<name>Endgaps</name>
<description>Score pairs with endgaps same as gap-gap pairs</description>
<optionNames>-E</optionNames>
- <optionNames>--endgaps</optionNames>
- <defaultValue>-E</defaultValue>
</options>
<options isRequired='false'>
<name>Most Informative Sequence</name>
<name>Partition Function</name>
<description>Output partition function and probability matrix</description>
<optionNames>-p</optionNames>
- <optionNames>--partfunc</optionNames>
- <defaultValue>-p</defaultValue>
- </options>
- <options isRequired='false'>
- <name>p0</name>
- <description>deactivates the calculation of the pair probabilities</description>
- <optionNames>-p0</optionNames>
- </options>
- <options isRequired='false'>
- <name>color</name>
- <description>Consensus structure plot is colored</description>
- <optionNames>--color</optionNames>
- </options>
- <options isRequired='false'>
- <name>Alignment</name>
- <description>Output structure annotated alignment</description>
- <optionNames>--aln</optionNames>
- </options>
- <options isRequired='false'>
- <name>No Postscript</name>
- <description>Do not produce postscript output</description>
- <optionNames>--noPS</optionNames>
</options>
<options isRequired='false'>
<name>Circular</name>
<description>Assume circular RNA molecule</description>
<optionNames>-c</optionNames>
- <optionNames>--circ</optionNames>
- <defaultValue>-c</defaultValue>
</options>
<!-- Not Currently available with circular structures (-c) -->
<options isRequired='false'>
<name>G-Quadruplex</name>
<description>Incorporate G-Quadruplex formation into prediction algorithm</description>
<optionNames>-g</optionNames>
- <optionNames>--gquad</optionNames>
- <defaultValue>-g</defaultValue>
</options>
<options isRequired='false'>
<name>d2</name>
<name>Ribosum Scoring</name>
<description>Use Ribosum Scoring Matrix</description>
<optionNames>-r</optionNames>
- <optionNames>--ribosum_scoring</optionNames>
- <defaultValue>-r</defaultValue>
</options>
<options isRequired='false'>
<name>d2</name>
<description>Maximum Expected Accuracy Structure</description>
<optionNames>--MEA</optionNames>
</options>
-<!-- Constraints are entered on the command line followed by the input .aln file
- Causing problems for a batch RNAalifold execution system -->
-<!--
- <option isRequired='false'>
- <name>Constraints</name>
- <description>Structures calculated subject to constraints</description>
- <optionNames>-C</optionNames>
- <validValue>
- <type>String</type>
- </validValue>
- </option> -->
<prmSeparator> </prmSeparator>
- <parameters isRequired='false'>
- <name>Stochastic Backtrack</name>
- <description>Compute a number of random structures</description>
- <optionNames>-s</optionNames>
-<!-- Having multiple optionNames requires a default value but -->
-<!-- in a parameter defaultValue refers to the argument -->
-<!-- <optionNames>-stochBT</optionNames> -->
- <defaultValue>5</defaultValue>
- <validValue>
- <type>Integer</type>
- <min>1</min>
- <max>100000</max>
- </validValue>
- </parameters>
- <parameters isRequired='false'>
- <name>stochBT_en</name>
- <description>Print Backtrack structures</description>
- <optionNames>--stochBT_en</optionNames>
- <defaultValue>5</defaultValue> <!-- arbitrary -->
- <validValue>
- <type>Integer</type>
- <min>1</min>
- <max>100000</max>
- </validValue>
- </parameters>
+
<parameters isRequired='false'>
<name>scaling factor</name>
<description>In calculating pf use scale*mfe as estimate for ensemble free energy]</description>
<optionNames>-S</optionNames>
-<!-- <optionNames>-pfScale</optionNames> -->
<defaultValue>1.07</defaultValue>
<validValue>
<type>Float</type>
</parameters>
<parameters isRequired='false'>
<name>Temperature</name>
- <description>Rescale Energy parameterss to Temperature</description>
+ <description>Rescale Energy parameters to Temperature</description>
<optionNames>-T</optionNames>
-<!-- <optionNames>-temp</optionNames> -->
<defaultValue>37</defaultValue>
<validValue>
<type>Float</type>
</validValue>
</parameters>
<parameters isRequired='false'>
- <name>Dangling End</name>
- <description>How to treat Dangling End energies for bases adjacent to helices</description>
- <optionNames>-d</optionNames>
-<!-- <optionNames>-dangles</optionNames> -->
- <defaultValue>2</defaultValue>
- <validValue>
- <type>Integer</type>
- <min>0</min>
- <max>100000</max>
- </validValue>
- </parameters>
- <parameters isRequired='false'>
<name>cfactor</name>
<description>weight of covariance term</description>
<optionNames>--cfactor</optionNames>
</validValue>
</parameters>
-<!-- How to deal with default/possible values for parameter files? -->
-<!-- <parameters isRequired='false'> -->
-<!-- <name>Ribosum File</name> -->
-<!-- <description>Use Specified Ribosum Matrix</description> -->
-<!-- <optionNames>-R</optionNames> -->
-<!-- <optionNames>-ribosum_file</optionNames> -->
-<!-- </parameters> -->
-<!-- <parameters isRequired='false'> -->
-<!-- <name>Paramfile</name> -->
-<!-- <description>Use Energy parameters from a file</description> -->
-<!-- <optionNames>-P</optionNames> -->
-<!-- <optionNames>-paramFile</optionNames> -->
-<!-- <validValue> -->
-<!-- <type>String</type> -->
-<!-- </validValue> -->
-<!-- </parameters> -->
-
- <!-- The values of this parameter are in the form of a comma separated
- list of allowed pairs. This makes a complete parameter list
- too large to be represented as a list of possible values
- How to deal with this? -->
- <!-- just support the most biologically viable pairs? -->
-
- <parameters isRequired='false'>
- <name>Allow Pairs</name>
- <description>allow pairs in addition to AU, GC and GU</description>
- <optionNames>--nsp</optionNames>
- <defaultValue>-GA</defaultValue>
- <possibleValues>-GA</possibleValues>
- <possibleValues>-AG</possibleValues>
- </parameters>
- <!-- Is dependant on -p (partfunc) -->
- <parameters isRequired='false'>
- <name>betaScale</name>
- <description>Set scaling of Boltzmann factors</description>
- <optionNames>--betaScale</optionNames>
- <defaultValue>1.0</defaultValue>
- <validValue>
- <type>Float</type>
- <min>0</min>
- <max>100000</max>
- </validValue>
- </parameters>
</runnerConfig>
\ No newline at end of file
// alifold out line patterns\r
static String ps = "\\s*";\r
static String alignmentP = "^"+seqP+ps+"$";\r
- static String stdStructP = "^"+structP+s+"\\("+ps+floatP+s+floatP+s+floatP+ps+"\\)"+ps+"$";\r
+ static String mfeStructP = "^"+structP+s+"\\("+ps+floatP+s+floatP+s+floatP+ps+"\\)"+ps+"$";\r
static String justStructP = "^"+structP+ps+"$";\r
static String stochBTStructP = "^"+structP+s+floatP+s+floatP+ps+"$";\r
static String PStructP = "^"+structP+s+"\\["+ps+floatP+ps+"\\]"+ps+"$";\r
static String MEAStructP = "^"+structP+s+"\\{"+ps+floatP+s+"MEA="+floatP+ps+"\\}"+ps+"$";\r
static String freeEnergyP = "^"+ps+"free energy of ensemble"+ps+"="+ps+floatP+ps+"kcal/mol"+ps+"$";\r
static String ensembleFreqP = "^"+ps+"frequency of mfe structure in ensemble "+floatP+ps+"$";\r
-\r
+ \r
+ \r
public static RNAStructScoreManager readRNAStructStream(InputStream stdout)\r
throws IOException {\r
\r
assert (Pattern.matches(AlifoldLine.alignment.regex, fline)) :\r
error + "Sequence Alignment Expected";\r
structs.add(fline.trim());\r
- data.add(newEmptyScore(AlifoldResult.alifoldSeq));\r
+ data.add(newEmptyScore(AlifoldResult.consensusAlignment));\r
\r
fline = reader.readLine();\r
- assert (Pattern.matches(AlifoldLine.stdStruct.regex, fline)) :\r
+ assert (Pattern.matches(AlifoldLine.mfeStruct.regex, fline)) :\r
error + "Consensus Structure and Energy Expected";\r
Scanner sc = new Scanner(fline);\r
structs.add(sc.next());\r
for (int i = 0; i < 3; i++) {\r
scores.add(Float.parseFloat(sc.findInLine(floatP)));\r
}\r
- data.add(newSetScore(AlifoldResult.alifold, scores));\r
+ data.add(newSetScore(AlifoldResult.mfeStructure, scores));\r
\r
// Now the alifold stdout file formats diverge based on arguments\r
fline = reader.readLine();\r
structs.add(sc.next());\r
scores.add(Float.parseFloat(sc.findInLine(floatP)));\r
scores.add(Float.parseFloat(nsc.findInLine(floatP)));\r
- data.add(newSetScore(AlifoldResult.alifoldP, scores));\r
+ data.add(newSetScore(AlifoldResult.contactProbabilityStructure, scores));\r
// Jump line\r
sline = reader.readLine();\r
}\r
for (int i = 0; i < 3; i++) {\r
scores.add(Float.parseFloat(sc.findInLine(floatP)));\r
}\r
- data.add(newSetScore(AlifoldResult.alifoldCentroid, scores));\r
+ data.add(newSetScore(AlifoldResult.centroidStructure, scores));\r
}\r
else if (ftype.equals(AlifoldLine.MEAStruct)) {\r
structs.add(sc.next());\r
for (int i = 0; i < 2; i++) {\r
scores.add(Float.parseFloat(sc.findInLine(floatP)));\r
}\r
- data.add(newSetScore(AlifoldResult.alifoldMEA, scores));\r
+ data.add(newSetScore(AlifoldResult.MEAStucture, scores));\r
}\r
else if (ftype.equals(AlifoldLine.justStruct)) {\r
structs.add(sc.next());\r
- data.add(newEmptyScore(AlifoldResult.alifoldStochBT));\r
+ data.add(newEmptyScore(AlifoldResult.stochBTStructure));\r
}\r
else if (ftype.equals(AlifoldLine.stochBTStruct)) {\r
structs.add(sc.next());\r
scores.add(sc.nextFloat());\r
scores.add(sc.nextFloat());\r
- data.add(newSetScore(AlifoldResult.alifoldStochBT, scores));\r
+ data.add(newSetScore(AlifoldResult.stochBTStructure, scores));\r
}\r
else if (ftype.equals(AlifoldLine.freeEnergy)) {\r
assert (sline != null \r
+ "frequency of mfe structure in ensemble");\r
scores.add(Float.parseFloat(sc.findInLine(floatP)));\r
scores.add(Float.parseFloat(nsc.findInLine(floatP)));\r
- data.add(newSetScore(AlifoldResult.alifoldMetadata, scores));\r
+ data.add(newSetScore(AlifoldResult.ensembleValues, scores));\r
// jump line\r
sline = reader.readLine();\r
}\r
\r
assert(!ftype.equals(AlifoldLine.ensembleFreq)) :\r
error + "Wasn't expecting 'frequency of mfe structure'!";\r
- assert(!ftype.equals(AlifoldLine.stdStruct)) :\r
+ assert(!ftype.equals(AlifoldLine.mfeStruct)) :\r
error + "'Standard output' line at a place other than line 2!";\r
assert(!ftype.equals(AlifoldLine.alignment)) :\r
error + "Wasn't expecting an alignment sequence!";\r
for (int i = 0; i < rangeHolder.size(); i++) {\r
ArrayList<Float> singleS = new ArrayList<Float>(Arrays.asList(scores.get(i)));\r
TreeSet<Range> singleR = new TreeSet<Range>(Arrays.asList(rangeHolder.get(i)));\r
- sHolder.add(new Score(AlifoldResult.alifoldSeq, singleS, singleR));\r
+ sHolder.add(new Score(AlifoldResult.contactProbabilities, singleS, singleR));\r
}\r
\r
data.set(0, sHolder);\r
}\r
\r
static enum AlifoldLine {\r
- stdStruct (stdStructP),\r
+ mfeStruct (mfeStructP),\r
justStruct (justStructP),\r
stochBTStruct (stochBTStructP),\r
PStruct (PStructP),\r
\r
//Something to put in the Score objects of the alifold result which gives information\r
//about what kind of sequence it is holding in its String Id.\r
- static enum AlifoldResult {\r
- alifold, alifoldP, alifoldMEA, alifoldCentroid, alifoldStochBT, alifoldSeq, alifoldMetadata\r
+\r
+ public static enum AlifoldResult {\r
+ mfeStructure, contactProbabilityStructure, MEAStucture, centroidStructure, stochBTStructure, consensusAlignment, ensembleValues, contactProbabilities\r
}\r
\r
- \r
\r
// Print the full regex Strings for testing \r
public static void main(String[] args) {\r
*/\r
\r
\r
+\r
+ \r
@Override\r
public int compareTo(Score o) {\r
if (this.method.compareTo(o.method) != 0) {\r
}\r
\r
private ScoreManager(Map<String, Set<Score>> data) {\r
- System.out.println("A ScoreManager was created!!");\r
\r
- \r
List<ScoreHolder> seqScores = new ArrayList<ScoreHolder>();\r
for (Map.Entry<String, Set<Score>> singleSeqScores : data.entrySet()) {\r
seqScores.add(new ScoreHolder(singleSeqScores.getKey(),\r
}\r
\r
public static ScoreManager newInstance(Map<String, Set<Score>> data) {\r
- System.out.println("A ScoreManager was created!!");\r
-\r
\r
return new ScoreManager(data);\r
}\r
public static ScoreManager newInstanceSingleScore(\r
Map<String, Score> seqScoresMap) {\r
\r
- System.out.println("A ScoreManager was created!!");\r
-\r
- \r
Map<String, Set<Score>> multipleScoresMap = new TreeMap<String, Set<Score>>();\r
for (Map.Entry<String, Score> seqScore : seqScoresMap.entrySet()) {\r
Set<Score> scores = new TreeSet<Score>();\r
}\r
\r
public static ScoreManager newInstanceSingleSequence(Set<Score> data) {\r
- System.out.println("A ScoreManager was created!!");\r
-\r
- \r
return new ScoreManager(ScoreManager.SINGLE_ENTRY_KEY,\r
new TreeSet(data));\r
}\r
public static final String CATEGORY_ALIGNMENT = "Alignment";\r
public static final String CATEGORY_DISORDER = "Protein Disorder";\r
public static final String CATEGORY_CONSERVATION = "Conservation";\r
+ public static final String CATEGORY_RNASTRUCT = "RNA Structure Prediction";\r
\r
public String name;\r
Set<Services> services;\r
Category conservation = new Category(CATEGORY_CONSERVATION,\r
conservation_services);\r
\r
+ Set<Services> rnastruct_services = new HashSet<Services>();\r
+ rnastruct_services.add(Services.RNAalifoldWS);\r
+ \r
+ Category rnastruct = new Category(CATEGORY_RNASTRUCT,\r
+ rnastruct_services);\r
+ \r
Set<Category> categories = new HashSet<Category>();\r
categories.add(alignment);\r
categories.add(disorder);\r
categories.add(conservation);\r
+ categories.add(rnastruct);\r
\r
return categories;\r
}\r
git://source.jalview.org / jabaws.git / commitdiff