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org.emboss.jemboss.parser
Class ParseAcd

java.lang.Object
  |
  +--org.emboss.jemboss.parser.ParseAcd

public class ParseAcd
extends java.lang.Object

ACD (Ajax command line definition) file parser.

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.

ApplicationFields[] getApplicationFields()
          Gets the application field.

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)

java.lang.String getGroups()
          Gets the list of groups defined by setGroups.

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.

int 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 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 getPrimaryGroup()
          Gets the primary groups the application is a member of.

java.lang.String getSecondaryGroup()
          Gets the secondary groups the application is a member of.

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.

boolean isPrimaryGroup()
          True if a primary group is defined.

boolean isSecondaryGroup()
          True if a secondary group is defined.

int parseParam(java.io.BufferedReader in, java.io.StreamTokenizer st)
          Parses each parameter in a field

void setGroups(int field)
          Finds the primary and secondary groups, defined in the ACD file.

void setParamValueStr(int field, int param, java.lang.String svalue)


Methods inherited from class java.lang.Object

, clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ParseAcd

public ParseAcd(java.lang.String acdText,
                boolean groups)

The constructor takes the ACD as a string.

Parameters:: acdText - String representation of the ACD file; groups - Boolean determing whether just to retieve the groups

Method Detail

getApplicationFields

public ApplicationFields[] getApplicationFields()

Gets the application field.

Returns:: ApplicationField

getGuiHandleNumber

public int getGuiHandleNumber(int field)

Gets the handle for a gui component on the Jemboss form.

Parameters:: int - field number in the ACD file
Returns:: Handle integer.

getNumTextf

public int getNumTextf()

Gets the number of float, string, seqout, outfile, infile, regexp, codon & featout data types in the ACD. These make up the number of JTextAreas in the Jemboss form.

Returns:: Number of TextArea's in the Jemboss form.

getNumNint

public int getNumNint()

Gets the number of int data types in the ACD.

Returns:: Number of TextFieldInt in the Jemboss form.

getNumNfloat

public int getNumNfloat()

Gets the number of float data types in the ACD.

Returns:: Number of TextFieldFloat in the Jemboss form.

getNumBool

public int getNumBool()

Gets the number of boolean data types in the ACD.

Returns:: Number of check boxes in the Jemboss form.

getNumSeq

public int getNumSeq()

Gets the number of seqset, seqall & sequence data types in the ACD

Returns:: Number of sequence inputs in the Jemboss form.

getNumList

public int getNumList()

Gets the number of list & selection data types in the ACD, using single list selection

Returns:: Number of selection lists in the Jemboss form.

getNumMList

public int getNumMList()

Gets the number of list & selection data types in the ACD, using multiple list selection

Returns:: Number of selection lists in the Jemboss form.

getNumRange

public int getNumRange()

Returns:: Number of range data types in the Jemboss form.

getNumSection

public int getNumSection()

Gets the number of sections in the ACD

Returns:: Number of sections in the Jemboss form.

getNumSubsection

public int getNumSubsection()

Gets the number of nested sections in the ACD

Returns:: Number of subsections in the Jemboss form.

getParameterAttribute

public java.lang.String getParameterAttribute(int field,
                                              int param)

Get a specified parameter attribute.

Parameters:: int - field number in the ACD file; int - parameter number in that field
Returns:: String of the value.

isParamValueStr

public boolean isParamValueStr(int field,
                               int param)

Determine if the value of the parameter is a String.

Returns:: True if the value of the parameter is a String.

getParamValueStr

public java.lang.String getParamValueStr(int field,
                                         int param)

Gets the String value of a parameter.

Returns:: String value of the parameter.

setParamValueStr

public void setParamValueStr(int field,
                             int param,
                             java.lang.String svalue)

getParamValueDbl

public double getParamValueDbl(int field,
                               int param)

Gets the double value of a parameter.

Returns:: Double value of the parameter.

isDefaultParamValueStr

public boolean isDefaultParamValueStr(int field)

Determine if there is a default parameter in a field of the ACD.

Parameters:: int - field number
Returns:: True if the default parameter value is a String

getDefaultParamValueDbl

public double getDefaultParamValueDbl(int field)

Return a double default parameter

Parameters:: int - field number
Returns:: Default parameter value as a double.

isDependents

public 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.

Parameters:: String - name of the attribute; int - field number; int - toatal number of fields
Returns:: True if there are dependent parameters.

getDependents

public Dependent[] getDependents()

Gets the dependents associated with the ACD.

Returns:: the Dependent array for those fields with dependents

getNumOfDependents

public int getNumOfDependents()

Gets the number of dependent parameters in the ACD.

Returns:: Number of Dependent making up the array

getMinParam

public java.lang.String getMinParam(int field)

Locates the min parameter in a field and returns it as a String.

Parameters:: int - field number
Returns:: The minimum value defined in a field.

getMaxParam

public java.lang.String getMaxParam(int field)

Locates the max parameter in a field and returns it as a String.

Parameters:: int - field number
Returns:: The maximum value defined in a field.

isMinParamValue

public boolean isMinParamValue(int field)

Determine if there is a min parameter in a field of the ACD.

Parameters:: int - field number
Returns:: True if there is a minimum value specified in a field.

isMaxParamValue

public boolean isMaxParamValue(int field)

Determine if there is a max parameter in a field of the ACD.

Parameters:: int - field number
Returns:: True if there is a maximum value specified in a field.

getInfoParamValue

public java.lang.String getInfoParamValue(int field)

Finds the prompt, info or help parameter in an ACD field, in that order.

Parameters:: int - field number
Returns:: Information specified by the prompt parameter, if present else the information parameter or the help parameter.

getHelpParamValue

public java.lang.String getHelpParamValue(int field)

Finds the help parameter in an ACD field.

Parameters:: int - field number
Returns:: Help parameter defined in a field or a blank String if not specified.

isBatchable

public boolean isBatchable()

Finds if the program is identifies as being able to run in a batch queue

Returns:: true if the program is suitable for putting in a batch queue

getExpectedCPU

public java.lang.String getExpectedCPU()

Finds any expected cpu level indicator (low, medium, high)

Returns:: cpu level indicator

formatHelpText

protected java.lang.String formatHelpText(java.lang.String help)

Limits the length of the line for the help text used in the tool tips.

Parameters:: String - help text
Returns:: formated help text.

isOptionalParamValue

public boolean isOptionalParamValue(int field)

Determine if there is a optional parameter in a field of the ACD.

Parameters:: int - field number
Returns:: True if this is an "optional" field.

isOutputSequence

public boolean isOutputSequence(int field)

Determine if data type of a field is seqout.

Parameters:: int - field number
Returns:: True if this is an "seqout" field.

getOutputSequenceFile

public java.lang.String getOutputSequenceFile(int field)

Gets the name of the output sequence field (seqout).

Parameters:: int - field number
Returns:: The parameter name for the seqout data type.

isOutputGraph

public boolean isOutputGraph(int field)

Determine if a field is data type graph or xygraph.

Parameters:: int - field number
Returns:: True if the field is of "graph" or "xygraph" type.

isOutputFile

public boolean isOutputFile(int field)

Determine if a field is data type outfile.

Parameters:: int - field number
Returns:: True if the field is of "outfile" type.

setGroups

public void setGroups(int field)

Finds the primary and secondary groups, defined in the ACD file. Call this before using the other group methods.

Parameters:: int - field number

isPrimaryGroup

public boolean isPrimaryGroup()

True if a primary group is defined.

Returns:: True if a primary group is defined.

isSecondaryGroup

public boolean isSecondaryGroup()

True if a secondary group is defined.

Returns:: True if a secondary group is defined.

getPrimaryGroup

public java.lang.String getPrimaryGroup()

Gets the primary groups the application is a member of.

Returns:: Primary groups the application is a member of.

getSecondaryGroup

public java.lang.String getSecondaryGroup()

Gets the secondary groups the application is a member of.

Returns:: Secondary groups the application is a member of.

getGroups

public java.lang.String getGroups()

Gets the list of groups defined by setGroups.

Returns:: Group list defined in setGroups().

getDefaultParamValueStr

public java.lang.String getDefaultParamValueStr(int field)

Gets a String default parameter.

Parameters:: int - field number
Returns:: Default parameter for this field.

getList

public java.lang.String[] getList(int field)

Used for a list data type to put the list items in a String array.

Parameters:: int - field number
Returns:: String array representation of the list type.

getListLabel

public java.lang.String getListLabel(int field,
                                     int index)

For a list data type determine the appropriate String entry.

Parameters:: int - field number; int - index into the list
Returns:: String for that entry.

getSelect

public java.lang.String[] getSelect(int field)

Used for a selection type to put the list items in a String array.

Parameters:: int - field number
Returns:: String array representation of the select type.

getListOrSelectDefault

public int getListOrSelectDefault()

Use this after getList or getSelect to retrieve default

Returns:: int default for list or select data type

isOptionalParam

public boolean isOptionalParam()

Determine if there is a optional parameter in any field of the ACD.

Parameters:: True - if there is an optional parameter in any field.

getNumofFields

public int getNumofFields()

Gets the number of fields in the ACD file.

Returns:: Total number of fields in an ACD file

getNumofParams

public int getNumofParams(int field)

Gets the number of parameters in a ACD field.

Parameters:: int - field number
Returns:: number of parameters in the field.

parseParam

public int parseParam(java.io.BufferedReader in,
                      java.io.StreamTokenizer st)
               throws java.io.IOException

Parses each parameter in a field

Parameters:: BufferedReader -; StreamTokenizer -
Returns:: int