- fi
- echo "Unpacking ${TARFILE}"
- JREDIR="${NAME}/${IMAGE_TYPE}"
- [ x$NAME != x -a -e "${JREDIR}" ] && $RM -rf "${JREDIR}"
- mkdir -p "${JREDIR}"
- if [ x$OS = xwindows ]; then
- echo "using unzip"
- unzip-strip "${TARFILE}" "${JREDIR}"
+for FEATURE_VERSION in 8 11 17; do
+ for OS_ARCH in mac:x64 mac:aarch64 windows:x64 linux:x64 linux:arm linux:aarch64; do
+ OS=${OS_ARCH%:*}
+ ARCH=${OS_ARCH#*:}
+ NAME="${IMAGE_TYPE}-${FEATURE_VERSION}-${OS}-${ARCH}"
+ TARFILE="${NAME}.tgz"
+ echo "* Downloading ${TARFILE}"
+ URL="${BASE}/${FEATURE_VERSION}/${RELEASE_TYPE}/${OS}/${ARCH}/${IMAGE_TYPE}/${JVM_IMPL}/${HEAP_SIZE}/${VENDOR}"
+ wget -q -O "${TARFILE}" "${URL}"
+ if [ "$?" != 0 ]; then
+ echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}'"
+ $RM -f "${TARFILE}"
+ continue;
+ fi
+ echo "Unpacking ${TARFILE}"
+ JREDIR="${NAME}/${IMAGE_TYPE}"
+ [ x$NAME != x -a -e "${JREDIR}" ] && $RM -rf "${JREDIR}"
+ mkdir -p "${JREDIR}"
+ if [ x$OS = xwindows ]; then
+ echo "using unzip"
+ unzip-strip "${TARFILE}" "${JREDIR}"
+ RET=$?
+ else
+ echo "using tar"
+ if [ x$OS = xmac -a x$STRIP_MAC_APP_BUNDLING = xtrue ]; then
+ $TAR --strip-components=3 -C "${JREDIR}" -zxf "${TARFILE}" "*/Contents/Home"
RET=$?
else
- echo "using tar"
- if [ x$OS = xmac -a x$STRIP_MAC_APP_BUNDLING = xtrue ]; then
- $TAR --strip-components=3 -C "${JREDIR}" -zxf "${TARFILE}" "*/Contents/Home"
- RET=$?
- else
- $TAR --strip-components=1 -C "${JREDIR}" -zxf "${TARFILE}"
- RET=$?
- fi
- fi
- if [ "$RET" != 0 ]; then
- echo "Error unpacking ${TARFILE}"
- exit 1
- fi
- $RM "${TARFILE}"
- if [ \! -z "$CREATE_ARCHIVES" ]; then
- for CREATEARCHIVE in ${CREATE_ARCHIVES}; do
- ARCHIVEDIR=$CREATEARCHIVE
- case $CREATEARCHIVE in
- zip)
- EXT=${CREATEARCHIVE}
- echo "Creating ${NAME}.${EXT} for getdown updates"
- [ \! -d ${ARCHIVEDIR} ] && mkdir -p "${ARCHIVEDIR}"
- ABSARCHIVEDIR="${PWD}/$ARCHIVEDIR"
- ZIPFILE="${ABSARCHIVEDIR}/${NAME}.${CREATEARCHIVE}"
- [ -e "${ZIPFILE}" ] && $RM "${ZIPFILE}"
- cd ${NAME}
- $ZIP -X -r "${ZIPFILE}" "${IMAGE_TYPE}"
- cd -
- ;;
- tgz)
- EXT=tar.gz
- echo "Creating ${NAME}.${EXT} for install4j bundling"
- [ \! -d ${ARCHIVEDIR} ] && mkdir -p "${ARCHIVEDIR}"
- $TAR -C "${JREDIR}" -zcf "${ARCHIVEDIR}/${NAME}.${EXT}" .
- ;;
- *)
- echo "Archiving as '${CREATEARCHIVE}' file not supported"
- ;;
- esac
- done
+ $TAR --strip-components=1 -C "${JREDIR}" -zxf "${TARFILE}"
+ RET=$?
fi
- done
+ fi
+ if [ "$RET" != 0 ]; then
+ echo "Error unpacking ${TARFILE}"
+ exit 1
+ fi
+ $RM "${TARFILE}"
+ if [ \! -z "$CREATE_ARCHIVES" ]; then
+ for CREATEARCHIVE in ${CREATE_ARCHIVES}; do
+ ARCHIVEDIR=$CREATEARCHIVE
+ case $CREATEARCHIVE in
+ zip)
+ EXT=${CREATEARCHIVE}
+ echo "Creating ${NAME}.${EXT} for getdown updates"
+ [ \! -d ${ARCHIVEDIR} ] && mkdir -p "${ARCHIVEDIR}"
+ ABSARCHIVEDIR="${PWD}/$ARCHIVEDIR"
+ ZIPFILE="${ABSARCHIVEDIR}/${NAME}.${CREATEARCHIVE}"
+ [ -e "${ZIPFILE}" ] && $RM "${ZIPFILE}"
+ cd ${NAME}
+ $ZIP -X -r "${ZIPFILE}" "${IMAGE_TYPE}"
+ cd -
+ ;;
+ tgz)
+ EXT=tar.gz
+ echo "Creating ${NAME}.${EXT} for install4j bundling"
+ [ \! -d ${ARCHIVEDIR} ] && mkdir -p "${ARCHIVEDIR}"
+ $TAR -C "${JREDIR}" -zcf "${ARCHIVEDIR}/${NAME}.${EXT}" .
+ # make symbolic link with _ instead of - for install4j9
+ NEWNAME=${NAME//-/_}
+ echo "Linking from ${NEWNAME}.${EXT} for install4j9"
+ ln -s "${NAME}.${EXT}" "${ARCHIVEDIR}/${NEWNAME}.${EXT}"
+ ;;
+ *)
+ echo "Archiving as '${CREATEARCHIVE}' file not supported"
+ ;;
+ esac
+ done
+ fi
done
done
annotations => {shortname=>"annotations",name=>"Jalview Annotations",extensions=>["annotations","jvannotations"]},
mmcif => {shortname=>"mmcif",name=>"CIF",extensions=>["cif"]},
mmcif2 => {shortname=>"mmcif2",name=>"mmCIF",extensions=>["mcif","mmcif"]},
- jvl => {shortname=>"jvl",name=>"Jalview Launch",extensions=>["jvl"],iconfile=>"Jalview-Launch"},
+ jvl => {shortname=>"jvl",name=>"Jalview Launch",extensions=>["jvl"],iconfile=>"jvl_file"},
jnet => {shortname=>"jnet",name=>"JnetFile",extensions=>["concise","jnet"]},
scorematrix => {shortname=>"scorematrix",name=>"Substitution Matrix",extensions=>["mat"]},
};
<key>CFBundleTypeName</key>
<string>Jalview Launch File</string>
<key>CFBundleTypeIconFile</key>
-<string>Jalview-Launch.icns</string>
+<string>jvl_file.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
<key>CFBundleTypeMIMETypes</key>
<dict>
<key>CFBundleTypeExtensions</key>
<array>
+<string>txt</string>
+</array>
+<key>CFBundleTypeName</key>
+<string>ENA Flatfile File</string>
+<key>CFBundleTypeIconFile</key>
+<string>Jalview-File.icns</string>
+<key>CFBundleTypeRole</key>
+<string>Editor</string>
+<key>CFBundleTypeMIMETypes</key>
+<array>
+<string>application/x-embl+txt</string>
+</array>
+<key>LSIsAppleDefaultForType</key>
+<true/>
+</dict>
+
+<dict>
+<key>CFBundleTypeExtensions</key>
+<array>
<string>fa</string>
<string>fasta</string>
</array>
<dict>
<key>CFBundleTypeExtensions</key>
<array>
+<string>gb</string>
+<string>gbk</string>
+</array>
+<key>CFBundleTypeName</key>
+<string>GenBank Flatfile File</string>
+<key>CFBundleTypeIconFile</key>
+<string>Jalview-File.icns</string>
+<key>CFBundleTypeRole</key>
+<string>Editor</string>
+<key>CFBundleTypeMIMETypes</key>
+<array>
+<string>application/x-genbank+txt</string>
+</array>
+<key>LSIsAppleDefaultForType</key>
+<true/>
+</dict>
+
+<dict>
+<key>CFBundleTypeExtensions</key>
+<array>
<string>gff2</string>
</array>
<key>CFBundleTypeName</key>
<serializedBean>
<property name="description" type="string">Jalview File</property>
<property name="extension" type="string">jvp</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Jalview Launch File</property>
<property name="extension" type="string">jvl</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
- <string>Jalview-Launch.icns</string>
+ <string>jvl_file.icns</string>
</object>
</property>
<property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />
<property name="unix" type="boolean" value="true" />
<property name="unixIconFile">
<object class="com.install4j.api.beans.ExternalFile">
- <string>Jalview-Launch.png</string>
+ <string>jvl_file.png</string>
</object>
</property>
<property name="unixMimeType" type="string">application/x-jalview-jvl+text</property>
<property name="windowsIconFile">
<object class="com.install4j.api.beans.ExternalFile">
- <string>Jalview-Launch.ico</string>
+ <string>jvl_file.ico</string>
</object>
</property>
</serializedBean>
<serializedBean>
<property name="description" type="string">CIF File</property>
<property name="extension" type="string">cif</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
</serializedBean>
</action>
- <action name="mmCIF (.mcif, .mmcif) progress bar 13" id="10010" customizedId="mmCIF-mcif,mmcif-10010-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="mmCIF (.mcif, .mmcif) progress bar 12" id="10010" customizedId="mmCIF-mcif,mmcif-10010-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="13" />
+ <property name="percentValue" type="int" value="12" />
</serializedBean>
</action>
<serializedBean>
<property name="description" type="string">mmCIF File</property>
<property name="extension" type="string">mcif,mmcif</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
</serializedBean>
</action>
- <action name="PDB (.ent, .pdb) progress bar 17" id="10013" customizedId="PDB-ent,pdb-10013-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PDB (.ent, .pdb) progress bar 16" id="10013" customizedId="PDB-ent,pdb-10013-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="17" />
+ <property name="percentValue" type="int" value="16" />
</serializedBean>
</action>
<serializedBean>
<property name="description" type="string">PDB File</property>
<property name="extension" type="string">ent,pdb</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
</serializedBean>
</action>
- <action name="AMSA (.amsa) progress bar 21" id="10016" customizedId="AMSA-amsa-10016-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="AMSA (.amsa) progress bar 20" id="10016" customizedId="AMSA-amsa-10016-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="21" />
+ <property name="percentValue" type="int" value="20" />
</serializedBean>
</action>
<serializedBean>
<property name="description" type="string">AMSA File</property>
<property name="extension" type="string">amsa</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
</serializedBean>
</action>
- <action name="Jalview Annotations (.annotations, .jvannotations) progress bar 26" id="10019" customizedId="Jalview Annotations-annotations,jvannotations-10019-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Jalview Annotations (.annotations, .jvannotations) progress bar 24" id="10019" customizedId="Jalview Annotations-annotations,jvannotations-10019-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="26" />
+ <property name="percentValue" type="int" value="24" />
</serializedBean>
</action>
<serializedBean>
<property name="description" type="string">Jalview Annotations File</property>
<property name="extension" type="string">annotations,jvannotations</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
</serializedBean>
</action>
- <action name="BioJSON (.biojson) progress bar 30" id="10022" customizedId="BioJSON-biojson-10022-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="BioJSON (.biojson) progress bar 28" id="10022" customizedId="BioJSON-biojson-10022-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="30" />
+ <property name="percentValue" type="int" value="28" />
</serializedBean>
</action>
<serializedBean>
<property name="description" type="string">BioJSON File</property>
<property name="extension" type="string">biojson</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
</serializedBean>
</action>
- <action name="BLC (.blc) progress bar 34" id="10025" customizedId="BLC-blc-10025-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="BLC (.blc) progress bar 32" id="10025" customizedId="BLC-blc-10025-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="34" />
+ <property name="percentValue" type="int" value="32" />
</serializedBean>
</action>
<serializedBean>
<property name="description" type="string">BLC File</property>
<property name="extension" type="string">blc</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
</serializedBean>
</action>
- <action name="Clustal (.aln) progress bar 39" id="10028" customizedId="Clustal-aln-10028-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Clustal (.aln) progress bar 36" id="10028" customizedId="Clustal-aln-10028-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="39" />
+ <property name="percentValue" type="int" value="36" />
</serializedBean>
</action>
<serializedBean>
<property name="description" type="string">Clustal File</property>
<property name="extension" type="string">aln</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
</action>
<!-- END -->
+<!-- ENA Flatfile (.txt) BEGIN -->
+ <action name="ENA Flatfile (.txt) message" id="10030" customizedId="ENA Flatfile-txt-10030-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">ENA Flatfile (.txt)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="ENA Flatfile (.txt) progress bar 40" id="10031" customizedId="ENA Flatfile-txt-10031-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="40" />
+ </serializedBean>
+ </action>
+
+ <action name="ENA Flatfile (.txt) file association" id="10032" customizedId="ENA Flatfile-txt-10032-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .txt file association">
+ <serializedBean>
+ <property name="description" type="string">ENA Flatfile File</property>
+ <property name="extension" type="string">txt</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-embl+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
<!-- Fasta (.fa, .fasta) BEGIN -->
- <action name="Fasta (.fa, .fasta) message" id="10030" customizedId="Fasta-fa,fasta-10030-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Fasta (.fa, .fasta) message" id="10033" customizedId="Fasta-fa,fasta-10033-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="detailMessage" type="string">Fasta (.fa, .fasta)</property>
<property name="statusMessage" type="string">Creating file associations...</property>
</serializedBean>
</action>
- <action name="Fasta (.fa, .fasta) progress bar 43" id="10031" customizedId="Fasta-fa,fasta-10031-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Fasta (.fa, .fasta) progress bar 44" id="10034" customizedId="Fasta-fa,fasta-10034-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="43" />
+ <property name="percentValue" type="int" value="44" />
</serializedBean>
</action>
- <action name="Fasta (.fa, .fasta) file association" id="10032" customizedId="Fasta-fa,fasta-10032-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .fa,fasta file association">
+ <action name="Fasta (.fa, .fasta) file association" id="10035" customizedId="Fasta-fa,fasta-10035-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .fa,fasta file association">
<serializedBean>
<property name="description" type="string">Fasta File</property>
<property name="extension" type="string">fa,fasta</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<!-- END -->
<!-- Jalview Features (.features, .jvfeatures) BEGIN -->
- <action name="Jalview Features (.features, .jvfeatures) message" id="10033" customizedId="Jalview Features-features,jvfeatures-10033-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Jalview Features (.features, .jvfeatures) message" id="10036" customizedId="Jalview Features-features,jvfeatures-10036-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="detailMessage" type="string">Jalview Features (.features, .jvfeatures)</property>
<property name="statusMessage" type="string">Creating file associations...</property>
</serializedBean>
</action>
- <action name="Jalview Features (.features, .jvfeatures) progress bar 47" id="10034" customizedId="Jalview Features-features,jvfeatures-10034-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Jalview Features (.features, .jvfeatures) progress bar 48" id="10037" customizedId="Jalview Features-features,jvfeatures-10037-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="47" />
+ <property name="percentValue" type="int" value="48" />
</serializedBean>
</action>
- <action name="Jalview Features (.features, .jvfeatures) file association" id="10035" customizedId="Jalview Features-features,jvfeatures-10035-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .features,jvfeatures file association">
+ <action name="Jalview Features (.features, .jvfeatures) file association" id="10038" customizedId="Jalview Features-features,jvfeatures-10038-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .features,jvfeatures file association">
<serializedBean>
<property name="description" type="string">Jalview Features File</property>
<property name="extension" type="string">features,jvfeatures</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
</action>
<!-- END -->
+<!-- GenBank Flatfile (.gb, .gbk) BEGIN -->
+ <action name="GenBank Flatfile (.gb, .gbk) message" id="10039" customizedId="GenBank Flatfile-gb,gbk-10039-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">GenBank Flatfile (.gb, .gbk)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="GenBank Flatfile (.gb, .gbk) progress bar 52" id="10040" customizedId="GenBank Flatfile-gb,gbk-10040-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="52" />
+ </serializedBean>
+ </action>
+
+ <action name="GenBank Flatfile (.gb, .gbk) file association" id="10041" customizedId="GenBank Flatfile-gb,gbk-10041-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .gb,gbk file association">
+ <serializedBean>
+ <property name="description" type="string">GenBank Flatfile File</property>
+ <property name="extension" type="string">gb,gbk</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-genbank+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
<!-- Generic Features Format v2 (.gff2) BEGIN -->
- <action name="Generic Features Format v2 (.gff2) message" id="10036" customizedId="Generic Features Format v2-gff2-10036-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Generic Features Format v2 (.gff2) message" id="10042" customizedId="Generic Features Format v2-gff2-10042-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="detailMessage" type="string">Generic Features Format v2 (.gff2)</property>
<property name="statusMessage" type="string">Creating file associations...</property>
</serializedBean>
</action>
- <action name="Generic Features Format v2 (.gff2) progress bar 52" id="10037" customizedId="Generic Features Format v2-gff2-10037-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Generic Features Format v2 (.gff2) progress bar 56" id="10043" customizedId="Generic Features Format v2-gff2-10043-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="52" />
+ <property name="percentValue" type="int" value="56" />
</serializedBean>
</action>
- <action name="Generic Features Format v2 (.gff2) file association" id="10038" customizedId="Generic Features Format v2-gff2-10038-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .gff2 file association">
+ <action name="Generic Features Format v2 (.gff2) file association" id="10044" customizedId="Generic Features Format v2-gff2-10044-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .gff2 file association">
<serializedBean>
<property name="description" type="string">Generic Features Format v2 File</property>
<property name="extension" type="string">gff2</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<!-- END -->
<!-- Generic Features Format v3 (.gff3) BEGIN -->
- <action name="Generic Features Format v3 (.gff3) message" id="10039" customizedId="Generic Features Format v3-gff3-10039-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Generic Features Format v3 (.gff3) message" id="10045" customizedId="Generic Features Format v3-gff3-10045-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="detailMessage" type="string">Generic Features Format v3 (.gff3)</property>
<property name="statusMessage" type="string">Creating file associations...</property>
</serializedBean>
</action>
- <action name="Generic Features Format v3 (.gff3) progress bar 56" id="10040" customizedId="Generic Features Format v3-gff3-10040-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Generic Features Format v3 (.gff3) progress bar 60" id="10046" customizedId="Generic Features Format v3-gff3-10046-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="56" />
+ <property name="percentValue" type="int" value="60" />
</serializedBean>
</action>
- <action name="Generic Features Format v3 (.gff3) file association" id="10041" customizedId="Generic Features Format v3-gff3-10041-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .gff3 file association">
+ <action name="Generic Features Format v3 (.gff3) file association" id="10047" customizedId="Generic Features Format v3-gff3-10047-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .gff3 file association">
<serializedBean>
<property name="description" type="string">Generic Features Format v3 File</property>
<property name="extension" type="string">gff3</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<!-- END -->
<!-- JnetFile (.concise, .jnet) BEGIN -->
- <action name="JnetFile (.concise, .jnet) message" id="10042" customizedId="JnetFile-concise,jnet-10042-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="JnetFile (.concise, .jnet) message" id="10048" customizedId="JnetFile-concise,jnet-10048-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="detailMessage" type="string">JnetFile (.concise, .jnet)</property>
<property name="statusMessage" type="string">Creating file associations...</property>
</serializedBean>
</action>
- <action name="JnetFile (.concise, .jnet) progress bar 60" id="10043" customizedId="JnetFile-concise,jnet-10043-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="JnetFile (.concise, .jnet) progress bar 64" id="10049" customizedId="JnetFile-concise,jnet-10049-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="60" />
+ <property name="percentValue" type="int" value="64" />
</serializedBean>
</action>
- <action name="JnetFile (.concise, .jnet) file association" id="10044" customizedId="JnetFile-concise,jnet-10044-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .concise,jnet file association">
+ <action name="JnetFile (.concise, .jnet) file association" id="10050" customizedId="JnetFile-concise,jnet-10050-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .concise,jnet file association">
<serializedBean>
<property name="description" type="string">JnetFile File</property>
<property name="extension" type="string">concise,jnet</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<!-- END -->
<!-- MSF (.msf) BEGIN -->
- <action name="MSF (.msf) message" id="10045" customizedId="MSF-msf-10045-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="MSF (.msf) message" id="10051" customizedId="MSF-msf-10051-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="detailMessage" type="string">MSF (.msf)</property>
<property name="statusMessage" type="string">Creating file associations...</property>
</serializedBean>
</action>
- <action name="MSF (.msf) progress bar 65" id="10046" customizedId="MSF-msf-10046-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="MSF (.msf) progress bar 68" id="10052" customizedId="MSF-msf-10052-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="65" />
+ <property name="percentValue" type="int" value="68" />
</serializedBean>
</action>
- <action name="MSF (.msf) file association" id="10047" customizedId="MSF-msf-10047-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .msf file association">
+ <action name="MSF (.msf) file association" id="10053" customizedId="MSF-msf-10053-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .msf file association">
<serializedBean>
<property name="description" type="string">MSF File</property>
<property name="extension" type="string">msf</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<!-- END -->
<!-- PFAM (.pfam) BEGIN -->
- <action name="PFAM (.pfam) message" id="10048" customizedId="PFAM-pfam-10048-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PFAM (.pfam) message" id="10054" customizedId="PFAM-pfam-10054-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="detailMessage" type="string">PFAM (.pfam)</property>
<property name="statusMessage" type="string">Creating file associations...</property>
</serializedBean>
</action>
- <action name="PFAM (.pfam) progress bar 69" id="10049" customizedId="PFAM-pfam-10049-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PFAM (.pfam) progress bar 72" id="10055" customizedId="PFAM-pfam-10055-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="69" />
+ <property name="percentValue" type="int" value="72" />
</serializedBean>
</action>
- <action name="PFAM (.pfam) file association" id="10050" customizedId="PFAM-pfam-10050-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .pfam file association">
+ <action name="PFAM (.pfam) file association" id="10056" customizedId="PFAM-pfam-10056-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .pfam file association">
<serializedBean>
<property name="description" type="string">PFAM File</property>
<property name="extension" type="string">pfam</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<!-- END -->
<!-- PHYLIP (.phy) BEGIN -->
- <action name="PHYLIP (.phy) message" id="10051" customizedId="PHYLIP-phy-10051-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PHYLIP (.phy) message" id="10057" customizedId="PHYLIP-phy-10057-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="detailMessage" type="string">PHYLIP (.phy)</property>
<property name="statusMessage" type="string">Creating file associations...</property>
</serializedBean>
</action>
- <action name="PHYLIP (.phy) progress bar 73" id="10052" customizedId="PHYLIP-phy-10052-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PHYLIP (.phy) progress bar 76" id="10058" customizedId="PHYLIP-phy-10058-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="73" />
+ <property name="percentValue" type="int" value="76" />
</serializedBean>
</action>
- <action name="PHYLIP (.phy) file association" id="10053" customizedId="PHYLIP-phy-10053-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .phy file association">
+ <action name="PHYLIP (.phy) file association" id="10059" customizedId="PHYLIP-phy-10059-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .phy file association">
<serializedBean>
<property name="description" type="string">PHYLIP File</property>
<property name="extension" type="string">phy</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<!-- END -->
<!-- PileUp (.pileup) BEGIN -->
- <action name="PileUp (.pileup) message" id="10054" customizedId="PileUp-pileup-10054-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PileUp (.pileup) message" id="10060" customizedId="PileUp-pileup-10060-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="detailMessage" type="string">PileUp (.pileup)</property>
<property name="statusMessage" type="string">Creating file associations...</property>
</serializedBean>
</action>
- <action name="PileUp (.pileup) progress bar 78" id="10055" customizedId="PileUp-pileup-10055-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PileUp (.pileup) progress bar 80" id="10061" customizedId="PileUp-pileup-10061-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="78" />
+ <property name="percentValue" type="int" value="80" />
</serializedBean>
</action>
- <action name="PileUp (.pileup) file association" id="10056" customizedId="PileUp-pileup-10056-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .pileup file association">
+ <action name="PileUp (.pileup) file association" id="10062" customizedId="PileUp-pileup-10062-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .pileup file association">
<serializedBean>
<property name="description" type="string">PileUp File</property>
<property name="extension" type="string">pileup</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<!-- END -->
<!-- PIR (.pir) BEGIN -->
- <action name="PIR (.pir) message" id="10057" customizedId="PIR-pir-10057-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PIR (.pir) message" id="10063" customizedId="PIR-pir-10063-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="detailMessage" type="string">PIR (.pir)</property>
<property name="statusMessage" type="string">Creating file associations...</property>
</serializedBean>
</action>
- <action name="PIR (.pir) progress bar 82" id="10058" customizedId="PIR-pir-10058-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PIR (.pir) progress bar 84" id="10064" customizedId="PIR-pir-10064-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="82" />
+ <property name="percentValue" type="int" value="84" />
</serializedBean>
</action>
- <action name="PIR (.pir) file association" id="10059" customizedId="PIR-pir-10059-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .pir file association">
+ <action name="PIR (.pir) file association" id="10065" customizedId="PIR-pir-10065-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .pir file association">
<serializedBean>
<property name="description" type="string">PIR File</property>
<property name="extension" type="string">pir</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<!-- END -->
<!-- RNAML (.rnaml) BEGIN -->
- <action name="RNAML (.rnaml) message" id="10060" customizedId="RNAML-rnaml-10060-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="RNAML (.rnaml) message" id="10066" customizedId="RNAML-rnaml-10066-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
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+java/util/spi/TimeZoneNameProvider.js
java/util/zip/CRC32.js
java/util/zip/Inflater.js
java/util/zip/InflaterInputStream.js
javajs/api/GenericLineReader.js
javajs/api/GenericOutputChannel.js
javajs/api/JSONEncodable.js
-javajs/awt/Font.js
-javajs/awt/FontManager.js
javajs/util/A4.js
+javajs/util/AU.js
+javajs/util/AjaxURLConnection.js
javajs/util/AjaxURLStreamHandler.js
+javajs/util/AjaxURLStreamHandlerFactory.js
javajs/util/BS.js
javajs/util/Base64.js
javajs/util/CU.js
javajs/util/CifDataParser.js
javajs/util/DF.js
javajs/util/Encoding.js
+javajs/util/JSThread.js
javajs/util/LimitedLineReader.js
+javajs/util/Lst.js
javajs/util/M3.js
javajs/util/M34.js
javajs/util/M4.js
javajs/util/P3.js
javajs/util/P3i.js
javajs/util/P4.js
+javajs/util/PT.js
javajs/util/Rdr.js
javajs/util/SB.js
javajs/util/T3.js
javajs/util/T3i.js
javajs/util/T4.js
javajs/util/V3.js
+javax/net/ssl/HttpsURLConnection.js
javax/swing/AbstractAction.js
-javax/swing/AbstractCellEditor.js
-javax/swing/AbstractSpinnerModel.js
+javax/swing/AbstractButton.js
+javax/swing/AbstractListModel.js
javax/swing/Action.js
+javax/swing/ActionMap.js
+javax/swing/AncestorNotifier.js
+javax/swing/ArrayTable.js
javax/swing/Autoscroller.js
-javax/swing/CellEditor.js
+javax/swing/BorderFactory.js
+javax/swing/BoundedRangeModel.js
+javax/swing/BoxLayout.js
+javax/swing/ButtonGroup.js
+javax/swing/ButtonModel.js
javax/swing/CellRendererPane.js
-javax/swing/ColorChooserDialog.js
+javax/swing/ClientPropertyKey.js
+javax/swing/ComboBoxEditor.js
+javax/swing/ComboBoxModel.js
javax/swing/ComponentInputMap.js
-javax/swing/DefaultCellEditor.js
+javax/swing/DefaultBoundedRangeModel.js
+javax/swing/DefaultButtonModel.js
+javax/swing/DefaultComboBoxModel.js
javax/swing/DefaultDesktopManager.js
javax/swing/DefaultListCellRenderer.js
javax/swing/DefaultListSelectionModel.js
javax/swing/DefaultRowSorter.js
+javax/swing/DefaultSingleSelectionModel.js
javax/swing/DesktopManager.js
javax/swing/DropMode.js
+javax/swing/FocusManager.js
javax/swing/Icon.js
javax/swing/ImageIcon.js
javax/swing/InputMap.js
-javax/swing/JColorChooser.js
+javax/swing/InternalFrameFocusTraversalPolicy.js
+javax/swing/JApplet.js
+javax/swing/JButton.js
+javax/swing/JCheckBox.js
+javax/swing/JCheckBoxMenuItem.js
+javax/swing/JComboBox.js
+javax/swing/JComponent.js
javax/swing/JDesktopPane.js
javax/swing/JDialog.js
-javax/swing/JFileChooser.js
-javax/swing/JFormattedTextField.js
+javax/swing/JFrame.js
javax/swing/JInternalFrame.js
+javax/swing/JLabel.js
+javax/swing/JLayeredPane.js
javax/swing/JList.js
+javax/swing/JMenu.js
+javax/swing/JMenuBar.js
+javax/swing/JMenuItem.js
javax/swing/JOptionPane.js
+javax/swing/JPanel.js
+javax/swing/JPopupMenu.js
javax/swing/JProgressBar.js
-javax/swing/JRadioButton.js
+javax/swing/JRadioButtonMenuItem.js
+javax/swing/JRootPane.js
+javax/swing/JScrollBar.js
javax/swing/JScrollPane.js
-javax/swing/JSlider.js
-javax/swing/JSpinner.js
+javax/swing/JSeparator.js
javax/swing/JTabbedPane.js
javax/swing/JTable.js
javax/swing/JTextArea.js
javax/swing/JTextField.js
+javax/swing/JToggleButton.js
javax/swing/JToolTip.js
javax/swing/JViewport.js
javax/swing/JWindow.js
javax/swing/KeyStroke.js
+javax/swing/KeyboardManager.js
+javax/swing/LayoutComparator.js
+javax/swing/LayoutFocusTraversalPolicy.js
javax/swing/ListCellRenderer.js
+javax/swing/ListModel.js
javax/swing/ListSelectionModel.js
+javax/swing/LookAndFeel.js
+javax/swing/MenuElement.js
javax/swing/MenuSelectionManager.js
+javax/swing/MutableComboBoxModel.js
javax/swing/Popup.js
javax/swing/PopupFactory.js
-javax/swing/RowFilter.js
+javax/swing/RepaintManager.js
+javax/swing/RootPaneContainer.js
javax/swing/RowSorter.js
javax/swing/ScrollPaneConstants.js
javax/swing/ScrollPaneLayout.js
javax/swing/Scrollable.js
+javax/swing/SingleSelectionModel.js
+javax/swing/SizeRequirements.js
javax/swing/SortOrder.js
-javax/swing/SpinnerModel.js
-javax/swing/SpinnerNumberModel.js
-javax/swing/Spring.js
-javax/swing/SpringLayout.js
+javax/swing/SortingFocusTraversalPolicy.js
+javax/swing/SwingConstants.js
+javax/swing/SwingContainerOrderFocusTraversalPolicy.js
+javax/swing/SwingDefaultFocusTraversalPolicy.js
+javax/swing/SwingPaintEventDispatcher.js
+javax/swing/SwingUtilities.js
javax/swing/Timer.js
javax/swing/ToolTipManager.js
+javax/swing/TransferHandler.js
+javax/swing/UIDefaults.js
+javax/swing/UIManager.js
javax/swing/ViewportLayout.js
+javax/swing/WindowConstants.js
+javax/swing/border/AbstractBorder.js
+javax/swing/border/BevelBorder.js
+javax/swing/border/Border.js
javax/swing/border/CompoundBorder.js
+javax/swing/border/EmptyBorder.js
+javax/swing/border/EtchedBorder.js
javax/swing/border/LineBorder.js
-javax/swing/border/MatteBorder.js
-javax/swing/border/TitledBorder.js
-javax/swing/colorchooser/AbstractColorChooserPanel.js
-javax/swing/colorchooser/CenterLayout.js
-javax/swing/colorchooser/ColorChooserComponentFactory.js
-javax/swing/colorchooser/ColorSelectionModel.js
-javax/swing/colorchooser/DefaultColorSelectionModel.js
-javax/swing/colorchooser/DefaultPreviewPanel.js
-javax/swing/colorchooser/DefaultRGBChooserPanel.js
-javax/swing/colorchooser/DefaultSwatchChooserPanel.js
-javax/swing/colorchooser/MainSwatchPanel.js
-javax/swing/colorchooser/RecentSwatchPanel.js
-javax/swing/colorchooser/SmartGridLayout.js
-javax/swing/colorchooser/SwatchPanel.js
+javax/swing/event/AncestorEvent.js
+javax/swing/event/AncestorListener.js
javax/swing/event/CaretEvent.js
javax/swing/event/CaretListener.js
javax/swing/event/CellEditorListener.js
+javax/swing/event/ChangeEvent.js
+javax/swing/event/ChangeListener.js
javax/swing/event/DocumentEvent.js
javax/swing/event/DocumentListener.js
+javax/swing/event/EventListenerList.js
+javax/swing/event/HyperlinkListener.js
javax/swing/event/InternalFrameAdapter.js
javax/swing/event/InternalFrameEvent.js
javax/swing/event/InternalFrameListener.js
+javax/swing/event/ListDataEvent.js
+javax/swing/event/ListDataListener.js
javax/swing/event/ListSelectionEvent.js
javax/swing/event/ListSelectionListener.js
+javax/swing/event/MenuEvent.js
javax/swing/event/MenuKeyListener.js
javax/swing/event/MenuListener.js
javax/swing/event/MouseInputListener.js
javax/swing/event/TableModelListener.js
javax/swing/event/UndoableEditEvent.js
javax/swing/event/UndoableEditListener.js
-javax/swing/filechooser/FileFilter.js
-javax/swing/filechooser/FileView.js
+javax/swing/plaf/ActionMapUIResource.js
+javax/swing/plaf/BorderUIResource.js
+javax/swing/plaf/ColorUIResource.js
javax/swing/plaf/ComponentInputMapUIResource.js
+javax/swing/plaf/ComponentUI.js
+javax/swing/plaf/DimensionUIResource.js
+javax/swing/plaf/FontUIResource.js
javax/swing/plaf/InputMapUIResource.js
+javax/swing/plaf/InsetsUIResource.js
+javax/swing/plaf/UIResource.js
javax/swing/plaf/basic/BasicBorders.js
+javax/swing/plaf/basic/BasicGraphicsUtils.js
javax/swing/table/AbstractTableModel.js
javax/swing/table/DefaultTableCellRenderer.js
javax/swing/table/DefaultTableColumnModel.js
javax/swing/table/DefaultTableModel.js
javax/swing/table/JTableHeader.js
-javax/swing/table/TableCellEditor.js
javax/swing/table/TableCellRenderer.js
javax/swing/table/TableColumn.js
javax/swing/table/TableColumnModel.js
javax/swing/table/TableRowSorter.js
javax/swing/text/AbstractDocument.js
javax/swing/text/AttributeSet.js
+javax/swing/text/BoxView.js
javax/swing/text/Caret.js
+javax/swing/text/CompositeView.js
javax/swing/text/DefaultCaret.js
javax/swing/text/DefaultEditorKit.js
-javax/swing/text/DefaultFormatter.js
-javax/swing/text/DefaultFormatterFactory.js
javax/swing/text/Document.js
-javax/swing/text/DocumentFilter.js
javax/swing/text/EditorKit.js
javax/swing/text/Element.js
javax/swing/text/GapContent.js
javax/swing/text/GapVector.js
-javax/swing/text/InternationalFormatter.js
javax/swing/text/JTextComponent.js
javax/swing/text/MutableAttributeSet.js
-javax/swing/text/NumberFormatter.js
javax/swing/text/PlainDocument.js
javax/swing/text/PlainView.js
javax/swing/text/Position.js
javax/swing/text/TextAction.js
javax/swing/text/Utilities.js
javax/swing/text/View.js
-javax/swing/tree/TreeCellEditor.js
+javax/swing/text/WrappedPlainView.js
javax/swing/tree/TreeNode.js
javax/swing/undo/AbstractUndoableEdit.js
javax/swing/undo/CompoundEdit.js
javax/xml/bind/annotation/adapters/XmlAdapter.js
javax/xml/bind/helpers/AbstractUnmarshallerImpl.js
javax/xml/bind/helpers/DefaultValidationEventHandler.js
-javax/xml/datatype/DatatypeFactory.js
javax/xml/datatype/XMLGregorianCalendar.js
javax/xml/namespace/QName.js
javax/xml/stream/XMLInputFactory.js
+javax/xml/stream/XMLStreamConstants.js
javax/xml/stream/XMLStreamReader.js
-mc_view/Atom.js
-mc_view/Bond.js
-mc_view/PDBChain.js
-mc_view/Residue.js
net/miginfocom/layout/AC.js
net/miginfocom/layout/AnimSpec.js
net/miginfocom/layout/BoundSize.js
net/miginfocom/swing/MigLayout.js
net/miginfocom/swing/SwingComponentWrapper.js
net/miginfocom/swing/SwingContainerWrapper.js
-org/apache/xerces/jaxp/datatype/DatatypeFactoryImpl.js
org/apache/xerces/jaxp/datatype/XMLGregorianCalendarImpl.js
org/jmol/adapter/readers/cif/CifReader.js
org/jmol/adapter/readers/cif/MMCifReader.js
org/jmol/adapter/smarter/SmarterJmolAdapter.js
org/jmol/adapter/smarter/Structure.js
org/jmol/adapter/smarter/StructureIterator.js
-org/jmol/adapter/smarter/XtalSymmetry.js
org/jmol/api/AtomIndexIterator.js
org/jmol/api/EventManager.js
+org/jmol/api/FontManager.js
org/jmol/api/GenericFileInterface.js
org/jmol/api/GenericMouseInterface.js
org/jmol/api/GenericPlatform.js
org/jmol/api/JmolAdapterBondIterator.js
org/jmol/api/JmolAdapterStructureIterator.js
org/jmol/api/JmolCallbackListener.js
+org/jmol/api/JmolFilesReaderInterface.js
org/jmol/api/JmolGraphicsInterface.js
org/jmol/api/JmolMeasurementClient.js
-org/jmol/api/JmolPropertyManager.js
org/jmol/api/JmolRendererInterface.js
org/jmol/api/JmolRepaintManager.js
org/jmol/api/JmolScriptEvaluator.js
org/jmol/c/STER.js
org/jmol/c/STR.js
org/jmol/c/VDW.js
+org/jmol/dssx/Bridge.js
+org/jmol/dssx/DSSP.js
org/jmol/g3d/CylinderRenderer.js
org/jmol/g3d/G3DRenderer.js
org/jmol/g3d/Graphics3D.js
org/jmol/i18n/Language.js
org/jmol/i18n/Resource.js
org/jmol/io/FileReader.js
+org/jmol/io/FilesReader.js
org/jmol/modelset/Atom.js
org/jmol/modelset/AtomCollection.js
org/jmol/modelset/AtomIteratorWithinModel.js
org/jmol/modelset/BondIteratorSelected.js
org/jmol/modelset/Chain.js
org/jmol/modelset/Group.js
+org/jmol/modelset/HBond.js
org/jmol/modelset/LabelToken.js
org/jmol/modelset/Measurement.js
org/jmol/modelset/MeasurementData.js
+org/jmol/modelset/MeasurementPending.js
org/jmol/modelset/Model.js
org/jmol/modelset/ModelLoader.js
org/jmol/modelset/ModelSet.js
org/jmol/modelsetbio/BioResolver.js
org/jmol/modelsetbio/Helix.js
org/jmol/modelsetbio/Monomer.js
-org/jmol/modelsetbio/NucleicMonomer.js
-org/jmol/modelsetbio/NucleicPolymer.js
-org/jmol/modelsetbio/PhosphorusMonomer.js
-org/jmol/modelsetbio/PhosphorusPolymer.js
org/jmol/modelsetbio/ProteinStructure.js
org/jmol/modelsetbio/Sheet.js
+org/jmol/modelsetbio/Turn.js
org/jmol/render/BallsRenderer.js
org/jmol/render/BbcageRenderer.js
org/jmol/render/CageRenderer.js
org/jmol/script/ScriptManager.js
org/jmol/script/ScriptMathProcessor.js
org/jmol/script/ScriptParam.js
+org/jmol/script/ScriptQueueThread.js
org/jmol/script/ScriptTokenParser.js
org/jmol/script/T.js
org/jmol/scriptext/CmdExt.js
org/jmol/shape/AtomShape.js
org/jmol/shape/Balls.js
org/jmol/shape/Bbcage.js
+org/jmol/shape/Echo.js
org/jmol/shape/FontLineShape.js
org/jmol/shape/Frank.js
org/jmol/shape/Hover.js
org/jmol/symmetry/UnitCell.js
org/jmol/thread/HoverWatcherThread.js
org/jmol/thread/JmolThread.js
+org/jmol/thread/TimeoutThread.js
org/jmol/util/BSUtil.js
org/jmol/util/BoxInfo.js
org/jmol/util/C.js
org/jmol/util/Edge.js
org/jmol/util/Elements.js
org/jmol/util/Escape.js
+org/jmol/util/Font.js
org/jmol/util/GData.js
org/jmol/util/Geodesic.js
org/jmol/util/Int2IntHash.js
org/jmol/viewer/ModelManager.js
org/jmol/viewer/MotionPoint.js
org/jmol/viewer/MouseState.js
-org/jmol/viewer/PropertyManager.js
org/jmol/viewer/SelectionManager.js
org/jmol/viewer/ShapeManager.js
org/jmol/viewer/StateManager.js
org/jmol/viewer/Viewer.js
org/jmol/viewer/binding/Binding.js
org/jmol/viewer/binding/JmolBinding.js
+org/json/simple/parser/ParseException.js
org/xml/sax/AttributeList.js
org/xml/sax/Attributes.js
org/xml/sax/ContentHandler.js
org/xml/sax/Parser.js
org/xml/sax/XMLReader.js
org/xml/sax/ext/Attributes2.js
-sun/awt/AWTAccessor.js
+sun/awt/AWTAutoShutdown.js
+sun/awt/AppContext.js
sun/awt/CausedFocusEvent.js
+sun/awt/ComponentFactory.js
sun/awt/EventQueueItem.js
-sun/awt/KeyboardFocusManagerPeerProvider.js
+sun/awt/MostRecentKeyValue.js
+sun/awt/MostRecentThreadAppContext.js
+sun/awt/PaintEventDispatcher.js
+sun/awt/PostEventQueue.js
+sun/awt/RequestFocusController.js
sun/awt/SunGraphicsCallback.js
+sun/awt/SunToolkit.js
sun/awt/image/DataStealer.js
sun/awt/image/IntegerComponentRaster.js
sun/awt/image/IntegerInterleavedRaster.js
sun/font/FontDesignMetrics.js
sun/java2d/StateTrackable.js
sun/java2d/StateTrackableDelegate.js
-sun/nio/cs/ArrayDecoder.js
-sun/nio/cs/HistoricallyNamedCharset.js
-sun/nio/cs/StandardCharsets.js
-sun/nio/cs/ThreadLocalCoders.js
-sun/nio/cs/UTF_8.js
-sun/nio/cs/Unicode.js
+sun/net/www/MessageHeader.js
sun/swing/DefaultLookup.js
sun/swing/StringUIClientPropertyKey.js
+sun/swing/SwingLazyValue.js
sun/swing/SwingUtilities2.js
sun/swing/UIAction.js
sun/swing/UIClientPropertyKey.js
sun/swing/table/DefaultTableCellHeaderRenderer.js
sun/text/resources/FormatData.js
-sun/text/resources/FormatData_en.js
+sun/text/resources/en/FormatData_en.js
+sun/text/resources/en/FormatData_en_GB.js
+sun/text/resources/en/FormatData_en_US.js
sun/util/calendar/AbstractCalendar.js
sun/util/calendar/BaseCalendar.js
sun/util/calendar/CalendarDate.js
sun/util/calendar/CalendarUtils.js
sun/util/calendar/Gregorian.js
sun/util/calendar/ZoneInfo.js
+sun/util/calendar/ZoneInfoFile.js
+sun/util/locale/BaseLocale.js
+sun/util/locale/LanguageTag.js
+sun/util/locale/LocaleUtils.js
+sun/util/locale/provider/AuxLocaleProviderAdapter.js
+sun/util/locale/provider/AvailableLanguageTags.js
+sun/util/locale/provider/CalendarDataProviderImpl.js
+sun/util/locale/provider/CalendarDataUtility.js
+sun/util/locale/provider/CalendarProviderImpl.js
+sun/util/locale/provider/DateFormatProviderImpl.js
+sun/util/locale/provider/JRELocaleProviderAdapter.js
+sun/util/locale/provider/LocaleDataMetaInfo.js
+sun/util/locale/provider/LocaleProviderAdapter.js
+sun/util/locale/provider/LocaleResources.js
+sun/util/locale/provider/LocaleServiceProviderPool.js
+sun/util/locale/provider/ResourceBundleBasedAdapter.js
+sun/util/locale/provider/SPILocaleProviderAdapter.js
sun/util/resources/LocaleData.js
-swingjs/JSAbstractDocument.js
-swingjs/JSCharSet.js
-swingjs/JSDnD.js
-swingjs/JSDocumentEvent.js
+sun/util/resources/ParallelListResourceBundle.js
+sun/util/spi/CalendarProvider.js
+swingjs/JSApp.js
+swingjs/JSAppletThread.js
+swingjs/JSAppletViewer.js
+swingjs/JSDummyApplet.js
+swingjs/JSFileSystem.js
swingjs/JSFocusPeer.js
-swingjs/JSGraphicsCompositor.js
+swingjs/JSFontMetrics.js
+swingjs/JSFrameViewer.js
+swingjs/JSGraphics2D.js
+swingjs/JSGraphicsConfiguration.js
+swingjs/JSGraphicsEnvironment.js
swingjs/JSImage.js
swingjs/JSImagekit.js
swingjs/JSKeyEvent.js
swingjs/JSMenuManager.js
-swingjs/JSPlainDocument.js
-swingjs/JSTempFile.js
+swingjs/JSMouse.js
+swingjs/JSScreenDevice.js
+swingjs/JSThreadGroup.js
+swingjs/JSToolkit.js
+swingjs/JSUtil.js
swingjs/a2s/A2SContainer.js
swingjs/a2s/Dialog.js
-swingjs/api/JSMinimalAbstractDocument.js
+swingjs/api/Interface.js
+swingjs/api/JSUtilI.js
+swingjs/api/js/DOMNode.js
+swingjs/api/js/HTML5Canvas.js
+swingjs/api/js/HTML5CanvasContext2D.js
+swingjs/api/js/JSFunction.js
+swingjs/api/js/JSInterface.js
+swingjs/jquery/JQueryUI.js
swingjs/json/JSON.js
swingjs/jzlib/Adler32.js
swingjs/jzlib/CRC32.js
swingjs/jzlib/Inflater.js
swingjs/jzlib/InflaterInputStream.js
swingjs/jzlib/ZStream.js
-swingjs/plaf/BasicArrowButton.js
+swingjs/plaf/BasicComboBoxEditor.js
+swingjs/plaf/BasicComboBoxRenderer.js
swingjs/plaf/BasicHTML.js
+swingjs/plaf/ButtonListener.js
swingjs/plaf/CellHolder.js
-swingjs/plaf/CenterLayout.js
+swingjs/plaf/DefaultMenuLayout.js
+swingjs/plaf/HTML5LookAndFeel.js
swingjs/plaf/JSAppletUI.js
-swingjs/plaf/JSColorChooserUI.js
+swingjs/plaf/JSButtonUI.js
+swingjs/plaf/JSCheckBoxMenuItemUI.js
+swingjs/plaf/JSCheckBoxUI.js
+swingjs/plaf/JSComboBoxUI.js
+swingjs/plaf/JSComboPopupList.js
+swingjs/plaf/JSComponentUI.js
swingjs/plaf/JSDesktopIconUI.js
swingjs/plaf/JSDesktopPaneUI.js
swingjs/plaf/JSDialogUI.js
-swingjs/plaf/JSFormattedTextFieldUI.js
+swingjs/plaf/JSEventHandler.js
+swingjs/plaf/JSFrameUI.js
swingjs/plaf/JSGraphicsUtils.js
swingjs/plaf/JSInternalFrameUI.js
+swingjs/plaf/JSLabelUI.js
+swingjs/plaf/JSLayeredPaneUI.js
+swingjs/plaf/JSLightweightUI.js
swingjs/plaf/JSListUI.js
+swingjs/plaf/JSMenuBarUI.js
+swingjs/plaf/JSMenuItemUI.js
+swingjs/plaf/JSMenuUI.js
+swingjs/plaf/JSOptionPaneUI.js
+swingjs/plaf/JSPanelUI.js
+swingjs/plaf/JSPopupMenuSeparatorUI.js
+swingjs/plaf/JSPopupMenuUI.js
swingjs/plaf/JSPopupUI.js
swingjs/plaf/JSProgressBarUI.js
+swingjs/plaf/JSRadioButtonMenuItemUI.js
+swingjs/plaf/JSRadioButtonUI.js
+swingjs/plaf/JSRootPaneUI.js
+swingjs/plaf/JSScrollBarUI.js
swingjs/plaf/JSScrollPaneUI.js
-swingjs/plaf/JSSpinnerUI.js
+swingjs/plaf/JSSeparatorUI.js
+swingjs/plaf/JSSliderUI.js
swingjs/plaf/JSTabbedPaneUI.js
swingjs/plaf/JSTableHeaderUI.js
swingjs/plaf/JSTableUI.js
swingjs/plaf/JSTextAreaUI.js
swingjs/plaf/JSTextFieldUI.js
swingjs/plaf/JSTextUI.js
-swingjs/plaf/JSTextViewUI.js
swingjs/plaf/JSToolTipUI.js
swingjs/plaf/JSViewportUI.js
+swingjs/plaf/JSWindowUI.js
+swingjs/plaf/LazyActionMap.js
+swingjs/plaf/Resizer.js
swingjs/plaf/TextListener.js
swingjs/xml/JSJAXBClass.js
swingjs/xml/JSJAXBContext.js
swingjs/xml/JSJAXBContextFactory.js
-swingjs/xml/JSJAXBDatatypeFactory.js
swingjs/xml/JSJAXBField.js
swingjs/xml/JSJAXBUnmarshaller.js
swingjs/xml/JSSAXAttributes.js
swingjs/xml/JSSAXParser.js
swingjs/xml/JSXMLGregorianCalendarImpl.js
swingjs/xml/JSXMLInputFactory.js
-swingjs/xml/JSXMLStreamReader.jscom/stevesoft/pat/Any.js
-swingjs/xml/JSXMLStreamReader.jscom/stevesoft/pat/Boundary.js
+swingjs/xml/JSXMLStreamReader.js
--- /dev/null
+#!/usr/bin/env bash
+
+FILENAME512=$1
+BASENAME=${FILENAME512%-512.png}
+
+usage () {
+ echo "$(basename "$0") <LOGO_NAME>-512.png"
+}
+
+[ "$1" = "-h" ] && usage && exit 0
+[ -r "$FILENAME512" ] || ( usage && echo "'${FILENAME512}' must exist and be readable" && exit 1 )
+[ "$BASENAME" = "$FILENAME512" ] && usage && echo "Must have '-512.png' at end of filename" && exit 2
+
+set -e
+
+SIZES="16 32 38 48 64 128 256"
+declare -a ICOFILES=()
+declare -a ICNSFILES=()
+for n in $SIZES
+do
+ NEWFILE="${BASENAME}-${n}.png"
+ [ -e "{$NEWFILE}" ] && continue
+ convert -geometry "${n}x${n}" "${BASENAME}-512.png" "${NEWFILE}"
+ [ "${n}" != 38 ] && ICOFILES=( "${ICOFILES[@]}" "${NEWFILE}" )
+ [ "${n}" != 64 ] && [ "${n}" != 38 ] && ICNSFILES=( "${ICNSFILES[@]}" "${NEWFILE}" )
+done
+
+# make the .ico
+ICOFILE="${BASENAME}.ico"
+echo "Creating ${ICOFILE}"
+convert "${ICOFILES[@]}" "${ICOFILE}"
+
+# make the .icns
+ICNSFILE="${BASENAME}.icns"
+echo "Creating ${ICNSFILE}"
+png2icns "${ICNSFILE}" "${ICNSFILES[@]}"
+
+# make the rotatable icon
+ROTATABLEFILE="rotatable_${BASENAME}-38.png"
+convert "${BASENAME}-38.png" -gravity center -background white -extent 60x60 "${ROTATABLEFILE}"
+
+exit 0
git://source.jalview.org / jalview.git / commitdiff
