description "Build the site"
dependsOn jalviewjsBuildSite
}
+
--- /dev/null
+--open[B]=./examples/uniref50.fa
+--colour[B]=clustal
+--image[B]=outputB.html
+--close[B]
--- /dev/null
+--open[{++n}]=./examples/test_fab41.result/sample.a2m
+--colour[{n}]=clustal
+--structure[{n}]=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb
+--paematrix[{n}]=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json
+--structure[{n}]=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb
+--paematrix[{n}]=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4_scores.json
+--structure[{n}]=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb
+--paematrix[{n}]=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2_scores.json
+--structure[{n}]=./examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5.pdb
+--paematrix[{n}]=./examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5_scores.json
+--structure[{n}]=./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1.pdb
+--paematrix[{n}]=./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1_scores.json
+--image[{n}]=output1.html
+--close
--- /dev/null
+--open=./examples/test_fab41.result/sample.a2m
+--colour=gecos:flower
+--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb
+--paematrix=[label=pAE R1-M3]./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json
+--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb
+--paematrix=[label=pAE R2-M4]./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4_scores.json
+--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb
+--paematrix=[label=pAE R3-M2]./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2_scores.json
+--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5.pdb
+--paematrix=[label=pAE R4-M5]./examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5_scores.json
+--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1.pdb
+--paematrix=[label=pAE R5-M1]./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1_scores.json
+--image=output1.html
--- /dev/null
+--debug
+--nonews
+--nosplash
+--substitutions
+--open={argfiledirname}/sample.a2m
+--colour=gecos:flower
+--structure={dirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
+--paematrix=[seqid=101;label=PAE R1-M3]{dirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json
+--structure={dirname}/test_fab41_unrelaxed_rank_2_model_4.pdb
+--paematrix=[label=PAE R2-M4]{dirname}/test_fab41_unrelaxed_rank_2_model_4_scores.json
+--structure={dirname}/test_fab41_unrelaxed_rank_3_model_2.pdb
+--paematrix=[label=PAE R3-M2]{dirname}/test_fab41_unrelaxed_rank_3_model_2_scores.json
+--structure={dirname}/test_fab41_unrelaxed_rank_4_model_5.pdb
+--paematrix=[label=PAE R4-M5]{dirname}/test_fab41_unrelaxed_rank_4_model_5_scores.json
+--structure={dirname}/test_fab41_unrelaxed_rank_5_model_1.pdb
+--paematrix=[label=PAE R5-M1]{dirname}/test_fab41_unrelaxed_rank_5_model_1_scores.json
+--image={dirname}/{basename}.html
+#--headless
+++ /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.bin;
-
-import java.io.File;
-import java.io.IOException;
-import java.net.URLDecoder;
-import java.nio.file.Files;
-import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.EnumSet;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Locale;
-import java.util.Map;
-import java.util.Set;
-
-import jalview.util.Platform;
-
-public class ArgParser
-{
- private static final String NEGATESTRING = "no";
-
- private static final String DEFAULTLINKEDID = "";
-
- private static enum Opt
- {
- BOOLEAN, STRING, UNARY, MULTI, LINKED, NODUPLICATEVALUES
- }
-
- // These bootstrap args are simply parsed before a full parse of arguments and
- // so are accessible at an earlier stage to (e.g.) set debug log leve, provide
- // a props file (that might set log level), run headlessly, read an argfile
- // instead of other args.
- private static final Collection<Arg> bootstrapArgs = new ArrayList(
- Arrays.asList(Arg.PROPS, Arg.DEBUG, Arg.HEADLESS, Arg.ARGFILE));
-
- public enum Arg
- {
- /*
- NOCALCULATION, NOMENUBAR, NOSTATUS, SHOWOVERVIEW, ANNOTATIONS, COLOUR,
- FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, NOANNOTATION, NOANNOTATION2,
- NODISPLAY, NOGUI, NONEWS, NOQUESTIONNAIRE, NOSORTBYTREE, NOUSAGESTATS,
- OPEN, OPEN2, PROPS, QUESTIONNAIRE, SETPROP, SORTBYTREE, TREE, VDOC,
- VSESS;
- */
- HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, ANNOTATIONS,
- COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, ANNOTATION,
- ANNOTATION2, DISPLAY, GUI, NEWS, NOQUESTIONNAIRE, SORTBYTREE,
- USAGESTATS, OPEN, OPEN2, PROPS, QUESTIONNAIRE, SETPROP, TREE, VDOC,
- VSESS, OUTPUT, OUTPUTTYPE, SSANNOTATION, NOTEMPFAC, TEMPFAC,
- TEMPFAC_LABEL, TEMPFAC_DESC, TEMPFAC_SHADING, TITLE, PAEMATRIX, WRAP,
- NOSTRUCTURE, STRUCTURE, IMAGE, QUIT, DEBUG("d"), ARGFILE;
-
- static
- {
- HELP.setOptions(Opt.UNARY);
- CALCULATION.setOptions(true, Opt.BOOLEAN); // default "true" implies only
- // expecting "--nocalculation"
- MENUBAR.setOptions(true, Opt.BOOLEAN);
- STATUS.setOptions(true, Opt.BOOLEAN);
- SHOWOVERVIEW.setOptions(Opt.UNARY, Opt.LINKED);
- ANNOTATIONS.setOptions(Opt.STRING, Opt.LINKED);
- COLOUR.setOptions(Opt.STRING, Opt.LINKED);
- FEATURES.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
- GROOVY.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
- GROUPS.setOptions(Opt.STRING, Opt.LINKED);
- HEADLESS.setOptions(Opt.UNARY);
- JABAWS.setOptions(Opt.STRING);
- ANNOTATION.setOptions(true, Opt.BOOLEAN);
- ANNOTATION2.setOptions(true, Opt.BOOLEAN);
- DISPLAY.setOptions(true, Opt.BOOLEAN);
- GUI.setOptions(true, Opt.BOOLEAN);
- NEWS.setOptions(true, Opt.BOOLEAN);
- NOQUESTIONNAIRE.setOptions(Opt.UNARY); // unary as --questionnaire=val
- // expects a string value
- SORTBYTREE.setOptions(true, Opt.BOOLEAN);
- USAGESTATS.setOptions(true, Opt.BOOLEAN);
- OPEN.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
- OPEN2.setOptions(Opt.STRING, Opt.LINKED);
- PROPS.setOptions(Opt.STRING);
- QUESTIONNAIRE.setOptions(Opt.STRING);
- SETPROP.setOptions(Opt.STRING);
- TREE.setOptions(Opt.STRING);
-
- VDOC.setOptions(Opt.UNARY);
- VSESS.setOptions(Opt.UNARY);
-
- OUTPUT.setOptions(Opt.STRING, Opt.LINKED);
- OUTPUTTYPE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
-
- SSANNOTATION.setOptions(Opt.BOOLEAN, Opt.LINKED);
- NOTEMPFAC.setOptions(Opt.UNARY, Opt.LINKED);
- TEMPFAC.setOptions(Opt.STRING, Opt.LINKED);
- TEMPFAC_LABEL.setOptions(Opt.STRING, Opt.LINKED);
- TEMPFAC_DESC.setOptions(Opt.STRING, Opt.LINKED);
- TEMPFAC_SHADING.setOptions(Opt.BOOLEAN, Opt.LINKED);
- TITLE.setOptions(Opt.STRING, Opt.LINKED);
- PAEMATRIX.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
- NOSTRUCTURE.setOptions(Opt.UNARY, Opt.LINKED);
- STRUCTURE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
- WRAP.setOptions(Opt.BOOLEAN, Opt.LINKED);
- IMAGE.setOptions(Opt.STRING, Opt.LINKED);
- QUIT.setOptions(Opt.UNARY);
- DEBUG.setOptions(Opt.BOOLEAN);
- ARGFILE.setOptions(Opt.STRING);
- }
-
- private final String[] argNames;
-
- private Opt[] argOptions;
-
- private boolean defaultBoolValue = false;
-
- public String toLongString()
- {
- StringBuilder sb = new StringBuilder();
- sb.append("Arg: ").append(this.name());
- for (String name : getNames())
- {
- sb.append(", '").append(name).append("'");
- }
- sb.append("\nOptions: ");
- boolean first = true;
- for (Opt o : argOptions)
- {
- if (!first)
- {
- sb.append(", ");
- }
- sb.append(o.toString());
- first = false;
- }
- sb.append("\n");
- return sb.toString();
- }
-
- private Arg()
- {
- this(new String[0]);
- }
-
- private Arg(String... names)
- {
- int length = (names == null || names.length == 0
- || (names.length == 1 && names[0] == null)) ? 1
- : names.length + 1;
- this.argNames = new String[length];
- this.argNames[0] = this.getName();
- if (length > 1)
- System.arraycopy(names, 0, this.argNames, 1, names.length);
- }
-
- public String[] getNames()
- {
- return argNames;
- }
-
- public String getName()
- {
- return this.name().toLowerCase(Locale.ROOT).replace('_', '-');
- }
-
- @Override
- public final String toString()
- {
- return getName();
- }
-
- public boolean hasOption(Opt o)
- {
- if (argOptions == null)
- return false;
- for (Opt option : argOptions)
- {
- if (o == option)
- return true;
- }
- return false;
- }
-
- protected void setOptions(Opt... options)
- {
- setOptions(false, options);
- }
-
- protected void setOptions(boolean defaultBoolValue, Opt... options)
- {
- this.defaultBoolValue = defaultBoolValue;
- argOptions = options;
- }
-
- protected boolean getDefaultBoolValue()
- {
- return defaultBoolValue;
- }
- }
-
- public static class ArgValues
- {
- private static final String ID = "id";
-
- private Arg arg;
-
- private int argCount = 0;
-
- private boolean boolValue = false;
-
- private boolean negated = false;
-
- private int boolIndex = -1;
-
- private List<Integer> argsIndexes;
-
- private List<ArgValue> argValueList;
-
- private Map<String, ArgValue> idMap = new HashMap<>();
-
- protected ArgValues(Arg a)
- {
- this.arg = a;
- this.argValueList = new ArrayList<ArgValue>();
- this.boolValue = arg.getDefaultBoolValue();
- }
-
- public Arg arg()
- {
- return arg;
- }
-
- protected int getCount()
- {
- return argCount;
- }
-
- protected void incrementCount()
- {
- argCount++;
- }
-
- protected void setNegated(boolean b)
- {
- this.negated = b;
- }
-
- protected boolean isNegated()
- {
- return this.negated;
- }
-
- protected void setBoolean(boolean b, int i)
- {
- this.boolValue = b;
- this.boolIndex = i;
- }
-
- protected boolean getBoolean()
- {
- return this.boolValue;
- }
-
- @Override
- public String toString()
- {
- if (argValueList == null)
- return null;
- StringBuilder sb = new StringBuilder();
- sb.append(arg.toLongString());
- if (arg.hasOption(Opt.BOOLEAN) || arg.hasOption(Opt.UNARY))
- sb.append("Boolean: ").append(boolValue).append("; Default: ")
- .append(arg.getDefaultBoolValue()).append("; Negated: ")
- .append(negated).append("\n");
- if (arg.hasOption(Opt.STRING))
- {
- sb.append("Values:");
- boolean first = true;
- for (ArgValue av : argValueList)
- {
- String v = av.getValue();
- if (!first)
- sb.append(",");
- sb.append("\n '");
- sb.append(v).append("'");
- first = false;
- }
- sb.append("\n");
- }
- sb.append("Count: ").append(argCount).append("\n");
- return sb.toString();
- }
-
- protected void addValue()
- {
- addValue(null, -1);
- }
-
- protected void addValue(String val, int argIndex)
- {
- addArgValue(new ArgValue(val, argIndex));
- }
-
- protected void addArgValue(ArgValue av)
- {
- if ((!arg.hasOption(Opt.MULTI) && argValueList.size() > 0)
- || (arg.hasOption(Opt.NODUPLICATEVALUES)
- && argValueList.contains(av.getValue())))
- return;
- if (argValueList == null)
- {
- argValueList = new ArrayList<ArgValue>();
- }
- SubVals sv = ArgParser.getSubVals(av.getValue());
- if (sv.has(ID))
- {
- String id = sv.get(ID);
- av.setId(id);
- idMap.put(id, av);
- }
- argValueList.add(av);
- }
-
- protected boolean hasValue(String val)
- {
- return argValueList.contains(val);
- }
-
- protected ArgValue getArgValue()
- {
- if (arg.hasOption(Opt.MULTI))
- Console.warn("Requesting single value for multi value argument");
- return argValueList.size() > 0 ? argValueList.get(0) : null;
- }
-
- protected List<ArgValue> getArgValueList()
- {
- return argValueList;
- }
-
- protected boolean hasId(String id)
- {
- return idMap.containsKey(id);
- }
-
- protected ArgValue getId(String id)
- {
- return idMap.get(id);
- }
- }
-
- // old style
- private List<String> vargs = null;
-
- private boolean isApplet;
-
- // private AppletParams appletParams;
-
- public boolean isApplet()
- {
- return isApplet;
- }
-
- public String nextValue()
- {
- return vargs.remove(0);
- }
-
- public int getSize()
- {
- return vargs.size();
- }
-
- public String getValue(String arg)
- {
- return getValue(arg, false);
- }
-
- public String getValue(String arg, boolean utf8decode)
- {
- int index = vargs.indexOf(arg);
- String dc = null;
- String ret = null;
- if (index != -1)
- {
- ret = vargs.get(index + 1).toString();
- vargs.remove(index);
- vargs.remove(index);
- if (utf8decode && ret != null)
- {
- try
- {
- dc = URLDecoder.decode(ret, "UTF-8");
- ret = dc;
- } catch (Exception e)
- {
- // TODO: log failure to decode
- }
- }
- }
- return ret;
- }
-
- /*
- public Object getAppletValue(String key, String def, boolean asString)
- {
- Object value;
- return (appletParams == null ? null
- : (value = appletParams.get(key.toLowerCase())) == null ? def
- : asString ? "" + value : value);
- }
- */
-
- // new style
- private static final Map<String, Arg> argMap;
-
- private Map<String, ArgValuesMap> linkedArgs = new HashMap<>();
-
- private List<String> linkedOrder = null;
-
- private List<Arg> argList;
-
- static
- {
- argMap = new HashMap<>();
- for (Arg a : EnumSet.allOf(Arg.class))
- {
- ARGNAME: for (String argName : a.getNames())
- {
- if (argMap.containsKey(argName))
- {
- Console.warn("Trying to add argument name multiple times: '"
- + argName + "'"); // RESTORE THIS WHEN MERGED
- if (argMap.get(argName) != a)
- {
- Console.error(
- "Trying to add argument name multiple times for different Args: '"
- + argMap.get(argName).getName() + ":" + argName
- + "' and '" + a.getName() + ":" + argName
- + "'");
- }
- continue ARGNAME;
- }
- argMap.put(argName, a);
- }
- }
- }
-
- public ArgParser(String[] args)
- {
- // old style
- vargs = new ArrayList<>();
- isApplet = (args.length > 0 && args[0].startsWith("<applet"));
- if (isApplet)
- {
- // appletParams = AppletParams.getAppletParams(args, vargs);
- }
- else
- {
- if (Platform.isJS())
-
- {
- isApplet = true;
- // appletParams =
- // AppletParams.getAppletParams(Platform.getAppletInfoAsMap(), vargs);
- }
- for (int i = 0; i < args.length; i++)
- {
- String arg = args[i].trim();
- if (arg.charAt(0) == '-')
- {
- arg = arg.substring(1);
- }
- vargs.add(arg);
- }
- }
-
- // new style
- Enumeration<String> argE = Collections.enumeration(Arrays.asList(args));
- int argIndex = 0;
- while (argE.hasMoreElements())
- {
- String arg = argE.nextElement();
- String argName = null;
- String val = null;
- String linkedId = null;
- if (arg.startsWith("--"))
- {
- int equalPos = arg.indexOf('=');
- if (equalPos > -1)
- {
- argName = arg.substring(2, equalPos);
- val = arg.substring(equalPos + 1);
- }
- else
- {
- argName = arg.substring(2);
- }
- int idOpen = argName.indexOf('[');
- int idClose = argName.indexOf(']');
-
- if (idOpen > -1 && idClose == argName.length() - 1)
- {
- linkedId = argName.substring(idOpen + 1, idClose);
- argName = argName.substring(0, idOpen);
- }
-
- Arg a = argMap.get(argName);
- // check for boolean prepended by "no"
- boolean negated = false;
- if (a == null && argName.startsWith(NEGATESTRING) && argMap
- .containsKey(argName.substring(NEGATESTRING.length())))
- {
- argName = argName.substring(NEGATESTRING.length());
- a = argMap.get(argName);
- negated = true;
- }
-
- // check for config errors
- if (a == null)
- {
- // arg not found
- Console.error("Argument '" + arg + "' not recognised. Ignoring.");
- continue;
- }
- if (!a.hasOption(Opt.BOOLEAN) && negated)
- {
- // used "no" with a non-boolean option
- Console.error("Argument '--" + NEGATESTRING + argName
- + "' not a boolean option. Ignoring.");
- continue;
- }
- if (!a.hasOption(Opt.STRING) && equalPos > -1)
- {
- // set --argname=value when arg does not accept values
- Console.error("Argument '--" + argName
- + "' does not expect a value (given as '" + arg
- + "'). Ignoring.");
- continue;
- }
- if (!a.hasOption(Opt.LINKED) && linkedId != null)
- {
- // set --argname[linkedId] when arg does not use linkedIds
- Console.error("Argument '--" + argName
- + "' does not expect a linked id (given as '" + arg
- + "'). Ignoring.");
- continue;
- }
-
- if (a.hasOption(Opt.STRING) && equalPos == -1)
- {
- // take next arg as value if required, and '=' was not found
- if (!argE.hasMoreElements())
- {
- // no value to take for arg, which wants a value
- Console.error("Argument '" + a.getName()
- + "' requires a value, none given. Ignoring.");
- continue;
- }
- val = argE.nextElement();
- }
-
- // use default linkedId for linked arguments
- if (a.hasOption(Opt.LINKED) && linkedId == null)
- linkedId = DEFAULTLINKEDID;
-
- if (!linkedArgs.containsKey(linkedId))
- linkedArgs.put(linkedId, new ArgValuesMap());
-
- ArgValuesMap avm = linkedArgs.get(linkedId);
-
- if (a.hasOption(Opt.NODUPLICATEVALUES) && avm.hasValue(a, val))
- {
- Console.error("Argument '--" + argName
- + "' cannot contain a duplicate value ('" + val
- + "'). Ignoring this and subsequent occurrences.");
- continue;
- }
-
- // check for unique id
- SubVals sv = ArgParser.getSubVals(val);
- String id = sv.get(ArgValues.ID);
- if (id != null && avm.hasId(a, id))
- {
- Console.error("Argument '--" + argName + "' has a duplicate id ('"
- + id + "'). Ignoring.");
- continue;
- }
-
- ArgValues avs = avm.getOrCreateArgValues(a);
- if (avs == null)
- {
- avs = new ArgValues(a);
- }
- // store appropriate value
- if (a.hasOption(Opt.STRING))
- {
- avs.addValue(val, argIndex);
- }
- else if (a.hasOption(Opt.BOOLEAN))
- {
- avs.setBoolean(!negated, argIndex);
- avs.setNegated(negated);
- }
- else if (a.hasOption(Opt.UNARY))
- {
- avs.setBoolean(true, argIndex);
- }
- avs.incrementCount();
-
- // store in appropriate place
- if (a.hasOption(Opt.LINKED))
- {
- // allow a default linked id for single usage
- if (linkedId == null)
- linkedId = DEFAULTLINKEDID;
- // store the order of linkedIds
- if (linkedOrder == null)
- linkedOrder = new ArrayList<>();
- if (!linkedOrder.contains(linkedId))
- linkedOrder.add(linkedId);
- }
-
- // store arg in the list of args used
- if (argList == null)
- argList = new ArrayList<>();
- if (!argList.contains(a))
- argList.add(a);
- }
- }
- }
-
- public boolean isSet(Arg a)
- {
- return a.hasOption(Opt.LINKED) ? isSet("", a) : isSet(null, a);
- }
-
- public boolean isSet(String linkedId, Arg a)
- {
- ArgValuesMap avm = linkedArgs.get(linkedId);
- return avm == null ? false : avm.containsArg(a);
- }
-
- public boolean getBool(Arg a)
- {
- if (!a.hasOption(Opt.BOOLEAN) && !a.hasOption(Opt.UNARY))
- {
- Console.warn("Getting boolean from non boolean Arg '" + a.getName()
- + "'.");
- }
- return a.hasOption(Opt.LINKED) ? getBool("", a) : getBool(null, a);
- }
-
- public boolean getBool(String linkedId, Arg a)
- {
- ArgValuesMap avm = linkedArgs.get(linkedId);
- if (avm == null)
- return a.getDefaultBoolValue();
- ArgValues avs = avm.getArgValues(a);
- return avs == null ? a.getDefaultBoolValue() : avs.getBoolean();
- }
-
- public List<String> linkedIds()
- {
- return linkedOrder;
- }
-
- public ArgValuesMap linkedArgs(String id)
- {
- return linkedArgs.get(id);
- }
-
- @Override
- public String toString()
- {
- StringBuilder sb = new StringBuilder();
- sb.append("UNLINKED\n");
- sb.append(argValuesMapToString(linkedArgs.get(null)));
- if (linkedIds() != null)
- {
- sb.append("LINKED\n");
- for (String id : linkedIds())
- {
- // already listed these as UNLINKED args
- if (id == null)
- continue;
-
- ArgValuesMap avm = linkedArgs(id);
- sb.append("ID: '").append(id).append("'\n");
- sb.append(argValuesMapToString(avm));
- }
- }
- return sb.toString();
- }
-
- private static String argValuesMapToString(ArgValuesMap avm)
- {
- if (avm == null)
- return null;
- StringBuilder sb = new StringBuilder();
- for (Arg a : avm.getArgKeys())
- {
- ArgValues v = avm.getArgValues(a);
- sb.append(v.toString());
- sb.append("\n");
- }
- return sb.toString();
- }
-
- public static SubVals getSubVals(String item)
- {
- return new SubVals(item);
- }
-
- /**
- * A helper class to keep an index of argument position with argument values
- */
- public static class ArgValue
- {
- private int argIndex;
-
- private String value;
-
- private String id;
-
- protected ArgValue(String value, int argIndex)
- {
- this.value = value;
- this.argIndex = argIndex;
- }
-
- protected String getValue()
- {
- return value;
- }
-
- protected int getArgIndex()
- {
- return argIndex;
- }
-
- protected void setId(String i)
- {
- id = i;
- }
-
- protected String getId()
- {
- return id;
- }
- }
-
- /**
- * A helper class to parse a string of the possible forms "content"
- * "[index]content", "[keyName=keyValue]content" and return the integer index,
- * the strings keyName and keyValue, and the content after the square brackets
- * (if present). Values not set `will be -1 or null.
- */
- public static class SubVals
- {
- private static int NOTSET = -1;
-
- private int index = NOTSET;
-
- private Map<String, String> subVals = null;
-
- private static char SEPARATOR = ';';
-
- private String content = null;
-
- public SubVals(String item)
- {
- this.parseVals(item);
- }
-
- public void parseVals(String item)
- {
- if (item == null)
- return;
- if (item.indexOf('[') == 0 && item.indexOf(']') > 1)
- {
- int openBracket = item.indexOf('[');
- int closeBracket = item.indexOf(']');
- String subvalsString = item.substring(openBracket + 1,
- closeBracket);
- this.content = item.substring(closeBracket + 1);
- boolean setIndex = false;
- for (String subvalString : subvalsString
- .split(Character.toString(SEPARATOR)))
- {
- int equals = subvalString.indexOf('=');
- if (equals > -1)
- {
- if (subVals == null)
- subVals = new HashMap<>();
- subVals.put(subvalString.substring(0, equals),
- subvalString.substring(equals + 1));
- }
- else
- {
- try
- {
- this.index = Integer.parseInt(subvalString);
- setIndex = true;
- } catch (NumberFormatException e)
- {
- Console.warn("Failed to obtain subvalue or index from '"
- + item + "'. Setting index=0 and using content='"
- + content + "'.");
- }
- }
- }
- if (!setIndex)
- this.index = NOTSET;
- }
- else
- {
- this.content = item;
- }
- }
-
- public boolean notSet()
- {
- // notSet is true if content present but nonsensical
- return index == NOTSET && subVals == null;
- }
-
- public String get(String key)
- {
- return subVals == null ? null : subVals.get(key);
- }
-
- public boolean has(String key)
- {
- return subVals == null ? false : subVals.containsKey(key);
- }
-
- public int getIndex()
- {
- return index;
- }
-
- public String getContent()
- {
- return content;
- }
- }
-
- /**
- * Helper class to allow easy extraction of information about specific
- * argument values (without having to check for null etc all the time)
- */
- protected static class ArgValuesMap
- {
- protected Map<Arg, ArgValues> m;
-
- protected ArgValuesMap()
- {
- this.newMap();
- }
-
- protected ArgValuesMap(Map<Arg, ArgValues> map)
- {
- this.m = map;
- }
-
- private Map<Arg, ArgValues> getMap()
- {
- return m;
- }
-
- private void newMap()
- {
- m = new HashMap<Arg, ArgValues>();
- }
-
- private void newArg(Arg a)
- {
- if (m == null)
- newMap();
- if (!containsArg(a))
- m.put(a, new ArgValues(a));
- }
-
- protected void addArgValue(Arg a, ArgValue av)
- {
- if (getMap() == null)
- m = new HashMap<Arg, ArgValues>();
-
- if (!m.containsKey(a))
- m.put(a, new ArgValues(a));
- ArgValues avs = m.get(a);
- avs.addArgValue(av);
- }
-
- protected ArgValues getArgValues(Arg a)
- {
- return m == null ? null : m.get(a);
- }
-
- protected ArgValues getOrCreateArgValues(Arg a)
- {
- ArgValues avs = m.get(a);
- if (avs == null)
- newArg(a);
- return getArgValues(a);
- }
-
- protected List<ArgValue> getArgValueList(Arg a)
- {
- ArgValues avs = getArgValues(a);
- return avs == null ? new ArrayList<>() : avs.getArgValueList();
- }
-
- protected ArgValue getArgValue(Arg a)
- {
- List<ArgValue> vals = getArgValueList(a);
- return (vals == null || vals.size() == 0) ? null : vals.get(0);
- }
-
- protected String getValue(Arg a)
- {
- ArgValue av = getArgValue(a);
- return av == null ? null : av.getValue();
- }
-
- protected boolean containsArg(Arg a)
- {
- if (m == null || !m.containsKey(a))
- return false;
- return a.hasOption(Opt.STRING) ? getArgValue(a) != null
- : this.getBoolean(a);
- }
-
- protected boolean hasValue(Arg a, String val)
- {
- if (m == null || !m.containsKey(a))
- return false;
- for (ArgValue av : getArgValueList(a))
- {
- String avVal = av.getValue();
- if ((val == null && avVal == null)
- || (val != null && val.equals(avVal)))
- {
- return true;
- }
- }
- return false;
- }
-
- protected boolean getBoolean(Arg a)
- {
- ArgValues av = getArgValues(a);
- return av == null ? false : av.getBoolean();
- }
-
- protected Set<Arg> getArgKeys()
- {
- return m.keySet();
- }
-
- protected ArgValue getClosestPreviousArgValueOfArg(ArgValue thisAv,
- Arg a)
- {
- ArgValue closestAv = null;
- int thisArgIndex = thisAv.getArgIndex();
- ArgValues compareAvs = this.getArgValues(a);
- int closestPreviousIndex = -1;
- for (ArgValue av : compareAvs.getArgValueList())
- {
- int argIndex = av.getArgIndex();
- if (argIndex < thisArgIndex && argIndex > closestPreviousIndex)
- {
- closestPreviousIndex = argIndex;
- closestAv = av;
- }
- }
- return closestAv;
- }
-
- protected ArgValue getClosestNextArgValueOfArg(ArgValue thisAv, Arg a)
- {
- // this looks for the *next* arg that *might* be referring back to
- // a thisAv. Such an arg would have no subValues (if it does it should
- // specify an id in the subValues so wouldn't need to be guessed).
- ArgValue closestAv = null;
- int thisArgIndex = thisAv.getArgIndex();
- ArgValues compareAvs = this.getArgValues(a);
- int closestNextIndex = Integer.MAX_VALUE;
- for (ArgValue av : compareAvs.getArgValueList())
- {
- int argIndex = av.getArgIndex();
- if (argIndex > thisArgIndex && argIndex < closestNextIndex)
- {
- closestNextIndex = argIndex;
- closestAv = av;
- }
- }
- return closestAv;
- }
-
- protected ArgValue[] getArgValuesReferringTo(String key, String value,
- Arg a)
- {
- // this looks for the *next* arg that *might* be referring back to
- // a thisAv. Such an arg would have no subValues (if it does it should
- // specify an id in the subValues so wouldn't need to be guessed).
- List<ArgValue> avList = new ArrayList<>();
- Arg[] args = a == null ? (Arg[]) this.getMap().keySet().toArray()
- : new Arg[]
- { a };
- for (Arg keyArg : args)
- {
- for (ArgValue av : this.getArgValueList(keyArg))
- {
-
- }
- }
- return (ArgValue[]) avList.toArray();
- }
-
- protected boolean hasId(Arg a, String id)
- {
- ArgValues avs = this.getArgValues(a);
- return avs == null ? false : avs.hasId(id);
- }
-
- protected ArgValue getId(Arg a, String id)
- {
- ArgValues avs = this.getArgValues(a);
- return avs == null ? null : avs.getId(id);
- }
- }
-
- public static Map<Arg, String> bootstrapArgs(String[] args)
- {
- Map<Arg, String> bootstrapArgMap = new HashMap<>();
- if (args == null)
- return bootstrapArgMap;
- Enumeration<String> argE = Collections.enumeration(Arrays.asList(args));
- while (argE.hasMoreElements())
- {
- String arg = argE.nextElement();
- String argName = null;
- String val = null;
- if (arg.startsWith("--"))
- {
- int equalPos = arg.indexOf('=');
- if (equalPos > -1)
- {
- argName = arg.substring(2, equalPos);
- val = arg.substring(equalPos + 1);
- }
- else
- {
- argName = arg.substring(2);
- }
- Arg a = argMap.get(argName);
- if (a != null && bootstrapArgs.contains(a))
- bootstrapArgMap.put(a, val);
- }
- }
- return bootstrapArgMap;
- }
-
- public static ArgParser parseArgFile(String argFilename)
- {
- List<String> argsList = null;
- File argFile = new File(argFilename);
- if (!argFile.exists())
- {
- System.err.println("--" + Arg.ARGFILE.name().toLowerCase(Locale.ROOT)
- + "=\"" + argFilename + "\": File does not exist.");
- System.exit(2);
- }
- try
- {
- argsList = Files.readAllLines(Paths.get(argFilename));
- } catch (IOException e)
- {
- System.err.println("--" + Arg.ARGFILE.name().toLowerCase(Locale.ROOT)
- + "=\"" + argFilename + "\": File could not be read.");
- System.exit(3);
- }
- return new ArgParser((String[]) argsList.toArray());
- }
-}
\ No newline at end of file
*/
public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
+ // for tests
+ public static final String BOOTSTRAP_TEST = "BOOTSTRAP_TEST";
+
/**
* Sifts settings
*/
}
private static final Collection<String> bootstrapProperties = new ArrayList<>(
- Arrays.asList(JALVIEWLOGLEVEL));
+ Arrays.asList(JALVIEWLOGLEVEL, BOOTSTRAP_TEST));
public static Properties bootstrapProperties(String filename)
{
import java.io.File;
import java.io.IOException;
+import java.util.AbstractMap;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.Locale;
import java.util.Map;
+import java.util.Map.Entry;
import jalview.analysis.AlignmentUtils;
import jalview.api.AlignmentViewPanel;
-import jalview.bin.ArgParser.Arg;
-import jalview.bin.ArgParser.ArgValue;
-import jalview.bin.ArgParser.ArgValuesMap;
-import jalview.bin.ArgParser.SubVals;
+import jalview.bin.argparser.Arg;
+import jalview.bin.argparser.ArgParser;
+import jalview.bin.argparser.ArgValue;
+import jalview.bin.argparser.ArgValues;
+import jalview.bin.argparser.ArgValuesMap;
+import jalview.bin.argparser.SubVals;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.gui.StructureViewer;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
import jalview.io.FileLoader;
{
Desktop desktop;
- private static boolean headless;
+ private boolean headless;
- private static ArgParser argParser;
+ private ArgParser argParser;
private Map<String, AlignFrame> afMap;
- private static boolean commandArgsProvided = false;
+ private boolean commandArgsProvided = false;
- public static boolean commandArgsProvided()
+ private boolean argsWereParsed = false;
+
+ public Commands(ArgParser argparser, boolean headless)
{
- return commandArgsProvided;
+ this(Desktop.instance, argparser, headless);
}
- public static boolean processArgs(ArgParser ap, boolean h)
+ public Commands(Desktop d, ArgParser argparser, boolean h)
{
- argParser = ap;
+ argParser = argparser;
headless = h;
- boolean argsWereParsed = true;
- if (headless)
+ desktop = d;
+ afMap = new HashMap<String, AlignFrame>();
+ if (argparser != null)
{
- System.setProperty("java.awt.headless", "true");
+ processArgs(argparser, headless);
}
+ }
+
+ private boolean processArgs(ArgParser argparser, boolean h)
+ {
+ argParser = argparser;
+ headless = h;
+ boolean theseArgsWereParsed = false;
if (argParser != null && argParser.linkedIds() != null)
{
for (String id : argParser.linkedIds())
{
- Commands cmds = new Commands();
+ ArgValuesMap avm = argParser.linkedArgs(id);
+ theseArgsWereParsed = true;
if (id == null)
{
- cmds.processUnlinked(id);
- argsWereParsed &= cmds.wereParsed();
+ theseArgsWereParsed &= processUnlinked(id);
}
else
{
- cmds.processLinked(id);
- argsWereParsed &= cmds.wereParsed();
+ theseArgsWereParsed &= processLinked(id);
}
- cmds.processImages(id);
- argsWereParsed &= cmds.wereParsed();
+ theseArgsWereParsed &= processImages(id);
+
+ // close ap
+ if (avm.getBoolean(Arg.CLOSE))
+ {
+ AlignFrame af = afMap.get(id);
+ if (af != null)
+ {
+ af.closeMenuItem_actionPerformed(true);
+ }
+ }
+
}
}
return true;
}
// carry on with jalview.bin.Jalview
+ argsWereParsed = theseArgsWereParsed;
return argsWereParsed;
}
- boolean argsWereParsed = true; // set false as soon as an arg is found
-
- private boolean wereParsed()
+ public boolean commandArgsProvided()
{
- return argsWereParsed;
- }
-
- public Commands()
- {
- this(Desktop.instance);
+ return commandArgsProvided;
}
- public Commands(Desktop d)
+ public boolean argsWereParsed()
{
- this.desktop = d;
- afMap = new HashMap<String, AlignFrame>();
+ return argsWereParsed;
}
- protected void processUnlinked(String id)
+ protected boolean processUnlinked(String id)
{
- processLinked(id);
+ return processLinked(id);
}
- protected void processLinked(String id)
+ protected boolean processLinked(String id)
{
+ boolean theseArgsWereParsed = false;
ArgValuesMap avm = argParser.linkedArgs(id);
if (avm == null)
- return;
- else
- argsWereParsed = false;
+ return true;
/*
- // script to execute after all loading is completed one way or another
- String groovyscript = m.get(Arg.GROOVY) == null ? null
- : m.get(Arg.GROOVY).getValue();
- String file = m.get(Arg.OPEN) == null ? null
- : m.get(Arg.OPEN).getValue();
- String data = null;
- FileFormatI format = null;
- DataSourceType protocol = null;
- */
- if (avm.containsArg(Arg.OPEN))
+ * // script to execute after all loading is completed one way or another String
+ * groovyscript = m.get(Arg.GROOVY) == null ? null :
+ * m.get(Arg.GROOVY).getValue(); String file = m.get(Arg.OPEN) == null ? null :
+ * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
+ * DataSourceType protocol = null;
+ */
+ if (avm.containsArg(Arg.OPEN) || avm.containsArg(Arg.OPENNEW))
{
commandArgsProvided = true;
long progress = -1;
boolean first = true;
boolean progressBarSet = false;
AlignFrame af;
- for (ArgValue av : avm.getArgValueList(Arg.OPEN))
+ // Combine the OPEN and OPENNEW files into one list, along with whether it
+ // was OPEN or OPENNEW
+ List<Entry<Arg, ArgValue>> openAvList = new ArrayList<>();
+ avm.getArgValueList(Arg.OPEN).stream()
+ .forEachOrdered(av -> openAvList.add(
+ new AbstractMap.SimpleEntry<Arg, ArgValue>(Arg.OPEN,
+ av)));
+ avm.getArgValueList(Arg.OPENNEW).stream()
+ .forEachOrdered(av -> openAvList
+ .add(new AbstractMap.SimpleEntry<Arg, ArgValue>(
+ Arg.OPENNEW, av)));
+ for (Entry<Arg, ArgValue> aav : openAvList)
{
+ Arg a = aav.getKey();
+ ArgValue av = aav.getValue();
String openFile = av.getValue();
if (openFile == null)
continue;
- argsWereParsed = true;
+ theseArgsWereParsed = true;
if (first)
{
first = false;
}
af = afMap.get(id);
- if (af == null)
+ if (af == null || "true".equals(av.getSubVal("new"))
+ || a == Arg.OPENNEW || format == FileFormat.Jalview)
{
/*
- * this approach isn't working yet
- // get default annotations before opening AlignFrame
- if (m.get(Arg.SSANNOTATION) != null)
- {
- Console.debug("***** SSANNOTATION="
- + m.get(Arg.SSANNOTATION).getBoolean());
- }
- if (m.get(Arg.NOTEMPFAC) != null)
- {
- Console.debug(
- "***** NOTEMPFAC=" + m.get(Arg.NOTEMPFAC).getBoolean());
- }
- boolean showSecondaryStructure = (m.get(Arg.SSANNOTATION) != null)
- ? m.get(Arg.SSANNOTATION).getBoolean()
- : false;
- boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null)
- ? !m.get(Arg.NOTEMPFAC).getBoolean()
- : false;
- Console.debug("***** tempfac=" + showTemperatureFactor
- + ", showSS=" + showSecondaryStructure);
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- if (ssm != null)
- {
- ssm.setAddTempFacAnnot(showTemperatureFactor);
- ssm.setProcessSecondaryStructure(showSecondaryStructure);
- }
+ * this approach isn't working yet // get default annotations before opening
+ * AlignFrame if (m.get(Arg.SSANNOTATION) != null) {
+ * Console.debug("##### SSANNOTATION=" + m.get(Arg.SSANNOTATION).getBoolean());
+ * } if (m.get(Arg.NOTEMPFAC) != null) { Console.debug( "##### NOTEMPFAC=" +
+ * m.get(Arg.NOTEMPFAC).getBoolean()); } boolean showSecondaryStructure =
+ * (m.get(Arg.SSANNOTATION) != null) ? m.get(Arg.SSANNOTATION).getBoolean() :
+ * false; boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null) ?
+ * !m.get(Arg.NOTEMPFAC).getBoolean() : false; Console.debug("##### tempfac=" +
+ * showTemperatureFactor + ", showSS=" + showSecondaryStructure);
+ * StructureSelectionManager ssm = StructureSelectionManager
+ * .getStructureSelectionManager(Desktop.instance); if (ssm != null) {
+ * ssm.setAddTempFacAnnot(showTemperatureFactor);
+ * ssm.setProcessSecondaryStructure(showSecondaryStructure); }
*/
// get kind of temperature factor annotation
} catch (IllegalArgumentException e)
{
// Just an error message!
- StringBuilder sb = new StringBuilder().append("Cannot set --")
- .append(Arg.TEMPFAC.getName()).append(" to '")
+ StringBuilder sb = new StringBuilder().append("Cannot set ")
+ .append(Arg.TEMPFAC.argString()).append(" to '")
.append(tempfacType)
.append("', ignoring. Valid values are: ");
Iterator<StructureImportSettings.TFType> it = Arrays
false, false);
}
else
- /* comment out hacky approach up to here and add this line:
- if (showTemperatureFactor)
- */
+ /*
+ * comment out hacky approach up to here and add this line: if
+ * (showTemperatureFactor)
+ */
{
if (avm.containsArg(Arg.TEMPFAC_LABEL))
{
{
Console.debug(
"Opening '" + openFile + "' in existing alignment frame");
- af.getCurrentView().addFile(new File(openFile), format);
+ af.getCurrentView().addFile(new File(openFile), format, false);
}
Console.debug("Command " + Arg.OPEN + " executed successfully!");
{
if (headless)
{
- Console.error("Could not open any files in headless mode");
- System.exit(1);
+ Jalview.exit("Could not open any files in headless mode", 1);
}
else
{
for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
{
String val = av.getValue();
- SubVals subId = new SubVals(val);
+ SubVals subId = av.getSubVals();
SequenceI seq = getSpecifiedSequence(af, subId);
if (seq == null)
{
- Console.warn("Could not find sequence for argument --"
- + Arg.STRUCTURE + "=" + val);
+ // Could not find sequence from subId, let's assume the first
+ // sequence in the alignframe
+ AlignmentI al = af.getCurrentView().getAlignment();
+ seq = al.getSequenceAt(0);
+ }
+
+ if (seq == null)
+ {
+ Console.warn("Could not find sequence for argument "
+ + Arg.STRUCTURE.argString() + "=" + val);
// you probably want to continue here, not break
// break;
continue;
Console.debug("Using structure file (from argument) '"
+ structureFile.getAbsolutePath() + "'");
}
-
// TRY THIS
/*
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(selectedPdbFileName,
- DataSourceType.FILE, selectedSequence, true,
- Desktop.instance);
-
- sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
- ap, new SequenceI[]
- { selectedSequence });
-
+ * PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+ * .associatePdbWithSeq(selectedPdbFileName, DataSourceType.FILE,
+ * selectedSequence, true, Desktop.instance);
+ *
+ * sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new
+ * SequenceI[] { selectedSequence });
+ *
*/
-
/* THIS DOESN'T WORK */
else if (seq.getAllPDBEntries() != null
&& seq.getAllPDBEntries().size() > 0)
// get tft, paeFilename, label?
/*
- ArgValue tftAv = avm.getArgValuesReferringTo("structid", structId,
- Arg.TEMPFAC);
+ * ArgValue tftAv = avm.getArgValuesReferringTo("structid", structId,
+ * Arg.TEMPFAC);
*/
StructureChooser.openStructureFileForSequence(null, null, ap, seq,
false, structureFile.getAbsolutePath(), null, null); // tft,
- // paeFilename);
+ // paeFilename);
}
}
}
- // load a pAE file if given
+ // load a PAE file if given
if (avm.containsArg(Arg.PAEMATRIX))
{
AlignFrame af = afMap.get(id);
for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
{
String val = av.getValue();
- SubVals subVals = ArgParser.getSubVals(val);
+ SubVals subVals = av.getSubVals();
+ String paeLabel = subVals.get("label");
File paeFile = new File(subVals.getContent());
String paePath = null;
try
Console.warn(
"Problem with the PAE file path: '" + paePath + "'");
}
- String structId = subVals.get("structid");
- if (subVals.notSet())
+ String structid = subVals.get("structid");
+ String structfile = subVals.get("structfile");
+ String seqid = subVals.get("seqid");
+ int seqindex = subVals.getIndex();
+
+ // let's find a structure
+ if (structfile == null && structid == null && seqid == null
+ && seqindex == SubVals.NOTSET)
+ {
+ ArgValue likelyStructure = avm
+ .getClosestPreviousArgValueOfArg(av, Arg.STRUCTURE);
+ if (likelyStructure != null)
+ {
+ SubVals sv = likelyStructure.getSubVals();
+ if (sv != null && sv.has(ArgValues.ID))
+ {
+ structid = sv.get(ArgValues.ID);
+ }
+ else
+ {
+ structfile = likelyStructure.getValue();
+ Console.debug(
+ "##### Using closest previous structure argument '"
+ + structfile + "'");
+ }
+ }
+ }
+
+ if (structfile != null)
{
- // take structid from pdbfilename
+ Console.debug("##### Attaching paeFile '" + paePath + "' to "
+ + "structfile=" + structfile);
+ EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+ paeFile, seqindex, structfile, true, false, paeLabel);
}
- if (subVals.has("structfile"))
+ else if (structid != null)
{
- Console.info("***** Attaching paeFile '" + paePath + "' to "
- + "structfile=" + subVals.get("structfile"));
+ Console.debug("##### Attaching paeFile '" + paePath + "' to "
+ + "structid=" + structid);
EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, subVals.getIndex(), subVals.get("structfile"),
- true, false);
+ paeFile, seqindex, structid, true, true, paeLabel);
}
- else if (subVals.has("structid"))
+ else if (seqid != null)
{
- Console.info("***** Attaching paeFile '" + paePath + "' to "
- + "structid=" + subVals.get("structid"));
+ Console.debug("##### Attaching paeFile '" + paePath + "' to "
+ + "seqid=" + seqid);
EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, subVals.getIndex(), subVals.get("structid"),
- true, true);
+ paeFile, seqindex, seqid, false, false, paeLabel);
}
- else
+ else if (seqindex >= 0)
{
- Console.debug("***** Attaching paeFile '" + paePath
- + "' to sequence index " + subVals.getIndex());
+ Console.debug("##### Attaching paeFile '" + paePath
+ + "' to sequence index " + seqindex);
EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, subVals.getIndex(), null, false, false);
- // required to readjust the height and position of the pAE
- // annotation
+ paeFile, seqindex, null, false, false, paeLabel);
}
for (AlignmentViewPanel ap : af.getAlignPanels())
{
+ // required to readjust the height and position of the PAE
+ // annotation
ap.adjustAnnotationHeight();
}
}
Console.info("Changed colour " + acg.toString());
}
}
+
+ return theseArgsWereParsed;
}
- protected void processImages(String id)
+ protected boolean processImages(String id)
{
ArgValuesMap avm = argParser.linkedArgs(id);
AlignFrame af = afMap.get(id);
if (af == null)
{
Console.warn("Did not have an alignment window for id=" + id);
- return;
+ return false;
}
if (avm.containsArg(Arg.IMAGE))
for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
{
String val = av.getValue();
- SubVals subVal = new SubVals(val);
+ SubVals subVal = av.getSubVals();
String type = "png"; // default
String fileName = subVal.getContent();
File file = new File(fileName);
htmlSVG.exportHTML(fileName);
break;
default:
- Console.warn("--image type '" + type + "' not known. Ignoring");
+ Console.warn(Arg.IMAGE.argString() + " type '" + type
+ + "' not known. Ignoring");
break;
}
}
}
+ return true;
}
private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
{
+ if (subId == null)
+ return null;
AlignmentI al = af.getCurrentView().getAlignment();
- if (-1 < subId.getIndex()
- && subId.getIndex() < al.getSequences().size())
+ if (subId.has("seqid"))
{
- return al.getSequenceAt(subId.getIndex());
+ return al.findName(subId.get("seqid"));
}
- else if (subId.has("seqid"))
+ else if (-1 < subId.getIndex()
+ && subId.getIndex() < al.getSequences().size())
{
- return al.findName(subId.get("seqid"));
+ return al.getSequenceAt(subId.getIndex());
}
return null;
}
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStreamReader;
+import java.io.OutputStream;
import java.io.OutputStreamWriter;
+import java.io.PrintStream;
import java.io.PrintWriter;
import java.net.MalformedURLException;
import java.net.URI;
import java.security.PermissionCollection;
import java.security.Permissions;
import java.security.Policy;
+import java.util.ArrayList;
import java.util.HashMap;
+import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Properties;
//import edu.stanford.ejalbert.launching.IBrowserLaunching;
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
-import jalview.bin.ArgParser.Arg;
+import jalview.bin.argparser.Arg;
+import jalview.bin.argparser.ArgParser;
+import jalview.bin.argparser.BootstrapArgs;
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
private Desktop desktop;
+ protected Commands cmds;
+
public static AlignFrame currentAlignFrame;
static
System.setSecurityManager(null);
}
+ // Move any new getdown-launcher-new.jar into place over old
+ // getdown-launcher.jar
+ String appdirString = System.getProperty("getdownappdir");
+ if (appdirString != null && appdirString.length() > 0)
+ {
+ final File appdir = new File(appdirString);
+ new Thread()
+ {
+ @Override
+ public void run()
+ {
+ LaunchUtil.upgradeGetdown(
+ new File(appdir, "getdown-launcher-old.jar"),
+ new File(appdir, "getdown-launcher.jar"),
+ new File(appdir, "getdown-launcher-new.jar"));
+ }
+ }.start();
+ }
+
// get args needed before proper ArgParser
- Map<ArgParser.Arg, String> bootstrapArgs = ArgParser
- .bootstrapArgs(args);
+ BootstrapArgs bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
+
+ if (!Platform.isJS())
+ {
+ // are we being --quiet ?
+ if (bootstrapArgs.contains(Arg.QUIET))
+ {
+ OutputStream devNull = new OutputStream()
+ {
+ @Override
+ public void write(int b)
+ {
+ // DO NOTHING
+ }
+ };
+ System.setOut(new PrintStream(devNull));
+ // redirecting stderr not working
+ if (bootstrapArgs.getList(Arg.QUIET).size() > 1)
+ {
+ System.setErr(new PrintStream(devNull));
+ }
+ }
+ }
System.out
.println("Java version: " + System.getProperty("java.version"));
try
{
- String logLevel = bootstrapArgs.containsKey(Arg.DEBUG) ? "DEBUG"
- : null;
+ String logLevel = bootstrapArgs.contains(Arg.DEBUG) ? "DEBUG" : null;
if (logLevel == null && !(bootstrapProperties == null))
{
logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
} catch (NoClassDefFoundError error)
{
error.printStackTrace();
- System.out.println("\nEssential logging libraries not found."
- + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
- System.exit(0);
+ String message = "\nEssential logging libraries not found."
+ + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
+ Jalview.exit(message, 0);
}
// register SIGTERM listener
}
});
- String usrPropsFile = bootstrapArgs.containsKey(Arg.PROPS)
+ String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
? bootstrapArgs.get(Arg.PROPS)
: aparser.getValue("props");
+ // if usrPropsFile == null, loadProperties will use the Channel
+ // preferences.file
Cache.loadProperties(usrPropsFile);
if (usrPropsFile != null)
{
// new ArgParser
ArgParser argparser;
// --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
- if (bootstrapArgs.containsKey(Arg.ARGFILE))
+ if (bootstrapArgs.contains(Arg.ARGFILE))
{
- argparser = ArgParser.parseArgFile(bootstrapArgs.get(Arg.ARGFILE));
+ argparser = ArgParser.parseArgFiles(
+ bootstrapArgs.getList(Arg.ARGFILE),
+ bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
}
else
{
- argparser = new ArgParser(args);
+ argparser = new ArgParser(args,
+ bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
}
if (!Platform.isJS())
* @j2sIgnore
*/
{
- if (aparser.contains("help") || aparser.contains("h")
- || argparser.getBool(Arg.HELP))
+ if (bootstrapArgs.contains(Arg.HELP))
+ {
+ System.out.println(Arg.usage());
+ Jalview.exit(null, 0);
+ }
+ if (aparser.contains("help") || aparser.contains("h"))
{
showUsage();
- System.exit(0);
+ Jalview.exit(null, 0);
}
- if (argparser.isSet(Arg.HEADLESS))
+ if (bootstrapArgs.contains(Arg.HEADLESS))
{
System.setProperty("java.awt.headless", "true");
// new
}
}
- String defs = aparser.getValue("setprop");
- while (defs != null)
+ List<String> setprops = new ArrayList<>();
+ if (bootstrapArgs.contains(Arg.SETPROP))
+ {
+ setprops = bootstrapArgs.getList(Arg.SETPROP);
+ }
+ else
+ {
+ String sp = aparser.getValue("setprop");
+ while (sp != null)
+ {
+ setprops.add(sp);
+ sp = aparser.getValue("setprop");
+ }
+ }
+ for (String setprop : setprops)
{
- int p = defs.indexOf('=');
+ int p = setprop.indexOf('=');
if (p == -1)
{
- System.err.println("Ignoring invalid setprop argument : " + defs);
+ System.err
+ .println("Ignoring invalid setprop argument : " + setprop);
}
else
{
- System.out.println("Executing setprop argument: " + defs);
+ System.out.println("Executing setprop argument: " + setprop);
if (Platform.isJS())
{
- Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
+ Cache.setProperty(setprop.substring(0, p),
+ setprop.substring(p + 1));
}
// DISABLED FOR SECURITY REASONS
// TODO: add a property to allow properties to be overriden by cli args
- // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+ // Cache.setProperty(setprop.substring(0,p), setprop.substring(p+1));
}
- defs = aparser.getValue("setprop");
}
if (System.getProperty("java.awt.headless") != null
&& System.getProperty("java.awt.headless").equals("true"))
NoClassDefFoundError error)
{
error.printStackTrace();
- System.out.println("\nEssential logging libraries not found."
- + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
- System.exit(0);
+ String message = "\nEssential logging libraries not found."
+ + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
+ Jalview.exit(message, 0);
}
desktop = null;
if (!(headless || headlessArg))
{
- Desktop.nosplash = aparser.contains("nosplash");
+ Desktop.nosplash = "false".equals(bootstrapArgs.get(Arg.SPLASH))
+ || aparser.contains("nosplash");
desktop = new Desktop();
desktop.setInBatchMode(true); // indicate we are starting up
.println("CMD [-noquestionnaire] executed successfully!");
}
- if (!aparser.contains("nonews")
- || Cache.getProperty("NONEWS") == null)
+ if ((!aparser.contains("nonews")
+ && Cache.getProperty("NONEWS") == null
+ && !"false".equals(bootstrapArgs.get(Arg.NEWS)))
+ || "true".equals(bootstrapArgs.get(Arg.NEWS)))
{
desktop.checkForNews();
}
if (!aparser.contains("nohtmltemplates")
- || Cache.getProperty("NOHTMLTEMPLATES") == null)
+ && Cache.getProperty("NOHTMLTEMPLATES") == null)
{
BioJsHTMLOutput.updateBioJS();
}
}
}
// Run Commands from cli
- boolean commandsSuccess = Commands.processArgs(argparser, headlessArg);
+ cmds = new Commands(argparser, headlessArg);
+ boolean commandsSuccess = cmds.argsWereParsed();
if (commandsSuccess)
{
- Console.info("Successfully completed commands");
if (headlessArg)
- System.exit(0);
+ {
+ Jalview.exit("Successfully completed commands in headless mode", 0);
+ }
+ Console.info("Successfully completed commands");
}
else
{
- Console.warn("Error when running commands");
if (headlessArg)
- System.exit(1);
+ {
+ Jalview.exit("Error when running Commands in headless mode", 1);
+ }
+ Console.warn("Error when running commands");
}
// Check if JVM and compile version might cause problems and log if it
+ LaunchUtils.getJavaCompileVersion() + ".");
}
- // Move any new getdown-launcher-new.jar into place over old
- // getdown-launcher.jar
- String appdirString = System.getProperty("getdownappdir");
- if (appdirString != null && appdirString.length() > 0)
- {
- final File appdir = new File(appdirString);
- new Thread()
- {
- @Override
- public void run()
- {
- LaunchUtil.upgradeGetdown(
- new File(appdir, "getdown-launcher-old.jar"),
- new File(appdir, "getdown-launcher.jar"),
- new File(appdir, "getdown-launcher-new.jar"));
- }
- }.start();
- }
-
String file = null, data = null;
FileFormatI format = null;
groovyscript = aparser.getValue("groovy", true);
file = aparser.getValue("open", true);
- if (file == null && desktop == null)
+ if (file == null && desktop == null && !commandsSuccess)
{
- System.out.println("No files to open!");
- System.exit(1);
+ Jalview.exit("No files to open!", 1);
}
long progress = -1;
{
if (!(new File(file)).exists())
{
- System.out.println("Can't find " + file);
if (headless)
{
- System.exit(1);
+ Jalview.exit(
+ "Can't find file '" + file + "' in headless mode", 1);
}
+ Console.warn("Can't find file'" + file + "'");
}
}
}
if (!Platform.isJS() && !headless && file == null
&& Cache.getDefault("SHOW_STARTUP_FILE", true)
- && !Commands.commandArgsProvided())
+ && !cmds.commandArgsProvided())
// don't open the startup file if command line args have been processed
// (&& !Commands.commandArgsProvided())
/**
public void quit()
{
// System.exit will run the shutdownHook first
- System.exit(0);
+ Jalview.exit("Quitting now. Bye!", 0);
}
public static AlignFrame getCurrentAlignFrame()
{
Jalview.currentAlignFrame = currentAlignFrame;
}
+
+ protected Commands getCommands()
+ {
+ return cmds;
+ }
+
+ public static void exit(String message, int exitcode)
+ {
+ Console.debug("Using Jalview.exit");
+ if (message != null)
+ if (exitcode == 0)
+ Console.info(message);
+ else
+ Console.error(message);
+ if (exitcode > -1)
+ System.exit(exitcode);
+ }
}
if (Boolean.parseBoolean(System.getProperty("launcherstop", "false")))
{
+ System.out.println(
+ "System property 'launcherstop' is set and not 'false'. Exiting.");
System.exit(0);
}
try
{
e.printStackTrace();
}
- // System.exit(0);
}
}
--- /dev/null
+package jalview.bin.argparser;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.EnumSet;
+import java.util.List;
+import java.util.Locale;
+import java.util.stream.Collectors;
+
+public enum Arg
+{
+ HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, ANNOTATIONS,
+ COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, ANNOTATION,
+ ANNOTATION2, DISPLAY, GUI, NEWS, SORTBYTREE, USAGESTATS, OPEN, OPENNEW,
+ PROPS, QUESTIONNAIRE, SETPROP, TREE, VDOC, VSESS, OUTPUT, OUTPUTTYPE,
+ SSANNOTATION, NOTEMPFAC, TEMPFAC, TEMPFAC_LABEL, TEMPFAC_DESC,
+ TEMPFAC_SHADING, TITLE, PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, IMAGE,
+ QUIT, CLOSE, DEBUG("d"), QUIET("q"), ARGFILE, INCREMENT, NPP("n++"),
+ SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE;
+
+ protected static enum Opt
+ {
+ BOOLEAN, STRING, UNARY, MULTI, LINKED, NODUPLICATEVALUES, BOOTSTRAP,
+ GLOB, NOACTION, ALLOWSUBSTITUTIONS, PRIVATE
+ }
+
+ static
+ {
+ HELP.setOptions("Display this help message", Opt.UNARY, Opt.BOOTSTRAP);
+ CALCULATION.setOptions(true, Opt.BOOLEAN); // default "true" implies only
+ // expecting "--nocalculation"
+ MENUBAR.setOptions(true, Opt.BOOLEAN);
+ STATUS.setOptions(true, Opt.BOOLEAN);
+ SHOWOVERVIEW.setOptions(Opt.UNARY, Opt.LINKED);
+ ANNOTATIONS.setOptions(Opt.STRING, Opt.LINKED);
+ COLOUR.setOptions(Opt.STRING, Opt.LINKED);
+ FEATURES.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
+ Opt.ALLOWSUBSTITUTIONS);
+ GROOVY.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
+ Opt.ALLOWSUBSTITUTIONS);
+ GROUPS.setOptions(Opt.STRING, Opt.LINKED);
+ HEADLESS.setOptions(Opt.UNARY, Opt.BOOTSTRAP);
+ JABAWS.setOptions(Opt.STRING);
+ ANNOTATION.setOptions(true, Opt.BOOLEAN, Opt.LINKED);
+ ANNOTATION2.setOptions(true, Opt.BOOLEAN, Opt.LINKED);
+ DISPLAY.setOptions(true, Opt.BOOLEAN);
+ GUI.setOptions(true, Opt.BOOLEAN);
+ NEWS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
+ SPLASH.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
+ // expects a string value
+ SORTBYTREE.setOptions(true, Opt.BOOLEAN);
+ USAGESTATS.setOptions(true, Opt.BOOLEAN);
+ OPEN.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
+ Opt.ALLOWSUBSTITUTIONS);
+ OPENNEW.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
+ Opt.ALLOWSUBSTITUTIONS);
+ PROPS.setOptions(Opt.STRING, Opt.BOOTSTRAP);
+ QUESTIONNAIRE.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
+ SETPROP.setOptions(Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP);
+ TREE.setOptions(Opt.STRING);
+
+ VDOC.setOptions(Opt.UNARY);
+ VSESS.setOptions(Opt.UNARY);
+
+ OUTPUT.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS);
+ OUTPUTTYPE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
+
+ SSANNOTATION.setOptions(Opt.BOOLEAN, Opt.LINKED);
+ NOTEMPFAC.setOptions(Opt.UNARY, Opt.LINKED);
+ TEMPFAC.setOptions(Opt.STRING, Opt.LINKED);
+ TEMPFAC_LABEL.setOptions(Opt.STRING, Opt.LINKED);
+ TEMPFAC_DESC.setOptions(Opt.STRING, Opt.LINKED);
+ TEMPFAC_SHADING.setOptions(Opt.BOOLEAN, Opt.LINKED);
+ TITLE.setOptions(Opt.STRING, Opt.LINKED);
+ PAEMATRIX.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
+ Opt.ALLOWSUBSTITUTIONS);
+ NOSTRUCTURE.setOptions(Opt.UNARY, Opt.LINKED);
+ STRUCTURE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
+ Opt.ALLOWSUBSTITUTIONS);
+ WRAP.setOptions(Opt.BOOLEAN, Opt.LINKED);
+ IMAGE.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS);
+ QUIT.setOptions(Opt.UNARY);
+ CLOSE.setOptions(Opt.UNARY, Opt.LINKED);
+ DEBUG.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
+ QUIET.setOptions(Opt.UNARY, Opt.MULTI, Opt.BOOTSTRAP);
+ ARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP, Opt.GLOB,
+ Opt.ALLOWSUBSTITUTIONS);
+ INCREMENT.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION);
+ NPP.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION);
+ SUBSTITUTIONS.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
+ INITSUBSTITUTIONS.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION);
+ NIL.setOptions(Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.NOACTION);
+ SETARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
+ UNSETARGFILE.setOptions(Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
+ // Opt.BOOTSTRAP args are parsed (not linked with no SubVals so using a
+ // simplified parser, see jalview.bin.argparser.BootstrapArgs)
+ // before a full parse of arguments and so can be accessible at an earlier
+ // stage to (e.g.) set debug log level, provide a props file (that might set
+ // log level), run headlessly, read an argfile instead of other args.
+ }
+
+ private final String[] argNames;
+
+ private Opt[] argOptions;
+
+ private boolean defaultBoolValue = false;
+
+ private String description = null;
+
+ private Arg()
+ {
+ this(new String[0]);
+ }
+
+ private Arg(String... names)
+ {
+ int length = (names == null || names.length == 0
+ || (names.length == 1 && names[0] == null)) ? 1
+ : names.length + 1;
+ this.argNames = new String[length];
+ this.argNames[0] = this.getName();
+ if (length > 1)
+ System.arraycopy(names, 0, this.argNames, 1, names.length);
+ }
+
+ public String argString()
+ {
+ return argString(false);
+ }
+
+ public String negateArgString()
+ {
+ return argString(true);
+ }
+
+ private String argString(boolean negate)
+ {
+ StringBuilder sb = new StringBuilder(ArgParser.DOUBLEDASH);
+ if (negate && hasOption(Opt.BOOLEAN))
+ sb.append(ArgParser.NEGATESTRING);
+ sb.append(getName());
+ return sb.toString();
+ }
+
+ public String toLongString()
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append(this.getClass().getName()).append('.').append(this.name());
+ sb.append('(');
+ if (getNames().length > 0)
+ sb.append('"');
+ sb.append(String.join("\", \"", getNames()));
+ if (getNames().length > 0)
+ sb.append('"');
+ sb.append(")\n");
+ sb.append("\nOpt: ");
+ // map List<Opt> to List<String> for the String.join
+ List<String> optList = Arrays.asList(argOptions).stream()
+ .map(opt -> opt.name()).collect(Collectors.toList());
+ sb.append(String.join(", ", optList));
+ sb.append("\n");
+ return sb.toString();
+ }
+
+ public String[] getNames()
+ {
+ return argNames;
+ }
+
+ public String getName()
+ {
+ return this.name().toLowerCase(Locale.ROOT).replace('_', '-');
+ }
+
+ @Override
+ public final String toString()
+ {
+ return getName();
+ }
+
+ public boolean hasOption(Opt o)
+ {
+ if (argOptions == null)
+ return false;
+ for (Opt option : argOptions)
+ {
+ if (o == option)
+ return true;
+ }
+ return false;
+ }
+
+ protected void setOptions(Opt... options)
+ {
+ setOptions("", false, options);
+ }
+
+ protected void setOptions(String desc, Opt... options)
+ {
+ setOptions(desc, false, options);
+ }
+
+ protected void setOptions(boolean defaultBoolValue, Opt... options)
+ {
+ setOptions("", defaultBoolValue, options);
+ }
+
+ protected void setOptions(String desc, boolean defaultBoolValue,
+ Opt... options)
+ {
+ this.description = desc;
+ this.defaultBoolValue = defaultBoolValue;
+ this.argOptions = options;
+ }
+
+ protected boolean getDefaultBoolValue()
+ {
+ return defaultBoolValue;
+ }
+
+ private void setDescription(String d)
+ {
+ description = d;
+ }
+
+ protected String getDescription()
+ {
+ return description;
+ }
+
+ public static String booleanArgString(Arg a)
+ {
+ StringBuilder sb = new StringBuilder(a.argString());
+ if (a.hasOption(Opt.BOOLEAN))
+ {
+ sb.append('/');
+ sb.append(a.negateArgString());
+ }
+ return sb.toString();
+ }
+
+ public static final String usage()
+ {
+ StringBuilder sb = new StringBuilder();
+
+ sb.append("Usage: jalview [args]");
+ sb.append(System.lineSeparator());
+
+ int maxArgLength = 0;
+ for (Arg a : EnumSet.allOf(Arg.class))
+ {
+ if (a.hasOption(Opt.PRIVATE))
+ continue;
+ StringBuilder argSb = new StringBuilder();
+ argSb.append(a.hasOption(Opt.BOOLEAN) ? booleanArgString(a)
+ : a.argString());
+ if (a.hasOption(Opt.STRING))
+ argSb.append("=value");
+ if (argSb.length() > maxArgLength)
+ maxArgLength = argSb.length();
+ }
+
+ // might want to sort these
+ for (Arg a : EnumSet.allOf(Arg.class))
+ {
+ if (a.hasOption(Opt.PRIVATE))
+ continue;
+ StringBuilder argSb = new StringBuilder();
+ argSb.append(a.hasOption(Opt.BOOLEAN) ? booleanArgString(a)
+ : a.argString());
+ if (a.hasOption(Opt.STRING))
+ argSb.append("=value");
+ sb.append(String.format("%-" + maxArgLength + "s - %s",
+ argSb.toString(), a.getDescription()));
+
+ List<String> options = new ArrayList<>();
+
+ if (a.hasOption(Opt.BOOLEAN))
+ {
+ options.add("default " + (a.getDefaultBoolValue() ? a.argString()
+ : a.negateArgString()));
+ }
+
+ if (a.hasOption(Opt.MULTI))
+ {
+ options.add("multiple");
+ }
+
+ if (a.hasOption(Opt.LINKED))
+ {
+ options.add("can be linked");
+ }
+
+ if (a.hasOption(Opt.GLOB))
+ {
+ options.add("allows file globs");
+ }
+
+ if (a.hasOption(Opt.ALLOWSUBSTITUTIONS))
+ {
+ options.add("allows substitutions");
+ }
+
+ if (options.size() > 0)
+ {
+ sb.append(" (");
+ sb.append(String.join("; ", options));
+ sb.append(')');
+ }
+ sb.append(System.lineSeparator());
+ }
+ return sb.toString();
+ }
+}
\ 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.bin.argparser;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.EnumSet;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import jalview.bin.Console;
+import jalview.bin.Jalview;
+import jalview.bin.argparser.Arg.Opt;
+import jalview.util.FileUtils;
+
+public class ArgParser
+{
+ protected static final String DOUBLEDASH = "--";
+
+ protected static final char EQUALS = '=';
+
+ protected static final String NEGATESTRING = "no";
+
+ // the default linked id prefix used for no id (not even square braces)
+ protected static final String DEFAULTLINKEDIDPREFIX = "JALVIEW:";
+
+ // the counter added to the default linked id prefix
+ private int defaultLinkedIdCounter = 0;
+
+ // the substitution string used to use the defaultLinkedIdCounter
+ private static final String DEFAULTLINKEDIDCOUNTER = "{}";
+
+ // the counter added to the default linked id prefix
+ private int opennewLinkedIdCounter = 0;
+
+ // the linked id prefix used for --opennew files
+ protected static final String OPENNEWLINKEDIDPREFIX = "OPENNEW:";
+
+ // the counter used for {n} substitutions
+ private int linkedIdAutoCounter = 0;
+
+ // the linked id substitution string used to increment the idCounter (and use
+ // the incremented value)
+ private static final String INCREMENTLINKEDIDAUTOCOUNTER = "{++n}";
+
+ // the linked id substitution string used to use the idCounter
+ private static final String LINKEDIDAUTOCOUNTER = "{n}";
+
+ // the linked id substitution string used to use the base filename of --open
+ // or --opennew
+ private static final String LINKEDIDBASENAME = "{basename}";
+
+ // the linked id substitution string used to use the dir path of --open
+ // or --opennew
+ private static final String LINKEDIDDIRNAME = "{dirname}";
+
+ // the current argfile
+ private String argFile = null;
+
+ // the linked id substitution string used to use the dir path of the latest
+ // --argfile name
+ private static final String ARGFILEBASENAME = "{argfilebasename}";
+
+ // the linked id substitution string used to use the dir path of the latest
+ // --argfile name
+ private static final String ARGFILEDIRNAME = "{argfiledirname}";
+
+ // flag to say whether {n} subtitutions in output filenames should be made.
+ // Turn on and off with --subs and --nosubs
+ private boolean substitutions = false;
+
+ protected static final Map<String, Arg> argMap;
+
+ protected Map<String, ArgValuesMap> linkedArgs = new HashMap<>();
+
+ protected List<String> linkedOrder = null;
+
+ protected List<Arg> argList;
+
+ private static final char ARGFILECOMMENT = '#';
+
+ static
+ {
+ argMap = new HashMap<>();
+ for (Arg a : EnumSet.allOf(Arg.class))
+ {
+ for (String argName : a.getNames())
+ {
+ if (argMap.containsKey(argName))
+ {
+ Console.warn("Trying to add argument name multiple times: '"
+ + argName + "'"); // RESTORE THIS WHEN
+ // MERGED
+ if (argMap.get(argName) != a)
+ {
+ Console.error(
+ "Trying to add argument name multiple times for different Args: '"
+ + argMap.get(argName).getName() + ":" + argName
+ + "' and '" + a.getName() + ":" + argName
+ + "'");
+ }
+ continue;
+ }
+ argMap.put(argName, a);
+ }
+ }
+ }
+
+ public ArgParser(String[] args)
+ {
+ this(args, false);
+ }
+
+ public ArgParser(String[] args, boolean initsubstitutions)
+ {
+ // Make a mutable new ArrayList so that shell globbing parser works.
+ // (When shell file globbing is used, there are a sequence of non-Arg
+ // arguments (which are the expanded globbed filenames) that need to be
+ // consumed by the --open/--argfile/etc Arg which is most easily done by
+ // removing these filenames from the list one at a time. This can't be done
+ // with an ArrayList made with only Arrays.asList(String[] args). )
+ this(new ArrayList<>(Arrays.asList(args)), initsubstitutions);
+ }
+
+ public ArgParser(List<String> args, boolean initsubstitutions)
+ {
+ this(args, initsubstitutions, false);
+ }
+
+ public ArgParser(List<String> args, boolean initsubstitutions,
+ boolean allowPrivate)
+ {
+ // do nothing if there are no "--" args and some "-" args
+ boolean d = false;
+ boolean dd = false;
+ for (String arg : args)
+ {
+ if (arg.startsWith(DOUBLEDASH))
+ {
+ dd = true;
+ break;
+ }
+ else if (arg.startsWith("-"))
+ {
+ d = true;
+ }
+ }
+ if (d && !dd)
+ {
+ // leave it to the old style -- parse an empty list
+ parse(new ArrayList<String>(), false, false);
+ return;
+ }
+ parse(args, initsubstitutions, allowPrivate);
+ }
+
+ private void parse(List<String> args, boolean initsubstitutions,
+ boolean allowPrivate)
+ {
+ this.substitutions = initsubstitutions;
+ int argIndex = 0;
+ boolean openEachInitialFilenames = true;
+ for (int i = 0; i < args.size(); i++)
+ {
+ String arg = args.get(i);
+
+ // If the first arguments do not start with "--" or "-" or is "open" and
+ // is a filename that exists it is probably a file/list of files to open
+ // so we fake an Arg.OPEN argument and when adding files only add the
+ // single arg[i] and increment the defaultLinkedIdCounter so that each of
+ // these files is opened separately.
+ if (openEachInitialFilenames && !arg.startsWith(DOUBLEDASH)
+ && !arg.startsWith("-") && new File(arg).exists())
+ {
+ arg = Arg.OPENNEW.argString();
+ }
+ else
+ {
+ openEachInitialFilenames = false;
+ }
+
+ String argName = null;
+ String val = null;
+ List<String> globVals = null; // for Opt.GLOB only
+ SubVals globSubVals = null; // also for use by Opt.GLOB only
+ String linkedId = null;
+ if (arg.startsWith(DOUBLEDASH))
+ {
+ int equalPos = arg.indexOf(EQUALS);
+ if (equalPos > -1)
+ {
+ argName = arg.substring(DOUBLEDASH.length(), equalPos);
+ val = arg.substring(equalPos + 1);
+ }
+ else
+ {
+ argName = arg.substring(DOUBLEDASH.length());
+ }
+ int idOpen = argName.indexOf('[');
+ int idClose = argName.indexOf(']');
+
+ if (idOpen > -1 && idClose == argName.length() - 1)
+ {
+ linkedId = argName.substring(idOpen + 1, idClose);
+ argName = argName.substring(0, idOpen);
+ }
+
+ Arg a = argMap.get(argName);
+ // check for boolean prepended by "no"
+ boolean negated = false;
+ if (a == null && argName.startsWith(NEGATESTRING) && argMap
+ .containsKey(argName.substring(NEGATESTRING.length())))
+ {
+ argName = argName.substring(NEGATESTRING.length());
+ a = argMap.get(argName);
+ negated = true;
+ }
+
+ // check for config errors
+ if (a == null)
+ {
+ // arg not found
+ Console.error("Argument '" + arg + "' not recognised. Ignoring.");
+ continue;
+ }
+ if (a.hasOption(Opt.PRIVATE) && !allowPrivate)
+ {
+ Console.error(
+ "Argument '" + a.argString() + "' is private. Ignoring.");
+ continue;
+ }
+ if (!a.hasOption(Opt.BOOLEAN) && negated)
+ {
+ // used "no" with a non-boolean option
+ Console.error("Argument '" + DOUBLEDASH + NEGATESTRING + argName
+ + "' not a boolean option. Ignoring.");
+ continue;
+ }
+ if (!a.hasOption(Opt.STRING) && equalPos > -1)
+ {
+ // set --argname=value when arg does not accept values
+ Console.error("Argument '" + a.argString()
+ + "' does not expect a value (given as '" + arg
+ + "'). Ignoring.");
+ continue;
+ }
+ if (!a.hasOption(Opt.LINKED) && linkedId != null)
+ {
+ // set --argname[linkedId] when arg does not use linkedIds
+ Console.error("Argument '" + a.argString()
+ + "' does not expect a linked id (given as '" + arg
+ + "'). Ignoring.");
+ continue;
+ }
+
+ // String value(s)
+ if (a.hasOption(Opt.STRING))
+ {
+ if (equalPos >= 0)
+ {
+ if (a.hasOption(Opt.GLOB))
+ {
+ // strip off and save the SubVals to be added individually later
+ globSubVals = new SubVals(val);
+ // make substitutions before looking for files
+ String fileGlob = makeSubstitutions(globSubVals.getContent(),
+ linkedId);
+ globVals = FileUtils.getFilenamesFromGlob(fileGlob);
+ }
+ else
+ {
+ // val is already set -- will be saved in the ArgValue later in
+ // the normal way
+ }
+ }
+ else
+ {
+ // There is no "=" so value is next arg or args (possibly shell
+ // glob-expanded)
+ if ((openEachInitialFilenames ? i : i + 1) >= args.size())
+ {
+ // no value to take for arg, which wants a value
+ Console.error("Argument '" + a.getName()
+ + "' requires a value, none given. Ignoring.");
+ continue;
+ }
+ // deal with bash globs here (--arg val* is expanded before reaching
+ // the JVM). Note that SubVals cannot be used in this case.
+ // If using the --arg=val then the glob is preserved and Java globs
+ // will be used later. SubVals can be used.
+ if (a.hasOption(Opt.GLOB))
+ {
+ // if this is the first argument with a file list at the start of
+ // the args we add filenames from index i instead of i+1
+ globVals = getShellGlobbedFilenameValues(a, args,
+ openEachInitialFilenames ? i : i + 1);
+ }
+ else
+ {
+ val = args.get(i + 1);
+ }
+ }
+ }
+
+ // make NOACTION adjustments
+ // default and auto counter increments
+ if (a == Arg.INCREMENT)
+ {
+ defaultLinkedIdCounter++;
+ }
+ else if (a == Arg.NPP)
+ {
+ linkedIdAutoCounter++;
+ }
+ else if (a == Arg.SUBSTITUTIONS)
+ {
+ substitutions = !negated;
+ }
+ else if (a == Arg.SETARGFILE)
+ {
+ argFile = val;
+ }
+ else if (a == Arg.UNSETARGFILE)
+ {
+ argFile = null;
+ }
+
+ String autoCounterString = null;
+ boolean usingAutoCounterLinkedId = false;
+ String defaultLinkedId = new StringBuilder(DEFAULTLINKEDIDPREFIX)
+ .append(Integer.toString(defaultLinkedIdCounter))
+ .toString();
+ boolean usingDefaultLinkedId = false;
+ if (a.hasOption(Opt.LINKED))
+ {
+ if (linkedId == null)
+ {
+ if (a == Arg.OPENNEW)
+ {
+ // use the next default prefixed OPENNEWLINKEDID
+ linkedId = new StringBuilder(OPENNEWLINKEDIDPREFIX)
+ .append(Integer.toString(opennewLinkedIdCounter))
+ .toString();
+ opennewLinkedIdCounter++;
+ }
+ else
+ {
+ // use default linkedId for linked arguments
+ linkedId = defaultLinkedId;
+ usingDefaultLinkedId = true;
+ Console.debug("Changing linkedId to '" + linkedId + "' from "
+ + arg);
+ }
+ }
+ else if (linkedId.contains(LINKEDIDAUTOCOUNTER))
+ {
+ // turn {n} to the autoCounter
+ autoCounterString = Integer.toString(linkedIdAutoCounter);
+ linkedId = linkedId.replace(LINKEDIDAUTOCOUNTER,
+ autoCounterString);
+ usingAutoCounterLinkedId = true;
+ Console.debug(
+ "Changing linkedId to '" + linkedId + "' from " + arg);
+ }
+ else if (linkedId.contains(INCREMENTLINKEDIDAUTOCOUNTER))
+ {
+ // turn {++n} to the incremented autoCounter
+ autoCounterString = Integer.toString(++linkedIdAutoCounter);
+ linkedId = linkedId.replace(INCREMENTLINKEDIDAUTOCOUNTER,
+ autoCounterString);
+ usingAutoCounterLinkedId = true;
+ Console.debug(
+ "Changing linkedId to '" + linkedId + "' from " + arg);
+ }
+ }
+
+ if (!linkedArgs.containsKey(linkedId))
+ linkedArgs.put(linkedId, new ArgValuesMap());
+
+ // do not continue for NOACTION args
+ if (a.hasOption(Opt.NOACTION))
+ continue;
+
+ ArgValuesMap avm = linkedArgs.get(linkedId);
+
+ // not dealing with both NODUPLICATEVALUES and GLOB
+ if (a.hasOption(Opt.NODUPLICATEVALUES) && avm.hasValue(a, val))
+ {
+ Console.error("Argument '" + a.argString()
+ + "' cannot contain a duplicate value ('" + val
+ + "'). Ignoring this and subsequent occurrences.");
+ continue;
+ }
+
+ // check for unique id
+ SubVals idsv = new SubVals(val);
+ String id = idsv.get(ArgValues.ID);
+ if (id != null && avm.hasId(a, id))
+ {
+ Console.error("Argument '" + a.argString()
+ + "' has a duplicate id ('" + id + "'). Ignoring.");
+ continue;
+ }
+
+ boolean argIndexIncremented = false;
+ ArgValues avs = avm.getOrCreateArgValues(a);
+
+ // store appropriate String value(s)
+ if (a.hasOption(Opt.STRING))
+ {
+ if (a.hasOption(Opt.GLOB) && globVals != null
+ && globVals.size() > 0)
+ {
+ for (String v : globVals)
+ {
+ v = makeSubstitutions(v, linkedId);
+ SubVals vsv = new SubVals(globSubVals, v);
+ avs.addValue(vsv, v, argIndex++);
+ argIndexIncremented = true;
+ }
+ }
+ else
+ {
+ avs.addValue(makeSubstitutions(val, linkedId), argIndex);
+ }
+ }
+ else if (a.hasOption(Opt.BOOLEAN))
+ {
+ avs.setBoolean(!negated, argIndex);
+ avs.setNegated(negated);
+ }
+ else if (a.hasOption(Opt.UNARY))
+ {
+ avs.setBoolean(true, argIndex);
+ }
+ avs.incrementCount();
+ if (!argIndexIncremented)
+ argIndex++;
+
+ // store in appropriate place
+ if (a.hasOption(Opt.LINKED))
+ {
+ // store the order of linkedIds
+ if (linkedOrder == null)
+ linkedOrder = new ArrayList<>();
+ if (!linkedOrder.contains(linkedId))
+ linkedOrder.add(linkedId);
+ }
+
+ // store arg in the list of args used
+ if (argList == null)
+ argList = new ArrayList<>();
+ if (!argList.contains(a))
+ argList.add(a);
+
+ }
+ }
+ }
+
+ private String makeSubstitutions(String val, String linkedId)
+ {
+ if (!this.substitutions)
+ return val;
+
+ String subvals;
+ String rest;
+ if (val.indexOf('[') == 0 && val.indexOf(']') > 1)
+ {
+ int closeBracket = val.indexOf(']');
+ if (val.length() == closeBracket)
+ return val;
+ subvals = val.substring(0, closeBracket + 1);
+ rest = val.substring(closeBracket + 1);
+ }
+ else
+ {
+ subvals = "";
+ rest = val;
+ }
+ if (rest.contains(LINKEDIDAUTOCOUNTER))
+ rest = rest.replace(LINKEDIDAUTOCOUNTER,
+ String.valueOf(linkedIdAutoCounter));
+ if (rest.contains(INCREMENTLINKEDIDAUTOCOUNTER))
+ rest = rest.replace(INCREMENTLINKEDIDAUTOCOUNTER,
+ String.valueOf(++linkedIdAutoCounter));
+ if (rest.contains(DEFAULTLINKEDIDCOUNTER))
+ rest = rest.replace(DEFAULTLINKEDIDCOUNTER,
+ String.valueOf(defaultLinkedIdCounter));
+ ArgValuesMap avm = linkedArgs.get(linkedId);
+ if (avm != null)
+ {
+ if (rest.contains(LINKEDIDBASENAME))
+ {
+ rest = rest.replace(LINKEDIDBASENAME, avm.getBasename());
+ }
+ if (rest.contains(LINKEDIDDIRNAME))
+ {
+ rest = rest.replace(LINKEDIDDIRNAME, avm.getDirname());
+ }
+ }
+ if (argFile != null)
+ {
+ if (rest.contains(ARGFILEBASENAME))
+ {
+ rest = rest.replace(ARGFILEBASENAME,
+ FileUtils.getBasename(new File(argFile)));
+ }
+ if (rest.contains(ARGFILEDIRNAME))
+ {
+ rest = rest.replace(ARGFILEDIRNAME,
+ FileUtils.getDirname(new File(argFile)));
+ }
+ }
+
+ return new StringBuilder(subvals).append(rest).toString();
+ }
+
+ /*
+ * A helper method to take a list of String args where we're expecting
+ * {"--previousargs", "--arg", "file1", "file2", "file3", "--otheroptionsornot"}
+ * and the index of the globbed arg, here 1. It returns a List<String> {"file1",
+ * "file2", "file3"} *and remove these from the original list object* so that
+ * processing can continue from where it has left off, e.g. args has become
+ * {"--previousargs", "--arg", "--otheroptionsornot"} so the next increment
+ * carries on from the next --arg if available.
+ */
+ protected static List<String> getShellGlobbedFilenameValues(Arg a,
+ List<String> args, int i)
+ {
+ List<String> vals = new ArrayList<>();
+ while (i < args.size() && !args.get(i).startsWith(DOUBLEDASH))
+ {
+ vals.add(FileUtils.substituteHomeDir(args.remove(i)));
+ if (!a.hasOption(Opt.GLOB))
+ break;
+ }
+ return vals;
+ }
+
+ public boolean isSet(Arg a)
+ {
+ return a.hasOption(Opt.LINKED) ? isSet("", a) : isSet(null, a);
+ }
+
+ public boolean isSet(String linkedId, Arg a)
+ {
+ ArgValuesMap avm = linkedArgs.get(linkedId);
+ return avm == null ? false : avm.containsArg(a);
+ }
+
+ public boolean getBool(Arg a)
+ {
+ if (!a.hasOption(Opt.BOOLEAN) && !a.hasOption(Opt.UNARY))
+ {
+ Console.warn("Getting boolean from non boolean Arg '" + a.getName()
+ + "'.");
+ }
+ return a.hasOption(Opt.LINKED) ? getBool("", a) : getBool(null, a);
+ }
+
+ public boolean getBool(String linkedId, Arg a)
+ {
+ ArgValuesMap avm = linkedArgs.get(linkedId);
+ if (avm == null)
+ return a.getDefaultBoolValue();
+ ArgValues avs = avm.getArgValues(a);
+ return avs == null ? a.getDefaultBoolValue() : avs.getBoolean();
+ }
+
+ public List<String> linkedIds()
+ {
+ return linkedOrder;
+ }
+
+ public ArgValuesMap linkedArgs(String id)
+ {
+ return linkedArgs.get(id);
+ }
+
+ @Override
+ public String toString()
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append("UNLINKED\n");
+ sb.append(argValuesMapToString(linkedArgs.get(null)));
+ if (linkedIds() != null)
+ {
+ sb.append("LINKED\n");
+ for (String id : linkedIds())
+ {
+ // already listed these as UNLINKED args
+ if (id == null)
+ continue;
+
+ ArgValuesMap avm = linkedArgs(id);
+ sb.append("ID: '").append(id).append("'\n");
+ sb.append(argValuesMapToString(avm));
+ }
+ }
+ return sb.toString();
+ }
+
+ private static String argValuesMapToString(ArgValuesMap avm)
+ {
+ if (avm == null)
+ return null;
+ StringBuilder sb = new StringBuilder();
+ for (Arg a : avm.getArgKeys())
+ {
+ ArgValues v = avm.getArgValues(a);
+ sb.append(v.toString());
+ sb.append("\n");
+ }
+ return sb.toString();
+ }
+
+ public static ArgParser parseArgFiles(List<String> argFilenameGlobs,
+ boolean initsubstitutions)
+ {
+ List<File> argFiles = new ArrayList<>();
+
+ for (String pattern : argFilenameGlobs)
+ {
+ // I don't think we want to dedup files, making life easier
+ argFiles.addAll(FileUtils.getFilesFromGlob(pattern));
+ }
+
+ return parseArgFileList(argFiles, initsubstitutions);
+ }
+
+ public static ArgParser parseArgFileList(List<File> argFiles,
+ boolean initsubstitutions)
+ {
+ List<String> argsList = new ArrayList<>();
+ for (File argFile : argFiles)
+ {
+ if (!argFile.exists())
+ {
+ String message = Arg.ARGFILE.argString() + EQUALS + "\""
+ + argFile.getPath() + "\": File does not exist.";
+ Jalview.exit(message, 2);
+ }
+ try
+ {
+ String setargfile = new StringBuilder(Arg.SETARGFILE.argString())
+ .append(EQUALS).append(argFile.getCanonicalPath())
+ .toString();
+ argsList.add(setargfile);
+ argsList.addAll(readArgFile(argFile));
+ argsList.add(Arg.UNSETARGFILE.argString());
+ } catch (IOException e)
+ {
+ String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath()
+ + "\": File could not be read.";
+ Jalview.exit(message, 3);
+ }
+ }
+ // Third param "true" uses Opt.PRIVATE args --setargile=argfile and
+ // --unsetargfile
+ return new ArgParser(argsList, initsubstitutions, true);
+ }
+
+ protected static List<String> readArgFile(File argFile)
+ {
+ List<String> args = new ArrayList<>();
+ if (argFile != null && argFile.exists())
+ {
+ try
+ {
+ for (String line : Files.readAllLines(Paths.get(argFile.getPath())))
+ {
+ if (line != null && line.length() > 0
+ && line.charAt(0) != ARGFILECOMMENT)
+ args.add(line);
+ }
+ } catch (IOException e)
+ {
+ String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath()
+ + "\": File could not be read.";
+ Console.debug(message, e);
+ Jalview.exit(message, 3);
+ }
+ }
+ return args;
+ }
+
+}
\ No newline at end of file
--- /dev/null
+package jalview.bin.argparser;
+
+/**
+ * A helper class to keep an index of argument position with argument values
+ */
+public class ArgValue
+{
+ private int argIndex;
+
+ private String value;
+
+ private String id;
+
+ private SubVals subVals;
+
+ protected ArgValue(SubVals sv, String content, int argIndex)
+ {
+ this.value = content;
+ this.argIndex = argIndex;
+ this.subVals = sv == null ? new SubVals("") : sv;
+ }
+
+ protected ArgValue(String value, int argIndex)
+ {
+ this.argIndex = argIndex;
+ this.subVals = new SubVals(value);
+ this.value = getSubVals().getContent();
+ }
+
+ public String getValue()
+ {
+ return value;
+ }
+
+ public int getArgIndex()
+ {
+ return argIndex;
+ }
+
+ protected void setId(String i)
+ {
+ id = i;
+ }
+
+ public String getId()
+ {
+ return id;
+ }
+
+ public SubVals getSubVals()
+ {
+ return subVals;
+ }
+
+ public String getSubVal(String key)
+ {
+ if (subVals == null || !subVals.has(key))
+ return null;
+ return subVals.get(key);
+ }
+
+ protected void putSubVal(String key, String val)
+ {
+ this.subVals.put(key, val);
+ }
+}
\ No newline at end of file
--- /dev/null
+package jalview.bin.argparser;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+import jalview.bin.Console;
+import jalview.bin.argparser.Arg.Opt;
+
+public class ArgValues
+{
+ public static final String ID = "id";
+
+ private Arg arg;
+
+ private int argCount = 0;
+
+ private boolean boolValue = false;
+
+ private boolean negated = false;
+
+ private int boolIndex = -1;
+
+ private List<Integer> argsIndexes;
+
+ private List<ArgValue> argValueList;
+
+ private Map<String, ArgValue> idMap = new HashMap<>();
+
+ protected ArgValues(Arg a)
+ {
+ this.arg = a;
+ this.argValueList = new ArrayList<ArgValue>();
+ this.boolValue = arg.getDefaultBoolValue();
+ }
+
+ public Arg arg()
+ {
+ return arg;
+ }
+
+ protected int getCount()
+ {
+ return argCount;
+ }
+
+ protected void incrementCount()
+ {
+ argCount++;
+ }
+
+ protected void setNegated(boolean b)
+ {
+ this.negated = b;
+ }
+
+ protected boolean isNegated()
+ {
+ return this.negated;
+ }
+
+ protected void setBoolean(boolean b, int i)
+ {
+ this.boolValue = b;
+ this.boolIndex = i;
+ }
+
+ protected boolean getBoolean()
+ {
+ return this.boolValue;
+ }
+
+ @Override
+ public String toString()
+ {
+ if (argValueList == null)
+ return null;
+ StringBuilder sb = new StringBuilder();
+ sb.append(arg.toLongString());
+ if (arg.hasOption(Opt.BOOLEAN) || arg.hasOption(Opt.UNARY))
+ sb.append("Boolean: ").append(boolValue).append("; Default: ")
+ .append(arg.getDefaultBoolValue()).append("; Negated: ")
+ .append(negated).append("\n");
+ if (arg.hasOption(Opt.STRING))
+ {
+ sb.append("Values:");
+ sb.append("'")
+ .append(String
+ .join("',\n '",
+ argValueList.stream().map(av -> av.getValue())
+ .collect(Collectors.toList())))
+ .append("'");
+ sb.append("\n");
+ }
+ sb.append("Count: ").append(argCount).append("\n");
+ return sb.toString();
+ }
+
+ protected void addValue()
+ {
+ addValue(null, -1);
+ }
+
+ protected void addValue(String val, int argIndex)
+ {
+ addArgValue(new ArgValue(val, argIndex));
+ }
+
+ protected void addValue(SubVals sv, String content, int argIndex)
+ {
+ addArgValue(new ArgValue(sv, content, argIndex));
+ }
+
+ protected void addArgValue(ArgValue av)
+ {
+ if ((!arg.hasOption(Opt.MULTI) && argValueList.size() > 0)
+ || (arg.hasOption(Opt.NODUPLICATEVALUES)
+ && argValueList.contains(av.getValue())))
+ return;
+ if (argValueList == null)
+ {
+ argValueList = new ArrayList<ArgValue>();
+ }
+ SubVals sv = new SubVals(av.getValue());
+ if (sv.has(ID))
+ {
+ String id = sv.get(ID);
+ av.setId(id);
+ idMap.put(id, av);
+ }
+ argValueList.add(av);
+ }
+
+ protected boolean hasValue(String val)
+ {
+ return argValueList.contains(val);
+ }
+
+ protected ArgValue getArgValue()
+ {
+ if (arg.hasOption(Opt.MULTI))
+ Console.warn("Requesting single value for multi value argument");
+ return argValueList.size() > 0 ? argValueList.get(0) : null;
+ }
+
+ protected List<ArgValue> getArgValueList()
+ {
+ return argValueList;
+ }
+
+ protected boolean hasId(String id)
+ {
+ return idMap.containsKey(id);
+ }
+
+ protected ArgValue getId(String id)
+ {
+ return idMap.get(id);
+ }
+}
\ No newline at end of file
--- /dev/null
+package jalview.bin.argparser;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import jalview.bin.argparser.Arg.Opt;
+import jalview.util.FileUtils;
+
+/**
+ * Helper class to allow easy extraction of information about specific argument
+ * values (without having to check for null etc all the time)
+ */
+public class ArgValuesMap
+{
+ protected Map<Arg, ArgValues> m;
+
+ protected ArgValuesMap()
+ {
+ this.newMap();
+ }
+
+ protected ArgValuesMap(Map<Arg, ArgValues> map)
+ {
+ this.m = map;
+ }
+
+ private Map<Arg, ArgValues> getMap()
+ {
+ return m;
+ }
+
+ private void newMap()
+ {
+ m = new HashMap<Arg, ArgValues>();
+ }
+
+ private void newArg(Arg a)
+ {
+ if (m == null)
+ newMap();
+ if (!containsArg(a))
+ m.put(a, new ArgValues(a));
+ }
+
+ protected void addArgValue(Arg a, ArgValue av)
+ {
+ if (getMap() == null)
+ m = new HashMap<Arg, ArgValues>();
+
+ if (!m.containsKey(a))
+ m.put(a, new ArgValues(a));
+ ArgValues avs = m.get(a);
+ avs.addArgValue(av);
+ }
+
+ public ArgValues getArgValues(Arg a)
+ {
+ return m == null ? null : m.get(a);
+ }
+
+ public ArgValues getOrCreateArgValues(Arg a)
+ {
+ ArgValues avs = m.get(a);
+ if (avs == null)
+ newArg(a);
+ return getArgValues(a);
+ }
+
+ public List<ArgValue> getArgValueList(Arg a)
+ {
+ ArgValues avs = getArgValues(a);
+ return avs == null ? new ArrayList<>() : avs.getArgValueList();
+ }
+
+ public ArgValue getArgValue(Arg a)
+ {
+ List<ArgValue> vals = getArgValueList(a);
+ return (vals == null || vals.size() == 0) ? null : vals.get(0);
+ }
+
+ public String getValue(Arg a)
+ {
+ ArgValue av = getArgValue(a);
+ return av == null ? null : av.getValue();
+ }
+
+ public boolean containsArg(Arg a)
+ {
+ if (m == null || !m.containsKey(a))
+ return false;
+ return a.hasOption(Opt.STRING) ? getArgValue(a) != null
+ : this.getBoolean(a);
+ }
+
+ public boolean hasValue(Arg a, String val)
+ {
+ if (m == null || !m.containsKey(a))
+ return false;
+ for (ArgValue av : getArgValueList(a))
+ {
+ String avVal = av.getValue();
+ if ((val == null && avVal == null)
+ || (val != null && val.equals(avVal)))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ public boolean getBoolean(Arg a)
+ {
+ ArgValues av = getArgValues(a);
+ return av == null ? false : av.getBoolean();
+ }
+
+ public Set<Arg> getArgKeys()
+ {
+ return m.keySet();
+ }
+
+ public ArgValue getClosestPreviousArgValueOfArg(ArgValue thisAv, Arg a)
+ {
+ ArgValue closestAv = null;
+ int thisArgIndex = thisAv.getArgIndex();
+ ArgValues compareAvs = this.getArgValues(a);
+ int closestPreviousIndex = -1;
+ for (ArgValue av : compareAvs.getArgValueList())
+ {
+ int argIndex = av.getArgIndex();
+ if (argIndex < thisArgIndex && argIndex > closestPreviousIndex)
+ {
+ closestPreviousIndex = argIndex;
+ closestAv = av;
+ }
+ }
+ return closestAv;
+ }
+
+ public ArgValue getClosestNextArgValueOfArg(ArgValue thisAv, Arg a)
+ {
+ // this looks for the *next* arg that *might* be referring back to
+ // a thisAv. Such an arg would have no subValues (if it does it should
+ // specify an id in the subValues so wouldn't need to be guessed).
+ ArgValue closestAv = null;
+ int thisArgIndex = thisAv.getArgIndex();
+ ArgValues compareAvs = this.getArgValues(a);
+ int closestNextIndex = Integer.MAX_VALUE;
+ for (ArgValue av : compareAvs.getArgValueList())
+ {
+ int argIndex = av.getArgIndex();
+ if (argIndex > thisArgIndex && argIndex < closestNextIndex)
+ {
+ closestNextIndex = argIndex;
+ closestAv = av;
+ }
+ }
+ return closestAv;
+ }
+
+ public ArgValue[] getArgValuesReferringTo(String key, String value, Arg a)
+ {
+ // this looks for the *next* arg that *might* be referring back to
+ // a thisAv. Such an arg would have no subValues (if it does it should
+ // specify an id in the subValues so wouldn't need to be guessed).
+ List<ArgValue> avList = new ArrayList<>();
+ Arg[] args = a == null ? (Arg[]) this.getMap().keySet().toArray()
+ : new Arg[]
+ { a };
+ for (Arg keyArg : args)
+ {
+ for (ArgValue av : this.getArgValueList(keyArg))
+ {
+
+ }
+ }
+ return (ArgValue[]) avList.toArray();
+ }
+
+ public boolean hasId(Arg a, String id)
+ {
+ ArgValues avs = this.getArgValues(a);
+ return avs == null ? false : avs.hasId(id);
+ }
+
+ public ArgValue getId(Arg a, String id)
+ {
+ ArgValues avs = this.getArgValues(a);
+ return avs == null ? null : avs.getId(id);
+ }
+
+ /*
+ * This method returns the basename of the first --open or --opennew value.
+ * Used primarily for substitutions in output filenames.
+ */
+ public String getBasename()
+ {
+ return getDirOrBasename(false);
+ }
+
+ /*
+ * This method returns the dirname of the first --open or --opennew value.
+ * Used primarily for substitutions in output filenames.
+ */
+ public String getDirname()
+ {
+ return getDirOrBasename(true);
+ }
+
+ public String getDirOrBasename(boolean dirname)
+ {
+ String filename = null;
+ String openVal = getValue(Arg.OPEN);
+ String opennewVal = getValue(Arg.OPENNEW);
+ if (openVal != null)
+ filename = openVal;
+ if (filename == null && opennewVal != null)
+ filename = opennewVal;
+ if (filename == null)
+ return null;
+
+ File file = new File(filename);
+ return dirname ? FileUtils.getDirname(file)
+ : FileUtils.getBasename(file);
+ }
+}
--- /dev/null
+package jalview.bin.argparser;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import jalview.bin.argparser.Arg.Opt;
+import jalview.util.FileUtils;
+
+public class BootstrapArgs
+{
+ // only need one
+ private Map<Arg, List<String>> bootstrapArgMap = new HashMap<>();
+
+ private Set<File> argFiles = new HashSet<>();
+
+ public static BootstrapArgs getBootstrapArgs(String[] args)
+ {
+ List<String> argList = new ArrayList<>(Arrays.asList(args));
+ return new BootstrapArgs(argList);
+ }
+
+ private BootstrapArgs(List<String> args)
+ {
+ parse(args, null);
+ }
+
+ private void parse(List<String> args, File inArgFile)
+ {
+ if (args == null)
+ return;
+ // avoid looping argFiles
+ if (inArgFile != null)
+ {
+ if (argFiles.contains(inArgFile))
+ {
+ System.err.println(
+ "Looped argfiles detected: '" + inArgFile.getPath() + "'");
+ return;
+ }
+ argFiles.add(inArgFile);
+ }
+
+ for (int i = 0; i < args.size(); i++)
+ {
+ String arg = args.get(i);
+ String argName = null;
+ String val = null;
+ if (arg.startsWith(ArgParser.DOUBLEDASH))
+ {
+ // remove "--"
+ arg = arg.substring(ArgParser.DOUBLEDASH.length());
+ int equalPos = arg.indexOf(ArgParser.EQUALS);
+ if (equalPos > -1
+ && ArgParser.argMap.containsKey(arg.substring(0, equalPos)))
+ {
+ argName = arg.substring(0, equalPos);
+ val = arg.substring(equalPos + 1);
+ }
+ // check for boolean prepended by "no"
+ else if (arg.startsWith(ArgParser.NEGATESTRING)
+ && ArgParser.argMap.containsKey(
+ arg.substring(ArgParser.NEGATESTRING.length())))
+ {
+ argName = arg.substring(ArgParser.NEGATESTRING.length());
+ val = "false";
+ }
+ else if (ArgParser.argMap.containsKey(arg))
+ {
+ argName = arg;
+ val = "true";
+ }
+
+ Arg a = ArgParser.argMap.get(argName);
+
+ if (a == null || !a.hasOption(Opt.BOOTSTRAP))
+ {
+ // not a valid bootstrap arg
+ continue;
+ }
+
+ if (a.hasOption(Opt.STRING))
+ {
+ List<String> vals = null;
+ if (equalPos == -1)
+ {
+ vals = ArgParser.getShellGlobbedFilenameValues(a, args, i + 1);
+ }
+ else
+ {
+ if (a.hasOption(Opt.GLOB))
+ {
+ vals = FileUtils.getFilenamesFromGlob(val);
+ }
+ else
+ {
+ vals = new ArrayList<>();
+ vals.add(val);
+ }
+ }
+ addAll(a, vals);
+
+ if (a == Arg.ARGFILE)
+ {
+ for (String filename : vals)
+ {
+ File argFile = new File(filename);
+ parse(ArgParser.readArgFile(argFile), argFile);
+ }
+ }
+ }
+ else
+ {
+ add(a, val);
+ }
+ }
+ }
+ }
+
+ public boolean contains(Arg a)
+ {
+ return bootstrapArgMap.containsKey(a);
+ }
+
+ public List<String> getList(Arg a)
+ {
+ return bootstrapArgMap.get(a);
+ }
+
+ private List<String> getOrCreateList(Arg a)
+ {
+ List<String> l = getList(a);
+ if (l == null)
+ {
+ l = new ArrayList<>();
+ putList(a, l);
+ }
+ return l;
+ }
+
+ private void putList(Arg a, List<String> l)
+ {
+ bootstrapArgMap.put(a, l);
+ }
+
+ /*
+ * Creates a new list if not used before,
+ * adds the value unless the existing list is non-empty
+ * and the arg is not MULTI (so first expressed value is
+ * retained).
+ */
+ private void add(Arg a, String s)
+ {
+ List<String> l = getOrCreateList(a);
+ if (a.hasOption(Opt.MULTI) || l.size() == 0)
+ {
+ l.add(s);
+ }
+ }
+
+ private void addAll(Arg a, List<String> al)
+ {
+ List<String> l = getOrCreateList(a);
+ if (a.hasOption(Opt.MULTI))
+ {
+ l.addAll(al);
+ }
+ else if (l.size() == 0 && al.size() > 0)
+ {
+ l.add(al.get(0));
+ }
+ }
+
+ /*
+ * Retrieves the first value even if MULTI.
+ * A convenience for non-MULTI args.
+ */
+ public String get(Arg a)
+ {
+ if (!bootstrapArgMap.containsKey(a))
+ return null;
+ List<String> aL = bootstrapArgMap.get(a);
+ return (aL == null || aL.size() == 0) ? null : aL.get(0);
+ }
+
+ public boolean getBoolean(Arg a, boolean d)
+ {
+ if (!bootstrapArgMap.containsKey(a))
+ return d;
+ return Boolean.parseBoolean(get(a));
+ }
+
+ public boolean getBoolean(Arg a)
+ {
+ if (!(a.hasOption(Opt.BOOLEAN) || a.hasOption(Opt.UNARY)))
+ {
+ return false;
+ }
+ if (bootstrapArgMap.containsKey(a))
+ return Boolean.parseBoolean(get(a));
+ else
+ return a.getDefaultBoolValue();
+ }
+}
--- /dev/null
+package jalview.bin.argparser;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import jalview.bin.Console;
+
+/**
+ * A helper class to parse a string of the possible forms "content"
+ * "[index]content", "[keyName=keyValue]content" and return the integer index,
+ * the strings keyName and keyValue, and the content after the square brackets
+ * (if present). Values not set `will be -1 or null.
+ */
+public class SubVals
+{
+ public static int NOTSET = -1;
+
+ private int index = NOTSET;
+
+ private Map<String, String> subValMap;
+
+ private static char SEPARATOR = ';';
+
+ private static char EQUALS = '=';
+
+ private String content = null;
+
+ protected SubVals(SubVals sv, String c)
+ {
+ if (sv == null)
+ {
+ this.subValMap = new HashMap<>();
+ }
+ else
+ {
+ this.subValMap = sv == null ? new HashMap<>() : sv.getSubValMap();
+ this.index = sv.getIndex();
+ }
+ this.content = c;
+ }
+
+ protected SubVals(String item)
+ {
+ if (subValMap == null)
+ subValMap = new HashMap<>();
+ this.parseVals(item);
+ }
+
+ public void parseVals(String item)
+ {
+ if (item == null)
+ return;
+ if (item.indexOf('[') == 0 && item.indexOf(']') > 1)
+ {
+ int openBracket = 0;
+ int closeBracket = item.indexOf(']');
+ String subvalsString = item.substring(openBracket + 1, closeBracket);
+ this.content = item.substring(closeBracket + 1);
+ boolean setIndex = false;
+ for (String subvalString : subvalsString
+ .split(Character.toString(SEPARATOR)))
+ {
+ int equals = subvalString.indexOf(EQUALS);
+ if (equals > -1)
+ {
+ this.put(subvalString.substring(0, equals),
+ subvalString.substring(equals + 1));
+ }
+ else
+ {
+ try
+ {
+ this.index = Integer.parseInt(subvalString);
+ setIndex = true;
+ } catch (NumberFormatException e)
+ {
+ // store this non-numeric key as a "true" value
+ this.put(subvalString, "true");
+ }
+ }
+ }
+ if (!setIndex)
+ this.index = NOTSET;
+ else
+ Console.debug("SubVals from '" + subvalsString + "' has index "
+ + this.index + " set");
+ }
+ else
+ {
+ this.content = item;
+ }
+ }
+
+ protected void put(String key, String val)
+ {
+ subValMap.put(key, val);
+ }
+
+ public boolean notSet()
+ {
+ // notSet is true if content present but nonsensical
+ return index == NOTSET && (subValMap == null || subValMap.size() == 0);
+ }
+
+ public String get(String key)
+ {
+ return subValMap.get(key);
+ }
+
+ public boolean has(String key)
+ {
+ return subValMap.containsKey(key);
+ }
+
+ public int getIndex()
+ {
+ return index;
+ }
+
+ public String getContent()
+ {
+ return content;
+ }
+
+ protected Map<String, String> getSubValMap()
+ {
+ return subValMap;
+ }
+
+ public String toString()
+ {
+ if (subValMap == null && getIndex() == NOTSET)
+ return "";
+
+ StringBuilder sb = new StringBuilder();
+ List<String> entries = new ArrayList<>();
+ subValMap.entrySet().stream().forEachOrdered(
+ m -> entries.add(m.getValue().equals("true") ? m.getKey()
+ : new StringBuilder().append(m.getKey()).append(EQUALS)
+ .append(m.getValue()).toString()));
+ if (getIndex() != NOTSET)
+ entries.add(Integer.toString(getIndex()));
+ sb.append('[');
+ sb.append(String.join(Character.toString(SEPARATOR), entries));
+ sb.append(']');
+ return sb.toString();
+ }
+}
\ No newline at end of file
package jalview.datamodel;
import java.awt.Color;
-import java.math.BigInteger;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.HashMap;
import java.util.List;
-import java.util.Spliterator;
import java.util.StringTokenizer;
import jalview.bin.Console;
{
return "Contact Matrix";
}
- List<BitSet> groups=null;
+
+ List<BitSet> groups = null;
+
@Override
public void updateGroups(List<BitSet> colGroups)
{
groups = colGroups;
- colorMap=new HashMap<>();
+ colorMap = new HashMap<>();
}
+
@Override
public boolean hasGroups()
{
- return groups!=null && groups.size()>0;
+ return groups != null && groups.size() > 0;
}
+
@Override
public List<BitSet> getGroups()
{
return groups;
}
+
@Override
public BitSet getGroupsFor(int column)
{
- for (BitSet gp:groups) {
+ for (BitSet gp : groups)
+ {
if (gp.get(column))
{
return gp;
}
return ContactMatrixI.super.getGroupsFor(column);
}
- HashMap<BitSet,Color> colorMap = new HashMap<>();
- @Override
+
+ HashMap<BitSet, Color> colorMap = new HashMap<>();
+
+ @Override
public Color getColourForGroup(BitSet bs)
{
- if (bs==null) {
+ if (bs == null)
+ {
return Color.white;
}
- Color groupCol=colorMap.get(bs);
- if (groupCol==null)
+ Color groupCol = colorMap.get(bs);
+ if (groupCol == null)
{
return Color.white;
}
return groupCol;
}
- @Override
- public void setColorForGroup(BitSet bs,Color color)
+
+ @Override
+ public void setColorForGroup(BitSet bs, Color color)
{
- colorMap.put(bs,color);
+ colorMap.put(bs, color);
}
+
public static String contactToFloatString(ContactMatrixI cm)
{
StringBuilder sb = new StringBuilder();
- for (int c=0;c<cm.getWidth();c++)
+ for (int c = 0; c < cm.getWidth(); c++)
{
- ContactListI cl=cm.getContactList(c);
- if (cl!=null) {
- for (int h=0;h<=cl.getContactHeight();h++)
+ ContactListI cl = cm.getContactList(c);
+ if (cl != null)
{
- if (sb.length()>0) {
- sb.append('\t');
+ for (int h = 0; h <= cl.getContactHeight(); h++)
+ {
+ if (sb.length() > 0)
+ {
+ sb.append('\t');
+ }
+ sb.append(cl.getContactAt(h));
}
- sb.append(cl.getContactAt(h));
- }
}
}
return sb.toString();
int rows)
{
float[][] vals = new float[cols][rows];
- StringTokenizer tabsep = new StringTokenizer(values,""+'\t');
- int c=0,r=0;
-
+ StringTokenizer tabsep = new StringTokenizer(values, "" + '\t');
+ int c = 0, r = 0;
+
while (tabsep.hasMoreTokens())
{
double elem = Double.valueOf(tabsep.nextToken());
- vals[c][r++]=(float) elem;
- if (r>=vals[c].length)
+ vals[c][r++] = (float) elem;
+ if (r >= vals[c].length)
{
- r=0;
+ r = 0;
c++;
}
- if (c>=vals.length)
+ if (c >= vals.length)
{
-
+
break;
}
}
if (tabsep.hasMoreElements())
{
- Console.warn("Ignoring additional elements for Float string to contact matrix parsing.");
+ Console.warn(
+ "Ignoring additional elements for Float string to contact matrix parsing.");
}
-
+
return vals;
}
}
String getAnnotLabel();
/**
- * string indicating how the contactMatrix should be rendered - stored in calcId
- * @return
+ * string indicating how the contactMatrix should be rendered - stored in
+ * calcId
+ *
+ * @return
*/
String getType();
int getWidth();
+
int getHeight();
default boolean hasGroups() {
public class SeqDistanceContactMatrix implements ContactMatrixI
{
private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
+
private int width = 0;
public SeqDistanceContactMatrix(int width)
{
Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
- null, false, false);
+ null, false, false, null);
if (al.getAlignmentAnnotation() != null)
{
viewStyle.setFontName(font.getName());
viewStyle.setFontStyle(font.getStyle());
viewStyle.setFontSize(font.getSize());
-
+
validCharWidth = true;
}
*/
public void addFile(File file, FileFormatI format)
{
+ addFile(file, format, true);
+ }
+
+ public void addFile(File file, FileFormatI format, boolean async)
+ {
DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
if (format == null)
}
}
- new FileLoader().LoadFile(this, file, DataSourceType.FILE, format);
+ new FileLoader().LoadFile(this, file, DataSourceType.FILE, format,
+ async);
}
public void addFile(File file)
// TODO - write tests and fix AlignFrame.paste() which doesn't track if
// clipboard has come from a different alignment window than the one where
// paste has been called! JAL-4151
-
+
if (Desktop.jalviewClipboard != null)
{
// The clipboard was filled from within Jalview, we must use the
}
Desktop.addInternalFrame(af, newtitle, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_HEIGHT);
- } else {
- try
+ }
+ else
{
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
- Transferable contents = c.getContents(this);
-
- if (contents != null)
+ try
{
- String file = (String) contents
- .getTransferData(DataFlavor.stringFlavor);
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ Transferable contents = c.getContents(this);
- FileFormatI format = new IdentifyFile().identify(file,
- DataSourceType.PASTE);
+ if (contents != null)
+ {
+ String file = (String) contents
+ .getTransferData(DataFlavor.stringFlavor);
- new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
+ 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);
- }
}
}
// this will run the shutdownHook but QuitHandler.getQuitResponse() should
// not run a second time if gotQuitResponse flag has been set (i.e. user
// confirmed quit of some kind).
- System.exit(0);
+ Jalview.exit("Desktop exiting.", 0);
}
private void storeLastKnownDimensions(String string, Rectangle jc)
public void LoadFile(AlignViewport viewport, Object file,
DataSourceType protocol, FileFormatI format)
{
+ LoadFile(viewport, file, protocol, format, true);
+ }
+
+ public void LoadFile(AlignViewport viewport, Object file,
+ DataSourceType protocol, FileFormatI format, boolean async)
+ {
this.viewport = viewport;
if (file instanceof File)
{
this.selectedFile = (File) file;
file = selectedFile.getPath();
}
- LoadFile(file.toString(), protocol, format);
+ LoadFile(file.toString(), protocol, format, async);
}
public void LoadFile(String file, DataSourceType protocol,
FileFormatI format)
{
+ LoadFile(file, protocol, format, true);
+ }
+
+ public void LoadFile(String file, DataSourceType protocol,
+ FileFormatI format, boolean async)
+ {
this.file = file;
this.protocol = protocol;
this.format = format;
- final Thread loader = new Thread(this);
-
- SwingUtilities.invokeLater(new Runnable()
+ if (async)
{
- @Override
- public void run()
+ final Thread loader = new Thread(this);
+
+ SwingUtilities.invokeLater(new Runnable()
{
- loader.start();
- }
- });
+ @Override
+ public void run()
+ {
+ loader.start();
+ }
+ });
+ }
+ else
+ {
+ this.run();
+ }
}
/**
// TODO: Extended SequenceNodeI to hold parsed NHX strings
package jalview.io;
-import java.util.Locale;
-
-import jalview.datamodel.BinaryNode;
-import jalview.datamodel.SequenceNode;
-import jalview.util.MessageManager;
-
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
+import java.util.Locale;
import java.util.StringTokenizer;
import com.stevesoft.pat.Regex;
+import jalview.bin.Jalview;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.SequenceNode;
+import jalview.util.MessageManager;
+
/**
* Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
* tree distances and topology are unreliable when they are parsed. TODO: on
{
try
{
- distance = (Double.valueOf(ndist.stringMatched(1))).floatValue();
+ distance = (Double.valueOf(ndist.stringMatched(1)))
+ .floatValue();
HasDistances = true;
nodehasdistance = true;
} catch (Exception e)
{
if (root.isDummy())
{
- _print(tf, root.right());
- _print(tf, root.left());
+ _print(tf, root.right());
+ _print(tf, root.left());
}
else
{
tf.append("(");
- _print(tf, root.right());
+ _print(tf, root.right());
if (root.left() != null)
{
tf.append(",");
}
- _print(tf, root.left());
+ _print(tf, root.left());
tf.append(")" + printRootField(root));
}
}
{
if (c.isDummy())
{
- _print(tf, c.left());
+ _print(tf, c.left());
if (c.left() != null)
{
tf.append(",");
}
- _print(tf, c.right());
+ _print(tf, c.right());
}
else
{
tf.append("(");
- _print(tf, c.right());
+ _print(tf, c.right());
if (c.left() != null)
{
tf.append(",");
}
- _print(tf, c.left());
+ _print(tf, c.left());
tf.append(")" + printNodeField(c));
}
}
{
if (args == null || args.length != 1)
{
- System.err.println(
- "Takes one argument - file name of a newick tree file.");
- System.exit(0);
+ Jalview.exit(
+ "Takes one argument - file name of a newick tree file.", 0);
}
File fn = new File(args[0]);
import java.io.PipedOutputStream;
import java.io.PrintStream;
+import jalview.bin.Jalview;
+
public class AWTConsole extends WindowAdapter
implements WindowListener, ActionListener, Runnable
{
} catch (Exception e)
{
}
- System.exit(0);
+ Jalview.exit("Window closing. Bye!", 0);
}
@Override
*/
package jalview.util;
+import java.util.Arrays;
+
public class ArrayUtils
{
/**
}
}
}
+
+ public static <T> T[] concatArrays(T[]... arrays)
+ {
+ if (arrays == null)
+ return null;
+ if (arrays.length == 1)
+ return arrays[0];
+
+ T[] result = arrays[0];
+ for (int i = 1; i < arrays.length; i++)
+ {
+ result = concatTwoArrays(result, arrays[i]);
+ }
+ return result;
+ }
+
+ private static <T> T[] concatTwoArrays(T[] array1, T[] array2)
+ {
+ T[] result = Arrays.copyOf(array1, array1.length + array2.length);
+ System.arraycopy(array2, 0, result, array1.length, array2.length);
+ return result;
+ }
+
}
--- /dev/null
+package jalview.util;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.FileSystems;
+import java.nio.file.FileVisitOption;
+import java.nio.file.FileVisitResult;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.PathMatcher;
+import java.nio.file.Paths;
+import java.nio.file.SimpleFileVisitor;
+import java.nio.file.attribute.BasicFileAttributes;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.EnumSet;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import jalview.bin.Console;
+
+public class FileUtils
+{
+ /*
+ * Given string glob pattern (see
+ * https://docs.oracle.com/javase/7/docs/api/java/nio/file/FileSystem.html#getPathMatcher(java.lang.String)
+ * ) return a List of Files that match the pattern.
+ * Note this is a java style glob, not necessarily a bash-style glob, though there are sufficient similarities.
+ */
+ public static List<File> getFilesFromGlob(String pattern)
+ {
+ return getFilesFromGlob(pattern, true);
+ }
+
+ public static List<File> getFilesFromGlob(String pattern,
+ boolean allowSingleFilenameThatDoesNotExist)
+ {
+ pattern = substituteHomeDir(pattern);
+ List<File> files = new ArrayList<>();
+ /*
+ * For efficiency of the Files.walkFileTree(), let's find the longest path that doesn't need globbing.
+ * We look for the first glob character * { ? and then look for the last File.separator before that.
+ * Then we can reset the path to look at and shorten the globbing pattern.
+ * Relative paths can be used in pattern, which work from the pwd (though these are converted into
+ * full paths in the match).
+ */
+ int firstGlobChar = -1;
+ boolean foundGlobChar = false;
+ for (char c : new char[] { '*', '{', '?' })
+ {
+ if (pattern.indexOf(c) > -1
+ && (pattern.indexOf(c) < firstGlobChar || !foundGlobChar))
+ {
+ firstGlobChar = pattern.indexOf(c);
+ foundGlobChar = true;
+ }
+ }
+ int lastFS = pattern.lastIndexOf(File.separatorChar, firstGlobChar);
+ if (foundGlobChar)
+ {
+ String pS = pattern.substring(0, lastFS + 1);
+ String rest = pattern.substring(lastFS + 1);
+ Path parentDir = Paths.get(pS).toAbsolutePath();
+ if (parentDir.toFile().exists())
+ {
+ try
+ {
+ String glob = "glob:" + parentDir.toString() + File.separator
+ + rest;
+ PathMatcher pm = FileSystems.getDefault().getPathMatcher(glob);
+ int maxDepth = rest.contains("**") ? 1028
+ : (int) (rest.chars()
+ .filter(ch -> ch == File.separatorChar).count())
+ + 1;
+
+ Files.walkFileTree(parentDir,
+ EnumSet.of(FileVisitOption.FOLLOW_LINKS), maxDepth,
+ new SimpleFileVisitor<Path>()
+ {
+ @Override
+ public FileVisitResult visitFile(Path path,
+ BasicFileAttributes attrs) throws IOException
+ {
+ if (pm.matches(path))
+ {
+ files.add(path.toFile());
+ }
+ return FileVisitResult.CONTINUE;
+ }
+
+ @Override
+ public FileVisitResult visitFileFailed(Path file,
+ IOException exc) throws IOException
+ {
+ return FileVisitResult.CONTINUE;
+ }
+ });
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+ else
+ {
+ // no wildcards
+ File f = new File(pattern);
+ if (allowSingleFilenameThatDoesNotExist || f.exists())
+ {
+ files.add(f);
+ }
+ }
+ Collections.sort(files);
+
+ return files;
+ }
+
+ public static List<String> getFilenamesFromGlob(String pattern)
+ {
+ // convert list of Files to list of File.getPath() Strings
+ return getFilesFromGlob(pattern).stream().map(f -> f.getPath())
+ .collect(Collectors.toList());
+ }
+
+ public static String substituteHomeDir(String path)
+ {
+ return path.startsWith("~" + File.separator)
+ ? System.getProperty("user.home") + path.substring(1)
+ : path;
+ }
+
+ /*
+ * This method returns the basename of the first --open or --opennew value.
+ * Used primarily for substitutions in output filenames.
+ */
+ public static String getBasename(File file)
+ {
+ if (file == null)
+ return null;
+
+ String basename = null;
+ String filename = file.getName();
+ int lastDot = filename.lastIndexOf('.');
+ if (lastDot > 0) // don't truncate if starts with '.'
+ {
+ basename = filename.substring(0, lastDot);
+ }
+ else
+ {
+ basename = filename;
+ }
+ return basename;
+ }
+
+ /*
+ * This method returns the dirname of the first --open or --opennew value.
+ * Used primarily for substitutions in output filenames.
+ */
+ public static String getDirname(File file)
+ {
+ if (file == null)
+ return null;
+
+ String dirname = null;
+ try
+ {
+ File p = file.getParentFile();
+ File d = new File(substituteHomeDir(p.getPath()));
+ dirname = d.getCanonicalPath();
+ } catch (IOException e)
+ {
+ Console.debug(
+ "Exception when getting dirname of '" + file.getPath() + "'",
+ e);
+ dirname = "";
+ }
+ return dirname;
+ }
+}
/*
* implementation of String.replaceLast.
+ * Replaces only the last occurrence of toReplace in string with replacement.
*/
public static String replaceLast(String string, String toReplace,
String replacement)
int pos = string.lastIndexOf(toReplace);
if (pos > -1)
{
- return string.substring(0, pos) + replacement
- + string.substring(pos + toReplace.length());
+ return new StringBuilder().append(string.substring(0, pos))
+ .append(replacement)
+ .append(string.substring(pos + toReplace.length()))
+ .toString();
}
else
{
@Override
public String getAnnotDescr()
{
- return "Predicted Alignment Error"+((refSeq==null) ? "" : (" for " + refSeq.getName()));
+ return "Predicted Alignment Error"
+ + ((refSeq == null) ? "" : (" for " + refSeq.getName()));
}
@Override
public String getAnnotLabel()
{
StringBuilder label = new StringBuilder("PAE Matrix");
- //if (this.getReferenceSeq() != null)
- //{
- // label.append(":").append(this.getReferenceSeq().getDisplayId(false));
- //}
+ // if (this.getReferenceSeq() != null)
+ // {
+ // label.append(":").append(this.getReferenceSeq().getDisplayId(false));
+ // }
return label.toString();
}
{
return length;
}
- List<BitSet> groups=null;
+
+ List<BitSet> groups = null;
+
@Override
public boolean hasGroups()
{
- return groups!=null;
+ return groups != null;
}
- String newick=null;
+
+ String newick = null;
+
@Override
public String getNewick()
{
return newick;
}
+
@Override
public boolean hasTree()
{
- return newick!=null && newick.length()>0;
+ return newick != null && newick.length() > 0;
}
+
boolean abs;
+
double thresh;
- String treeType=null;
- public void makeGroups(float thresh,boolean abs)
+
+ String treeType = null;
+
+ public void makeGroups(float thresh, boolean abs)
{
- AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null, this);
+ AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null,
+ this);
double height = clusterer.findHeight(clusterer.getTopNode());
- newick = new jalview.io.NewickFile(clusterer.getTopNode(),false,true).print();
+ newick = new jalview.io.NewickFile(clusterer.getTopNode(), false, true)
+ .print();
treeType = "UPGMA";
- Console.trace("Newick string\n"+newick);
+ Console.trace("Newick string\n" + newick);
List<BinaryNode> nodegroups;
if (abs ? height > thresh : 0 < thresh && thresh < 1)
{
float cut = abs ? (float) (thresh / height) : thresh;
- Console.debug("Threshold "+cut+" for height="+height);
+ Console.debug("Threshold " + cut + " for height=" + height);
nodegroups = clusterer.groupNodes(cut);
}
nodegroups = new ArrayList<BinaryNode>();
nodegroups.add(clusterer.getTopNode());
}
- this.abs=abs;
- this.thresh=thresh;
+ this.abs = abs;
+ this.thresh = thresh;
groups = new ArrayList<>();
- for (BinaryNode root:nodegroups)
+ for (BinaryNode root : nodegroups)
{
- BitSet gpset=new BitSet();
- for (BinaryNode leaf:clusterer.findLeaves(root))
+ BitSet gpset = new BitSet();
+ for (BinaryNode leaf : clusterer.findLeaves(root))
{
- gpset.set((Integer)leaf.element());
+ gpset.set((Integer) leaf.element());
}
groups.add(gpset);
}
}
+
@Override
public void updateGroups(List<BitSet> colGroups)
{
- if (colGroups!=null)
+ if (colGroups != null)
{
- groups=colGroups;
- }
+ groups = colGroups;
+ }
}
+
@Override
public BitSet getGroupsFor(int column)
{
- for (BitSet gp:groups) {
+ for (BitSet gp : groups)
+ {
if (gp.get(column))
{
return gp;
return ContactMatrixI.super.getGroupsFor(column);
}
- HashMap<BitSet,Color> colorMap = new HashMap<>();
- @Override
+ HashMap<BitSet, Color> colorMap = new HashMap<>();
+
+ @Override
public Color getColourForGroup(BitSet bs)
{
- if (bs==null) {
+ if (bs == null)
+ {
return Color.white;
}
- Color groupCol=colorMap.get(bs);
- if (groupCol==null)
+ Color groupCol = colorMap.get(bs);
+ if (groupCol == null)
{
return Color.white;
}
return groupCol;
}
- @Override
- public void setColorForGroup(BitSet bs,Color color)
+
+ @Override
+ public void setColorForGroup(BitSet bs, Color color)
{
- colorMap.put(bs,color);
+ colorMap.put(bs, color);
}
+
public void restoreGroups(List<BitSet> newgroups, String treeMethod,
String tree, double thresh2)
{
- treeType=treeMethod;
+ treeType = treeMethod;
groups = newgroups;
- thresh=thresh2;
- newick =tree;
-
+ thresh = thresh2;
+ newick = tree;
+
}
+
@Override
- public boolean hasCutHeight() {
- return groups!=null && thresh!=0;
+ public boolean hasCutHeight()
+ {
+ return groups != null && thresh != 0;
}
+
@Override
public double getCutHeight()
{
return thresh;
}
+
@Override
public String getTreeMethod()
{
AlignmentI pdbAlignment, String retrievalUrl) throws IOException
{
File pae = fetchAlphaFoldPAE(id, retrievalUrl);
- addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false);
+ addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false, null);
}
public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae,
- int index, String id, boolean isStruct, boolean isStructId)
+ int index, String id, boolean isStruct, boolean isStructId,
+ String label)
{
FileInputStream paeInput = null;
try
if (ssm != null)
{
String structFilename = isStructId ? ssm.findFileForPDBId(id) : id;
- addPAEToStructure(ssm, structFilename, pae);
+ addPAEToStructure(ssm, structFilename, pae, label);
}
}
try
{
if (!importPaeJSONAsContactMatrixToSequence(pdbAlignment, paeInput,
- index, id))
+ index, id, label))
{
Console.warn("Could not import contact matrix from '"
+ pae.getAbsolutePath() + "' to sequence.");
}
public static void addPAEToStructure(StructureSelectionManager ssm,
- String structFilename, File pae)
+ String structFilename, File pae, String label)
{
FileInputStream paeInput = null;
try
try
{
- if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput))
+ if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput,
+ label))
{
Console.warn("Could not import contact matrix from '"
+ pae.getAbsolutePath() + "' to structure.");
*/
public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input, int index,
- String seqId) throws IOException, ParseException
+ String seqId, String label) throws IOException, ParseException
{
SequenceI sequence = null;
if (seqId == null)
return false;
}
return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input,
- sequence);
+ sequence, label);
}
public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input,
- SequenceI sequence) throws IOException, ParseException
+ SequenceI sequence, String label)
+ throws IOException, ParseException
{
JSONObject paeDict = parseJSONtoPAEContactMatrix(pae_input);
if (paeDict == null)
((PAEContactMatrix) matrix).makeGroups(5f, true);
AlignmentAnnotation cmannot = sequence.addContactList(matrix);
+ if (label != null)
+ cmannot.label = label;
pdbAlignment.addAnnotation(cmannot);
return true;
}
public static boolean importPaeJSONAsContactMatrixToStructure(
- StructureMapping[] smArray, InputStream paeInput)
+ StructureMapping[] smArray, InputStream paeInput, String label)
throws IOException, ParseException
{
boolean someDone = false;
for (StructureMapping sm : smArray)
{
boolean thisDone = importPaeJSONAsContactMatrixToStructure(sm,
- paeInput);
+ paeInput, label);
someDone |= thisDone;
}
return someDone;
}
public static boolean importPaeJSONAsContactMatrixToStructure(
- StructureMapping sm, InputStream paeInput)
+ StructureMapping sm, InputStream paeInput, String label)
throws IOException, ParseException
{
JSONObject pae_obj = parseJSONtoPAEContactMatrix(paeInput);
return false;
}
- ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
+ SequenceI seq = sm.getSequence();
+ Console.debug("##### SEQUENCE FOUND=" + seq.getName());
+ ContactMatrixI matrix = new PAEContactMatrix(seq,
(Map<String, Object>) pae_obj);
((PAEContactMatrix) matrix).makeGroups(5f, true);
- AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
- sm.getSequence().addAlignmentAnnotation(cmannot);
+ AlignmentAnnotation cmannot = seq.addContactList(matrix);
+ seq.addAlignmentAnnotation(cmannot);
+ // seq.addAlignmentAnnotation(cmannot);
return true;
}
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.bin.ArgsParser;
import jalview.gui.JvOptionPane;
import org.testng.annotations.BeforeClass;
public void setUpForHeadlessCommandLineInputOperations()
throws IOException
{
- String cmds = "nodisplay -open examples/uniref50.fa -sortbytree --props=test/jalview/bin/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);
return new Object[][] {
// headless mode input operations
{ "CMD [-colour zappo] executed successfully!",
- "Failed command : -color zappo" },
+ "Failed command : -colour zappo" },
{ "CMD [-props test/jalview/bin/testProps.jvprops] executed successfully!",
- "Failed command : --props=File" },
+ "Failed command : -props File" },
{ "CMD [-sortbytree] executed successfully!",
"Failed command : -sortbytree" },
{ "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
--- /dev/null
+package jalview.bin;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.util.ArrayUtils;
+
+@Test
+public class CommandsTest
+{
+ private static final String testfiles = "test/jalview/bin/argparser/testfiles";
+
+ private static final String png1 = testfiles + "/dir1/test1.png";
+
+ private static final String png2 = testfiles + "/dir2/test1.png";
+
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ Cache.loadProperties("test/jalview/gui/quitProps.jvprops");
+ Date oneHourFromNow = new Date(
+ System.currentTimeMillis() + 3600 * 1000);
+ Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
+ }
+
+ @AfterClass(alwaysRun = true)
+ public static void resetProps()
+ {
+ Cache.loadProperties("test/jalview/testProps.jvprops");
+ }
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void tearDown()
+ {
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ /* --setprops is currently disabled so this test won't work
+ @Test(groups = "Functional")
+ public void setpropsTest()
+ {
+ final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
+ String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
+ String[] args = cmdLine.split("\\s+");
+ Jalview.main(args);
+ Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
+ "Earth");
+ }
+ */
+
+ @Test(groups = "Functional", dataProvider = "cmdLines")
+ public void commandsOpenTest(String cmdLine, boolean cmdArgs,
+ int numFrames, String[] sequences)
+ {
+ String[] args = cmdLine.split("\\s+");
+ Jalview.main(args);
+ Commands cmds = Jalview.getInstance().getCommands();
+ Assert.assertNotNull(cmds);
+ Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
+ "Commands were not provided in the args");
+ Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
+ "Overall command parse and operation is false");
+
+ Assert.assertEquals(Desktop.getAlignFrames().length, numFrames);
+
+ if (sequences != null)
+ {
+ Set<String> openedSequenceNames = new HashSet<>();
+ AlignFrame[] afs = Desktop.getAlignFrames();
+ for (AlignFrame af : afs)
+ {
+ openedSequenceNames
+ .addAll(af.getViewport().getAlignment().getSequenceNames());
+ }
+ for (String sequence : sequences)
+ {
+ Assert.assertTrue(openedSequenceNames.contains(sequence),
+ "Sequence '" + sequence
+ + "' was not found in opened alignment files: "
+ + cmdLine + ".\nOpened sequence names are:\n"
+ + String.join("\n", openedSequenceNames));
+ }
+ }
+
+ Assert.assertFalse(
+ lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
+ }
+
+ @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
+ public void argFilesGlobAndSubstitutionsTest(String cmdLine,
+ String[] filenames) throws IOException
+ {
+ cleanupFiles(filenames);
+ String[] args = cmdLine.split("\\s+");
+ Jalview.main(args);
+ Commands cmds = Jalview.getInstance().getCommands();
+ Assert.assertNotNull(cmds);
+ File lastFile = null;
+ for (String filename : filenames)
+ {
+ File file = new File(filename);
+ Assert.assertTrue(file.exists(), "File '" + filename
+ + "' was not created by '" + cmdLine + "'");
+ Assert.assertTrue(file.isFile(), "File '" + filename
+ + "' is not a file from '" + cmdLine + "'");
+ Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
+ + "' has no content from '" + cmdLine + "'");
+ // make sure the successive output files get bigger!
+ if (lastFile != null)
+ Assert.assertTrue(
+ Files.size(file.toPath()) > Files.size(lastFile.toPath()));
+ }
+ cleanupFiles(filenames);
+ tearDown();
+ }
+
+ @DataProvider(name = "argfileOutputFiles")
+ public Object[][] argfileOutputFiles()
+ {
+ return new Object[][] {
+ { "--argfile=" + testfiles + "/**/*.txt", new String[]
+ { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
+ testfiles + "/dir3/subdir/test0.png" } },
+ { "--argfile=" + testfiles + "/**/argfile.txt", new String[]
+ { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
+ { "--argfile=" + testfiles + "/dir*/argfile.txt", new String[]
+ { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
+ { "--initsubstitutions --open examples/uniref50.fa --image "
+ + testfiles + "/{basename}.png",
+ new String[]
+ { testfiles + "/uniref50.png" } },
+ { "--open examples/uniref50.fa --image " + testfiles
+ + "/{basename}.png",
+ new String[]
+ { testfiles + "/{basename}.png" } } };
+ }
+
+ @DataProvider(name = "cmdLines")
+ public Object[][] cmdLines()
+ {
+ String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
+ "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
+ String[] t1 = new String[] { "TEST1" };
+ String[] t2 = new String[] { "TEST2" };
+ String[] t3 = new String[] { "TEST3" };
+ return new Object[][] {
+ { "--open=examples/uniref50.fa", true, 1, someUniref50Seqs },
+ { "--open examples/uniref50.fa", true, 1, someUniref50Seqs },
+ { "--open=examples/uniref50*.fa", true, 1, someUniref50Seqs },
+ // NOTE we cannot use shell expansion in tests, so list all files!
+ { "--open examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
+ someUniref50Seqs },
+ { "--open=[new]examples/uniref50*.fa", true, 2, someUniref50Seqs },
+ { "--opennew=examples/uniref50*.fa", true, 2, someUniref50Seqs },
+ { "examples/uniref50.fa", true, 1, someUniref50Seqs },
+ { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
+ ArrayUtils.concatArrays(someUniref50Seqs, t1) },
+ { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
+ { "--argfile=" + testfiles + "/argfile0.txt", true, 1,
+ ArrayUtils.concatArrays(t1, t3) },
+ { "--argfile=" + testfiles + "/argfile*.txt", true, 4,
+ ArrayUtils.concatArrays(t1, t2, t3) },
+ { "--argfile=" + testfiles + "/argfile.autocounter", true, 3,
+ ArrayUtils.concatArrays(t1, t2) } };
+ }
+
+ public static boolean lookForSequenceName(String sequenceName)
+ {
+ AlignFrame[] afs = Desktop.getAlignFrames();
+ for (AlignFrame af : afs)
+ {
+ for (String name : af.getViewport().getAlignment().getSequenceNames())
+ {
+ if (sequenceName.equals(name))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ public static void cleanupFiles(String[] filenames)
+ {
+ for (String filename : filenames)
+ {
+ File file = new File(filename);
+ if (file.exists())
+ {
+ file.delete();
+ }
+ }
+ }
+
+}
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
+import jalview.util.Platform;
/*
* Testing a HiDPI display is difficult without running in a HiDPI display.
@AfterClass(alwaysRun = true)
public void tearDown()
{
- Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
}
@Test(groups = { "Functional" })
setMockScreen(1920, 1080, 96);
assertEquals(HiDPISetting.getScalePropertyArg(), null);
+ // currently HiDPISetting only operates for Linux
+
// 4K screen -- scale by 2
setMockScreen(3180, 2160, 80);
assertEquals(HiDPISetting.getScalePropertyArg(),
- "-D" + scalePropertyName + "=2");
+ Platform.isLinux() ? "-D" + scalePropertyName + "=2" : null);
// 4K screen with high dpi -- scale by 3
setMockScreen(3180, 2160, 450);
assertEquals(HiDPISetting.getScalePropertyArg(),
- "-D" + scalePropertyName + "=3");
+ Platform.isLinux() ? "-D" + scalePropertyName + "=3" : null);
// stupidly big screen -- scale by 8
setMockScreen(19200, 10800, 72);
assertEquals(HiDPISetting.getScalePropertyArg(),
- "-D" + scalePropertyName + "=8");
+ Platform.isLinux() ? "-D" + scalePropertyName + "=8" : null);
}
}
--- /dev/null
+package jalview.bin.argparser;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import java.util.Properties;
+
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
+
+@Test(singleThreaded = true)
+public class ArgParserTest
+{
+ @AfterClass(alwaysRun = true)
+ public static void resetProps()
+ {
+ Cache.loadProperties("test/jalview/testProps.jvprops");
+ }
+
+ @Test(groups = "Functional", dataProvider = "argLines")
+ public void parseArgsTest(String commandLineArgs, Arg a, String other)
+ {
+ String[] args = commandLineArgs.split("\\s+");
+ ArgParser argparser = new ArgParser(args);
+ }
+
+ @Test(groups = "Functional", dataProvider = "argSubValsAndLinkedIds")
+ public void parseSubValsAndLinkedIdsTest(String commandLineArgs,
+ String linkedId, Arg a, String subvalKey, String value,
+ boolean trueOrFalse)
+ {
+ String[] args = commandLineArgs.split("\\s+");
+ ArgParser argparser = new ArgParser(args);
+ ArgValuesMap avm = argparser.linkedArgs(linkedId);
+ ArgValue av = avm.getArgValue(a);
+ SubVals sv = av.getSubVals();
+ String testString = null;
+ if (subvalKey.equals("GETINDEX"))
+ {
+ testString = String.valueOf(sv.getIndex());
+ }
+ else
+ {
+ testString = sv.get(subvalKey);
+ }
+ if (trueOrFalse)
+ {
+ Assert.assertEquals(testString, value);
+ }
+ else
+ {
+ Assert.assertNotEquals(testString, value);
+ }
+ }
+
+ @Test(
+ groups = "Functional",
+ dataProvider = "argAutoIndexAndSubstitutions")
+ public void parseAutoIndexAndSubstitutionsTest(String commandLineArgs,
+ String linkedId, Arg a, String filename)
+ {
+ // { "--open=filename0 --increment --open=filename1", "JALVIEW:1", Arg.OPEN,
+ // "filename1" },
+ String[] args = commandLineArgs.split("\\s+");
+ ArgParser argparser = new ArgParser(args);
+ ArgValuesMap avm = argparser.linkedArgs(linkedId);
+ ArgValue av = avm.getArgValue(a);
+ Assert.assertEquals(av.getValue(), filename);
+ }
+
+ @Test(groups = "Functional", dataProvider = "argLines")
+ public void bootstrapArgsTest(String commandLineArgs, Arg a, String other)
+ {
+ String[] args = commandLineArgs.split("\\s+");
+ BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
+
+ Assert.assertTrue(b.contains(a));
+ if (a == Arg.PROPS)
+ {
+ Properties bP = Cache.bootstrapProperties(b.get(Arg.PROPS));
+ Assert.assertNotNull(bP);
+ Assert.assertTrue(other.equals(bP.get(Cache.BOOTSTRAP_TEST)));
+ Assert.assertFalse(bP.contains("NOT" + Cache.BOOTSTRAP_TEST));
+ }
+ else if (a == Arg.ARGFILE)
+ {
+ List<String> filenames = b.getList(a);
+ boolean found = false;
+ for (String s : filenames)
+ {
+ File f = new File(s);
+ File fo = new File(other);
+ try
+ {
+ if (fo.getCanonicalPath().equals(f.getCanonicalPath()))
+ {
+ found = true;
+ break;
+ }
+ } catch (IOException e)
+ {
+ }
+ }
+ Assert.assertTrue(found,
+ "File '" + other + "' not found in shell expanded glob '"
+ + commandLineArgs + "'");
+ }
+ }
+
+ @Test(groups = "Functional", dataProvider = "argFiles")
+ public void argFilesTest(String commandLineArgs, Arg a, String other)
+ {
+ String[] args = commandLineArgs.split("\\s+");
+ BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
+
+ Assert.assertTrue(b.contains(a));
+ Assert.assertFalse(b.contains(Arg.OPEN));
+ if (a == Arg.PROPS)
+ {
+ Properties bP = Cache.bootstrapProperties(b.get(Arg.PROPS));
+ Assert.assertTrue("true".equals(bP.get(Cache.BOOTSTRAP_TEST)));
+ }
+ }
+
+ @DataProvider(name = "argLinesNotworking")
+ public Object[][] argLinesTest()
+ {
+ return new Object[][] {
+ // can't use this one yet as it doesn't get shell glob expanded by the
+ // test
+ { "--argfile test/jalview/bin/argparser/testfiles/argfile*.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile0.txt" }, };
+ }
+
+ @DataProvider(name = "argLines")
+ public Object[][] argLines()
+ {
+ return new Object[][] { {
+ "--open=test/jalview/bin/argparser/testfiles/test1.fa --props=test/jalview/bin/argparser/testfiles/testProps.jvprops",
+ Arg.PROPS, "true" },
+ { "--debug --open=test/jalview/bin/argparser/testfiles/test1.fa",
+ Arg.DEBUG, null },
+ { "--open=test/jalview/bin/argparser/testfiles/test1.fa --headless",
+ Arg.HEADLESS, null },
+
+ { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile0.txt" },
+ // these next three are what a shell glob expansion would look like
+ { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile0.txt" },
+ { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile1.txt" },
+ { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile2.txt" },
+ { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile0.txt" },
+ { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile1.txt" },
+ { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile2.txt" } };
+ }
+
+ @DataProvider(name = "argSubValsAndLinkedIds")
+ public Object[][] argSubValsAndLinkedIds()
+ {
+ return new Object[][] { {
+ "--debug --open=[hi]test/jalview/bin/argparser/testfiles/test1.fa",
+ "JALVIEW:0", Arg.OPEN, "hi", "true", true },
+ { "--open[linkedId1]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+ "linkedId1", Arg.OPEN, "new", "true", true },
+ { "--open[linkedId2]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+ "linkedId2", Arg.OPEN, "hello", "world", true },
+ { "--open[linkedId3]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+ "linkedId3", Arg.OPEN, "GETINDEX", "1", true },
+ { "--open[linkedId4]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --open[linkedId5]=[notnew;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+ "linkedId5", Arg.OPEN, "new", "true", false },
+ { "--open[linkedId5]=[new;hello=worlddomination;1]test/jalview/bin/argparser/testfiles/test1.fa --open[linkedId2]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+ "linkedId5", Arg.OPEN, "hello", "world", false },
+ { "--open[linkedId6]=[new;hello=world;0]test/jalview/bin/argparser/testfiles/test1.fa --open[linkedId7]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+ "linkedId7", Arg.OPEN, "GETINDEX", "0", false }, };
+ }
+
+ @DataProvider(name = "argAutoIndexAndSubstitutions")
+ public Object[][] argAutoIndexAndSubstitutions()
+ {
+ return new Object[][] { { "--open=filename0 --open=filename1",
+ "JALVIEW:0", Arg.OPEN, "filename0" },
+ { "--open=filename0 --increment --open=filename1", "JALVIEW:1",
+ Arg.OPEN, "filename1" },
+ { "--open=filename0 --increment --increment --open=filename2",
+ "JALVIEW:0", Arg.OPEN, "filename0" },
+ { "--open=filename0 --increment --increment --open=filename2",
+ "JALVIEW:2", Arg.OPEN, "filename2" },
+ { "--open[linkA-{n}]=filenameA0 --open[linkA-{++n}]=filenameA1",
+ "linkA-0", Arg.OPEN, "filenameA0" },
+ { "--open[linkB-{n}]=filenameB0 --open[linkB-{++n}]=filenameB1",
+ "linkB-1", Arg.OPEN, "filenameB1" },
+ { "--open[linkC-{n}]=filenameC0 --image[linkC-{n}]=outputC{n}.txt",
+ "linkC-0", Arg.IMAGE, "outputC{n}.txt" },
+ { "--open[linkD-{n}]=filenameD0 --substitutions --image[linkD-{n}]=outputD{n}.txt",
+ "linkD-0", Arg.IMAGE, "outputD0.txt" },
+ { "--open[linkE-{n}]=filenameE0 --substitutions --image[linkE-{n}]=output-E{n}.txt --nil[{++n}] --image[linkE-{n}]=outputE{n}.txt",
+ "linkE-0", Arg.IMAGE, "output-E0.txt" },
+ { "--open[linkF-{n}]=filenameF0 --substitutions --image[linkF-{n}]=output-F{n}.txt --nil[{++n}] --image[linkF-{n}]=outputF{n}.txt",
+ "linkF-1", Arg.IMAGE, "outputF1.txt" },
+ { "--open[linkG-{n}]=filenameG0 --substitutions --image[linkG-{n}]=output-G{n}.txt --nil[{++n}] --nosubstitutions --image[linkG-{n}]=outputG{n}.txt",
+ "linkG-1", Arg.IMAGE, "outputG{n}.txt" },
+ { "--open[linkH-{n}]=filenameH0 --substitutions --image[linkH-{n}]=output-H{n}.txt --nil[{++n}] --nosubstitutions --image[linkH-{n}]=outputH{n}.txt",
+ "linkH-0", Arg.IMAGE, "output-H0.txt" }, };
+ }
+
+ @DataProvider(name = "argFiles")
+ public Object[][] argFiles()
+ {
+ return new Object[][] { {
+ "--argfile=test/jalview/bin/argparser/testfiles/argfile0.txt --open=shouldntbeabootstrap",
+ Arg.ARGFILE, "test/jalview/bin/argfiles/testfiles/test1.fa" } };
+ }
+}
--- /dev/null
+--open[{++n}]=test/jalview/bin/argparser/testfiles/test1.fa
+--colour[{n}]=gecos:flower
+--open[{++n}]=test/jalview/bin/argparser/testfiles/test2.fa
+--colour[{n}]=zappo
+--open[{++n}]=test/jalview/bin/argparser/testfiles/test1.fa
+--open[{n}]=test/jalview/bin/argparser/testfiles/test2.fa
+--colour[{n}]=taylor
--- /dev/null
+--open=test/jalview/bin/argparser/testfiles/test1.fa
+--open=test/jalview/bin/argparser/testfiles/test3.fa
--- /dev/null
+--open[all]=test/jalview/bin/argparser/testfiles/test1.fa
+--open[all]=test/jalview/bin/argparser/testfiles/test2.fa
+--open[1]=test/jalview/bin/argparser/testfiles/test1.fa
+--open[2]=test/jalview/bin/argparser/testfiles/test2.fa
--- /dev/null
+--open=test/jalview/bin/argparser/testfiles/test2.fa
--- /dev/null
+--substitutions
+--increment
+--open={argfiledirname}/*.fa
+--colour=gecos:flower
+--image={argfiledirname}/{basename}.png
+--close
--- /dev/null
+>TEST1
+AAAA
--- /dev/null
+>TEST2
+LLLL
--- /dev/null
+--substitutions
+--increment
+--open={argfiledirname}/*.fa
+--colour=gecos:flower
+--image={argfiledirname}/{basename}.png
+--close
--- /dev/null
+>TEST1
+AAAA
--- /dev/null
+>TEST2
+LLLL
--- /dev/null
+>TEST3
+AAARG
--- /dev/null
+--substitutions
+--increment
+--open={argfiledirname}/*.fa
+--colour=gecos:flower
+--image={argfiledirname}/{basename}.png
+--close
--- /dev/null
+>TEST0
+AAAA
--- /dev/null
+>TEST1
+AAAA
--- /dev/null
+>TEST2
+LLLL
--- /dev/null
+>TEST3
+AAARG
--- /dev/null
+>TEST1
+AAAA
--- /dev/null
+>TEST2
+LLLL
--- /dev/null
+>TEST3
+AAARG
--- /dev/null
+#---JalviewX Properties File---
+#Fri Apr 25 09:54:25 BST 2014
+SCREEN_Y=768
+SCREEN_X=936
+SHOW_WSDISCOVERY_ERRORS=true
+LATEST_VERSION=2.8.0b1
+SHOW_CONSERVATION=true
+JALVIEW_RSS_WINDOW_SCREEN_WIDTH=550
+JAVA_CONSOLE_SCREEN_WIDTH=450
+LAST_DIRECTORY=/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples
+ID_ITALICS=true
+SORT_ALIGNMENT=No sort
+SHOW_IDENTITY=true
+WSMENU_BYHOST=false
+SEQUENCE_LINKS=EMBL-EBI Search|http\://www.ebi.ac.uk/ebisearch/search.ebi?db\=allebi&query\=$SEQUENCE_ID$
+SHOW_FULLSCREEN=false
+RECENT_URL=http\://www.jalview.org/examples/exampleFile_2_7.jar
+FONT_NAME=SansSerif
+BLC_JVSUFFIX=true
+VERSION_CHECK=false
+YEAR=2011
+SHOW_DBREFS_TOOLTIP=true
+MSF_JVSUFFIX=true
+SCREENGEOMETRY_HEIGHT=1600
+JAVA_CONSOLE_SCREEN_Y=475
+JAVA_CONSOLE_SCREEN_X=830
+PFAM_JVSUFFIX=true
+PIR_JVSUFFIX=true
+STARTUP_FILE=http\://www.jalview.org/examples/exampleFile_2_3.jar
+JAVA_CONSOLE_SCREEN_HEIGHT=162
+PIR_MODELLER=false
+GAP_SYMBOL=-
+SHOW_QUALITY=true
+SHOW_GROUP_CONSERVATION=false
+SHOW_JWS2_SERVICES=true
+SHOW_NPFEATS_TOOLTIP=true
+FONT_STYLE=plain
+ANTI_ALIAS=false
+SORT_BY_TREE=false
+RSBS_SERVICES=|Multi-Harmony|Analysis|Sequence Harmony and Multi-Relief (Brandt et al. 2010)|hseparable,gapCharacter\='-',returns\='ANNOTATION'|?tool\=jalview|http\://zeus.few.vu.nl/programs/shmrwww/index.php?tool\=jalview&groups\=$PARTITION\:min\='2',minsize\='2',sep\=' '$&ali_file\=$ALIGNMENT\:format\='FASTA',writeasfile$
+AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+JALVIEW_RSS_WINDOW_SCREEN_HEIGHT=328
+SHOW_GROUP_CONSENSUS=false
+SHOW_CONSENSUS_HISTOGRAM=true
+SHOW_OVERVIEW=false
+AUTHORS=J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+FIGURE_AUTOIDWIDTH=false
+SCREEN_WIDTH=900
+ANNOTATIONCOLOUR_MIN=ffc800
+SHOW_STARTUP_FILE=false
+RECENT_FILE=examples/uniref50.fa\t/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples/RF00031_folded.stk\t/Volumes/Data/Users/jimp/bs_ig_mult.out
+DEFAULT_FILE_FORMAT=FASTA
+SHOW_JAVA_CONSOLE=false
+VERSION=2.8b1
+FIGURE_USERIDWIDTH=
+WSMENU_BYTYPE=false
+DEFAULT_COLOUR=None
+NOQUESTIONNAIRES=true
+JALVIEW_NEWS_RSS_LASTMODIFIED=Apr 23, 2014 2\:53\:26 PM
+BUILD_DATE=01 November 2013
+PILEUP_JVSUFFIX=true
+SHOW_CONSENSUS_LOGO=false
+SCREENGEOMETRY_WIDTH=2560
+SHOW_ANNOTATIONS=true
+JALVIEW_RSS_WINDOW_SCREEN_Y=0
+USAGESTATS=false
+JALVIEW_RSS_WINDOW_SCREEN_X=0
+SHOW_UNCONSERVED=false
+SHOW_JVSUFFIX=true
+DAS_LOCAL_SOURCE=
+SCREEN_HEIGHT=650
+ANNOTATIONCOLOUR_MAX=ff0000
+AUTO_CALC_CONSENSUS=true
+FASTA_JVSUFFIX=true
+DAS_ACTIVE_SOURCE=uniprot\t
+JWS2HOSTURLS=http\://www.compbio.dundee.ac.uk/jabaws
+PAD_GAPS=false
+CLUSTAL_JVSUFFIX=true
+SHOW_ENFIN_SERVICES=true
+FONT_SIZE=10
+RIGHT_ALIGN_IDS=false
+USE_PROXY=false
+WRAP_ALIGNMENT=false
+#DAS_REGISTRY_URL=http\://www.dasregistry.org/das/ # retired 01/05/2015
+DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
+BOOTSTRAP_TEST=true
+NOTBOOTSTRAP_TEST=true
import static org.testng.Assert.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
+import java.lang.reflect.InvocationTargetException;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.gui.Preferences;
import jalview.gui.StructureViewer;
import jalview.io.FileFormat;
import jalview.io.FileLoader;
-import java.lang.reflect.InvocationTargetException;
-
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
@Test(singleThreaded = true)
public class JmolViewerTest
{
@AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
- jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
}
@Test(groups = { "Functional" })
@AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
}
@AfterMethod(alwaysRun = true)
@AfterMethod(alwaysRun = true)
public void tearDown()
{
- Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
}
/**
import java.io.IOException;
import java.util.HashMap;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import jalview.api.FeatureColourI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcher;
public class FeatureSettingsTest
{
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ /*
+ * use read-only test properties file
+ */
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Jalview.main(new String[] { "-nonews" });
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void tearDown()
+ {
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
/**
* Test a roundtrip of save and reload of feature colours and filters as XML
*
doStuffInJalview(f);
- Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
checkUsedMemory(MAX_RESIDUAL_HEAP);
}
// reset mock response
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
// close desktop windows/frames
- Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
// reset debug delay
Jalview2XML.setDebugDelaySave(20);
+ // load normal testprops
+ Cache.loadProperties("test/jalview/testProps.jvprops");
}
@BeforeMethod(alwaysRun = true)
// reset mock response
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
// close desktop windows/frames
- Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
// reset debug delay
Cache.setProperty("DEBUG_DELAY_SAVE", "false");
Jalview2XML.setDebugDelaySave(3);
Assert.assertTrue(end - start < 500,
"Quit-with-no-save-needed took too long (" + (end - start)
+ "ms)");
- Desktop.instance.closeAll_actionPerformed(null);
}
@Test(groups = { "Functional" }, singleThreaded = true, priority = 10)
Assert.assertEquals(response, QResponse.QUIT);
Assert.assertTrue(end - start > 2900,
"Quit-whilst-saving was too short (" + (end - start) + "ms)");
-
- Desktop.instance.closeAll_actionPerformed(null);
}
@Test(groups = { "Functional" }, singleThreaded = true, priority = 9)
// if not saved this would be CANCEL_QUIT
Assert.assertEquals(response, QResponse.QUIT);
- Desktop.instance.closeAll_actionPerformed(null);
}
@Test(groups = { "Functional" }, singleThreaded = true, priority = 9)
// if not saved this would be CANCEL_QUIT
Assert.assertEquals(response, QResponse.QUIT);
- Desktop.instance.closeAll_actionPerformed(null);
}
@Test(groups = { "Functional" }, singleThreaded = true, priority = 1)
QResponse response = QuitHandler.getQuitResponse(true);
Assert.assertEquals(response, QResponse.CANCEL_QUIT);
- Desktop.instance.closeAll_actionPerformed(null);
}
@Test(groups = { "Functional" }, singleThreaded = true, priority = 1)
QResponse response = QuitHandler.getQuitResponse(false);
Assert.assertEquals(response, QResponse.QUIT);
- Desktop.instance.closeAll_actionPerformed(null);
}
@Test(groups = { "Functional" }, singleThreaded = true, priority = 11)
"Force-Quit-whilst-saving was too long (" + (end - start)
+ "ms)");
- Desktop.instance.closeAll_actionPerformed(null);
}
}
@AfterMethod(alwaysRun = true)
public void tearDown()
{
- Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
}
@Test(groups = "Functional")
}
assertEquals(dna.length(), 51200);
AlignFrame alignFrame = new FileLoader()
- .LoadFileWaitTillLoaded("dna "+dna, DataSourceType.PASTE);
+ .LoadFileWaitTillLoaded("dna " + dna, DataSourceType.PASTE);
SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
AlignViewport av = alignFrame.getViewport();
av.setScaleAboveWrapped(true);
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
+import java.io.File;
+import java.util.List;
+
+import org.junit.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.SequenceFeatures;
import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureImportSettings.StructureParser;
-import java.io.File;
-import java.util.List;
-
-import org.junit.Assert;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
public class AnnotatedPDBFileInputTest
{
@AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
- jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
-
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
}
@Test(groups = { "Functional" })
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
-import jalview.analysis.CrossRef;
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentTest;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.CrossRefAction;
-import jalview.gui.Desktop;
-import jalview.gui.JvOptionPane;
-import jalview.gui.SequenceFetcher;
-import jalview.project.Jalview2XML;
-import jalview.util.DBRefUtils;
-
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import jalview.analysis.CrossRef;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentTest;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.CrossRefAction;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.SequenceFetcher;
+import jalview.project.Jalview2XML;
+import jalview.util.DBRefUtils;
import junit.extensions.PA;
@Test(singleThreaded = true)
}
else
{
- Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
// recover stored project
af = new FileLoader(false).LoadFileWaitTillLoaded(
savedProjects.get(first).toString(), DataSourceType.FILE);
}
else
{
- Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
pass3 = 0;
// recover stored project
File storedProject = savedProjects.get(nextxref);
}
else
{
- Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
// recover stored project
File storedProject = savedProjects.get(nextnextxref);
if (storedProject == null)
cra_views2.add(af2.getViewport().getAlignPanel());
cra_views2.add(((jalview.gui.AlignViewport) af2
.getViewport().getCodingComplement())
- .getAlignPanel());
+ .getAlignPanel());
}
else
// bottom view, then top
cra_views2.add(((jalview.gui.AlignViewport) af2
.getViewport().getCodingComplement())
- .getAlignPanel());
+ .getAlignPanel());
cra_views2.add(af2.getViewport().getAlignPanel());
}
Assert.assertEquals(cra_views2.size(), 2);
*/
package jalview.io;
+import java.util.Date;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeTest;
+
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentAnnotation;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
-import java.util.Date;
-
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeTest;
-
public class Jalview2xmlBase
{
@AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
- jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
}
@BeforeTest(alwaysRun = true)
import static org.testng.AssertJUnit.assertTrue;
-import jalview.datamodel.SequenceGroup;
-import jalview.gui.AlignFrame;
-import jalview.gui.JvOptionPane;
-
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.datamodel.SequenceGroup;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+
/**
* tests which verify that properties and preferences are correctly interpreted
* when exporting/importing data
@AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
- jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
}
--- /dev/null
+15 157
+FER_CAPAA -----------------------------------------------------------A
+FER_CAPAN MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA
+FER1_SOLLC MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA
+Q93XJ9_SOLTU MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA
+FER1_PEA MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA
+Q7XA98_TRIPR MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMA
+FER1_MESCR MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMA
+FER1_SPIOL MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMA
+FER3_RAPSA -----------------------------------------------------------A
+FER2_ARATH MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMA
+FER_BRANA -----------------------------------------------------------A
+FER1_ARATH MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA
+Q93Z60_ARATH MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA
+FER1_MAIZE MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQA
+O80429_MAIZE MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQA
+
+SYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG
+SYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG
+SYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDG
+SYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDG
+SYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDG
+TYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDG
+AYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDG
+AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQ
+TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ
+TYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ
+TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDE
+TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ
+TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ
+TYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ
+TYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQ
+
+NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG-
+NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG-
+NFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA-
+KFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA-
+SFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA-
+SFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA-
+SFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA-
+SFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA-
+SFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV--
+SFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV--
+SFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV--
+SFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM--
+SFLDD--------------------------------
+SYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA
+SFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL--
--- /dev/null
+15 157
+FER_CAPAA -----------------------------------------------------------A
+FER_CAPAN MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA
+FER1_SOLLCMA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA
+Q93XJ9_SOLMA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA
+FER1_PEA MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA
+Q7XA98_TRIMATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMA
+FER1_MESCRMAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMA
+FER1_SPIOLMAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMA
+FER3_RAPSA-----------------------------------------------------------A
+FER2_ARATHMAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMA
+FER_BRANA -----------------------------------------------------------A
+FER1_ARATHMAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA
+Q93Z60_ARAMAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA
+FER1_MAIZEMATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQA
+O80429_MAIMAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQA
+
+SYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG
+SYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG
+SYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDG
+SYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDG
+SYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDG
+TYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDG
+AYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDG
+AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQ
+TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ
+TYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ
+TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDE
+TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ
+TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ
+TYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ
+TYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQ
+
+NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG-
+NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG-
+NFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA-
+KFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA-
+SFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA-
+SFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA-
+SFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA-
+SFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA-
+SFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV--
+SFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV--
+SFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV--
+SFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM--
+SFLDD--------------------------------
+SYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA
+SFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL--
--- /dev/null
+15 157
+FER_CAPAA -----------------------------------------------------------A
+FER_CAPAN MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA
+FER1_SOLLCMA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA
+Q93XJ9_SOLMA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA
+FER1_PEA MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA
+Q7XA98_TRIMATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMA
+FER1_MESCRMAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMA
+FER1_SPIOLMAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMA
+FER3_RAPSA-----------------------------------------------------------A
+FER2_ARATHMAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMA
+FER_BRANA -----------------------------------------------------------A
+FER1_ARATHMAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA
+Q93Z60_ARAMAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA
+FER1_MAIZEMATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQA
+O80429_MAIMAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQA
+
+SYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG
+SYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG
+SYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDG
+SYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDG
+SYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDG
+TYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDG
+AYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDG
+AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQ
+TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ
+TYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ
+TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDE
+TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ
+TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ
+TYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ
+TYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQ
+
+NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG-
+NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG-
+NFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA-
+KFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA-
+SFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA-
+SFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA-
+SFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA-
+SFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA-
+SFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV--
+SFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV--
+SFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV--
+SFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM--
+SFLDD--------------------------------
+SYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA
+SFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL--
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
}
PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
String content = ContactMatrix.contactToFloatString(dummyMat);
- Assert.assertTrue(content.contains("\t1.")); // at least one element must be 1
- float[][] vals = ContactMatrix.fromFloatStringToContacts(content, sq.getLength(), sq.getLength());
- assertEquals(vals[3][4],paevals[3][4]);
+ Assert.assertTrue(content.contains("\t1.")); // at least one element must be
+ // 1
+ float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
+ sq.getLength(), sq.getLength());
+ assertEquals(vals[3][4], paevals[3][4]);
dummyMat.makeGroups(0.5f, false);
Assert.assertNotSame(dummyMat.getNewick(), "");
AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups());
Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
- Assert.assertEquals( restoredMat.getNewick(),dummyMat.getNewick());
-
-
+ Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
+
}
}
import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
import jalview.analysis.GeneticCodes;
import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
import jalview.util.matcher.Condition;
import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.testng.annotations.Test;
-
public class FeatureRendererTest
{
+ @BeforeMethod(alwaysRun = true)
+ public void closeAll()
+ {
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
@Test(groups = "Functional")
public void testFindAllFeatures()
{
Jalview.main(
new String[]
- { "-nonews", "-props", "test/jalview/testProps.jvprops" });
+ { "-nonews", "--props", "test/jalview/testProps.jvprops" });
// codons for MCWHSE
String cdsSeq = ">cds\nATGtgtTGGcacTCAgaa";
import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
+import java.awt.Color;
+import java.util.Iterator;
+import java.util.Map;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.io.FileLoader;
import jalview.schemes.ClustalxColourScheme.ClustalColour;
-import java.awt.Color;
-import java.util.Iterator;
-import java.util.Map;
-
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
public class ColourSchemesTest
{
/*
@AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
}
@Test(groups = "Functional")
{
// for some reason 'BeforeMethod' (which should be inherited from
// Jalview2XmlBase isn't always called)...
- Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
try
{
Thread.sleep(200);
--- /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.File;
+import java.io.IOException;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+@Test
+public class FileUtilsTest
+{
+ @Test(groups = "Functional", dataProvider = "patternsAndMinNumFiles")
+ public void testJavaFileGlob(String pattern, int atLeast, int atMost)
+ {
+ List<File> files = FileUtils.getFilesFromGlob(pattern);
+ if (atLeast != -1)
+ {
+ Assert.assertTrue(files.size() > atLeast,
+ "Did not find more than " + atLeast + " files with " + pattern
+ + " (found " + files.size() + ")");
+ }
+ if (atLeast != -1)
+ {
+ Assert.assertTrue(files.size() > atLeast,
+ "Did not find more than " + atLeast + " files with " + pattern
+ + " (found " + files.size() + ")");
+ }
+ if (atMost != -1)
+ {
+ Assert.assertTrue(files.size() < atMost,
+ "Did not find fewer than " + atMost + " files with " + pattern
+ + " (found " + files.size() + ")");
+ }
+ }
+
+ @Test(groups = "Functional", dataProvider = "dirnamesAndBasenames")
+ public void testDirnamesAndBasenames(String filename, int where,
+ String dirname, String basename, String notInDirname)
+ {
+ File file = new File(filename);
+ String d = FileUtils.getDirname(file);
+ String b = FileUtils.getBasename(file);
+ Assert.assertEquals(b, basename);
+ if (where == 0)
+ Assert.assertEquals(d, dirname);
+ else if (where < 0)
+ Assert.assertTrue(d.startsWith(dirname),
+ "getDirname(" + file.getPath() + ")=" + d
+ + " didn't start with '" + dirname + "'");
+ else if (where > 0)
+ Assert.assertTrue(d.endsWith(dirname), "getDirname(" + file.getPath()
+ + ")=" + d + " didn't end with '" + d + "'");
+
+ // ensure dirname doesn't end with basename (which means you can't use same
+ // filename as dir in tests!)
+ Assert.assertFalse(d.endsWith(b));
+
+ if (notInDirname != null)
+ Assert.assertFalse(d.contains(notInDirname));
+ }
+
+ @DataProvider(name = "patternsAndMinNumFiles")
+ public Object[][] patternsAndMinNumFiles()
+ {
+ return new Object[][] { { "src/**/*.java", 900, 100000 },
+ { "src/**.java", 900, 100000 },
+ { "test/**/*.java", 250, 2500 },
+ { "test/**.java", 250, 2500 },
+ { "help/**/*.html", 100, 1000 },
+ { "test/**/F*.java", 15, 150 },
+ { "test/jalview/*/F*.java", 10, 15 }, // 12 at time of writing
+ { "test/jalview/**/F*.java", 18, 30 }, // 20 at time of writing
+ { "test/jalview/util/F**.java", 1, 5 }, // 2 at time of writing
+ { "src/jalview/b*/*.java", 14, 19 }, // 15 at time of writing
+ { "src/jalview/b**/*.java", 20, 25 }, // 22 at time of writing
+ };
+ }
+
+ @DataProvider(name = "dirnamesAndBasenames")
+ public Object[][] dirnamesAndBasenames()
+ {
+ String homeDir = null;
+ try
+ {
+ homeDir = new File(System.getProperty("user.home"))
+ .getCanonicalPath();
+ } catch (IOException e)
+ {
+ System.err.println("Problem getting canonical home dir");
+ e.printStackTrace();
+ }
+ return new Object[][] { // -1=startsWith, 0=equals, 1=endsWith
+ { "~/hello/sailor", -1, homeDir, "sailor", "~" }, //
+ { "~/hello/sailor", 1, "/hello", "sailor", "~" }, //
+ { "./examples/uniref50.fa", -1, "/", "uniref50", "." }, //
+ { "./examples/uniref50.fa", 1, "/examples", "uniref50", "." }, //
+ { "examples/uniref50.fa", 1, "/examples", "uniref50", ".fa" }, //
+ };
+ }
+}
git://source.jalview.org / jalview.git / commitdiff