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java.lang.Object | +--org.emboss.jemboss.parser.ParseAcd
ACD (Ajax command line definition) file parser.
| Field Summary | |
| private  java.lang.String | attrparameter data type | 
| private  Dependent[] | depaaray of dependent variables | 
| private  java.lang.String | groupListString of the groups application belongs to | 
| private  boolean | isPrimaryGptrue if primary group is defined | 
| private  boolean | isSecondaryGptrue if secondary group is defined | 
| private  java.util.Vector | listdefaultdefault for list or select data type | 
| private  int | mlistnumber of list & selection fields - multiple selection | 
| private  int | nboolnumber of checkbox fields | 
| private  int | nflistnumber of filelist fields | 
| private  int | nfloatnumber of float fields | 
| private  int | nintnumber of integer fields | 
| private  int | nlistnumber of list & selection fields - single selection | 
| private  int | nrangenumber of range fields | 
| private  int | nsectionnumber of sections | 
| private  int | nseqsnumber of sequence fields | 
| private  int | nsubsectionnumber of subsections | 
| private  int | ntextfnumber of text fields | 
| private  int | numOfDependentsnumber of dependent variables | 
| private  int | numofFieldsnumber of ACD fields | 
| private  int | numofParamsnumber of parameters in a field | 
| private  double | nvaluedouble value of a parameter | 
| private  java.lang.String | primaryGpprimary group | 
| private  java.lang.String | secondaryGpsecondary group | 
| private  java.lang.String | svaluestring value of a parameter | 
| private  java.util.Vector | vappFvector containing the application fields | 
| Constructor Summary | |
| ParseAcd(java.lang.String acdText,
         boolean groups)The constructor takes the ACD as a string. | |
| Method Summary | |
| protected  java.lang.String | formatHelpText(java.lang.String help)Limits the length of the line for the help text used in the tool tips. | 
|  double | getDefaultParamValueDbl(int field)Return a double default parameter | 
|  java.lang.String | getDefaultParamValueStr(int field)Gets a String default parameter. | 
|  Dependent[] | getDependents()Gets the dependents associated with the ACD. | 
|  java.lang.String | getExpectedCPU()Finds any expected cpu level indicator (low, medium, high) | 
|  int | getGuiHandleNumber(int field)Gets the handle for a gui component on the Jemboss form. | 
|  java.lang.String | getHelpParamValue(int field)Finds the help parameter in an ACD field. | 
|  java.lang.String | getInfoParamValue(int field)Finds the prompt, info or help parameter in an ACD field, in that order. | 
|  java.lang.String[] | getList(int field)Used for a list data type to put the list items in a String array. | 
|  java.lang.String | getListLabel(int field,
             int index)For a list data type determine the appropriate String entry. | 
|  java.util.Vector | getListOrSelectDefault()Use this after getList or getSelect to retrieve default | 
|  java.lang.String | getMaxParam(int field)Locates the max parameter in a field and returns it as a String. | 
|  java.lang.String | getMinParam(int field)Locates the min parameter in a field and returns it as a String. | 
|  int | getNumBool()Gets the number of boolean data types in the ACD. | 
|  int | getNumFileList()Gets the number of filelist data types in the ACD | 
|  int | getNumList()Gets the number of list & selection data types in the ACD, using single list selection | 
|  int | getNumMList()Gets the number of list & selection data types in the ACD, using multiple list selection | 
|  int | getNumNfloat()Gets the number of float data types in the ACD. | 
|  int | getNumNint()Gets the number of int data types in the ACD. | 
|  int | getNumOfDependents()Gets the number of dependent parameters in the ACD. | 
|  int | getNumofFields()Gets the number of fields in the ACD file. | 
|  int | getNumofParams(int field)Gets the number of parameters in a ACD field. | 
|  int | getNumRange() | 
|  int | getNumSection()Gets the number of sections in the ACD | 
|  int | getNumSeq()Gets the number of seqset, seqall & sequence data types in the ACD | 
|  int | getNumSubsection()Gets the number of nested sections in the ACD | 
|  int | getNumTextf()Gets the number of float, string, seqout, outfile, infile, regexp, codon & featout data types in the ACD. | 
|  java.lang.String | getOutputSequenceFile(int field)Gets the name of the output sequence field (seqout). | 
|  java.lang.String | getParameterAttribute(int field,
                      int param)Get a specified parameter attribute. | 
|  double | getParamValueDbl(int field,
                 int param)Gets the double value of a parameter. | 
|  java.lang.String | getParamValueStr(int field,
                 int param)Gets the String value of a parameter. | 
|  java.lang.String[] | getSelect(int field)Used for a selection type to put the list items in a String array. | 
|  boolean | isBatchable()Finds if the program is identifies as being able to run in a batch queue | 
|  boolean | isDefaultParamValueStr(int field)Determine if there is a default parameter in a field of the ACD. | 
|  boolean | isDependents(java.lang.String attr,
             int field,
             int numofFields)Always start by calling isDependents(), which calculates the number of dependents and construct the Dependent array. | 
|  boolean | isMaxParamValue(int field)Determine if there is a max parameter in a field of the ACD. | 
|  boolean | isMinParamValue(int field)Determine if there is a min parameter in a field of the ACD. | 
|  boolean | isOptionalParam()Determine if there is a optional parameter in any field of the ACD. | 
|  boolean | isOptionalParamValue(int field)Determine if there is a optional parameter in a field of the ACD. | 
|  boolean | isOutputFile(int field)Determine if a field is data type outfile. | 
|  boolean | isOutputGraph(int field)Determine if a field is data type graph or xygraph. | 
|  boolean | isOutputSequence(int field)Determine if data type of a field is seqout. | 
|  boolean | isParamValueStr(int field,
                int param)Determine if the value of the parameter is a String. | 
|  int | parseParam(java.io.BufferedReader in,
           java.io.StreamTokenizer st)Parses a parameter in a ACD field | 
| private  java.lang.String | resolveVariables(ApplicationFields[] variables,
                 int nvars,
                 java.lang.String svalue)Used to replace the "variable:" or "var:" shorthand notation in the ACD to the full expression it represent | 
| private  void | setGuiHandleNumber(java.lang.String dataType,
                   ApplicationFields appF)Sets the gui handle depending on the data type. | 
| Methods inherited from class java.lang.Object | 
| clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait | 
| Field Detail | 
private int numofFields
private int numofParams
private java.util.Vector vappF
private java.lang.String svalue
private double nvalue
private java.lang.String attr
private Dependent[] dep
private int numOfDependents
private java.lang.String groupList
private int nsection
private int nsubsection
private int ntextf
private int nint
private int nfloat
private int nbool
private int nseqs
private int nflist
private int nlist
private int mlist
private int nrange
private java.util.Vector listdefault
private boolean isPrimaryGp
private boolean isSecondaryGp
private java.lang.String primaryGp
private java.lang.String secondaryGp
| Constructor Detail | 
public ParseAcd(java.lang.String acdText,
                boolean groups)
acdText - String representation of the ACD filegroups - Boolean determing whether just to retieve the groups| Method Detail | 
private java.lang.String resolveVariables(ApplicationFields[] variables,
                                          int nvars,
                                          java.lang.String svalue)
public int getGuiHandleNumber(int field)
public int getNumTextf()
public int getNumNint()
public int getNumNfloat()
public int getNumBool()
public int getNumSeq()
public int getNumFileList()
public int getNumList()
public int getNumMList()
public int getNumRange()
public int getNumSection()
public int getNumSubsection()
public java.lang.String getParameterAttribute(int field,
                                              int param)
public boolean isParamValueStr(int field,
                               int param)
public java.lang.String getParamValueStr(int field,
                                         int param)
private void setGuiHandleNumber(java.lang.String dataType,
                                ApplicationFields appF)
public double getParamValueDbl(int field,
                               int param)
public boolean isDefaultParamValueStr(int field)
public double getDefaultParamValueDbl(int field)
public boolean isDependents(java.lang.String attr,
                            int field,
                            int numofFields)
public Dependent[] getDependents()
public int getNumOfDependents()
public java.lang.String getMinParam(int field)
public java.lang.String getMaxParam(int field)
public boolean isMinParamValue(int field)
public boolean isMaxParamValue(int field)
public java.lang.String getInfoParamValue(int field)
public java.lang.String getHelpParamValue(int field)
public boolean isBatchable()
public java.lang.String getExpectedCPU()
protected java.lang.String formatHelpText(java.lang.String help)
public boolean isOptionalParamValue(int field)
public boolean isOutputSequence(int field)
public java.lang.String getOutputSequenceFile(int field)
public boolean isOutputGraph(int field)
public boolean isOutputFile(int field)
public java.lang.String getDefaultParamValueStr(int field)
public java.lang.String[] getList(int field)
public java.lang.String getListLabel(int field,
                                     int index)
public java.lang.String[] getSelect(int field)
public java.util.Vector getListOrSelectDefault()
public boolean isOptionalParam()
public int getNumofFields()
public int getNumofParams(int field)
public int parseParam(java.io.BufferedReader in,
                      java.io.StreamTokenizer st)
               throws java.io.IOException
java.io.IOException| 
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