| Keyword | Field | Information |
| Analysing | 0 | general Information |
| Sequence | 0 | Sequence Data |
| with | 4 | all Patterns Data |
| Total | 0 | general Information, Condition for end of the loop |
| Keyword | Variables /Arrays | index | consists of | Comments |
| Analysing | seq_nr seq_file |
number of analysed SEQ file contains SEQ data |
||
| Sequence | sequence | [0 .. seq_nr] [0 .. 1] |
sequence_name sequence_length |
Name of all SEQ Length of all SEQ |
| with | pat_id_nr | Number of different PAT | ||
| pattern (data for each different PAT) |
[0 .. pat_nr] [0 .. 1] |
pattern_id full_pattern |
Id of the PAT complete PAT |
|
| length_of_pattern | -"- | pat_length | Lenght of every PAT | |
| abs_nr_of_pat | ||||
| Sequence_with_pattern (data for for each discovered Pattern) |
[0 .. abs_nr_of_pat] [0 .. 5] |
pattern_id pat_id_nr pat_seq_name pat_start pat_end pat_length pat_real |
Id of the PAT ID-Number of the PAT SEQ, where PAT is found Start Position of PAT End Position of PAT Lenght of PAT real complete PAT |
|
| Total | success end time |
pointer for a success of the process pointer for the end of the process running time of Pratt |
All important data for the JAVA applet before calling the applet inside
of the CGI script (module call_java_applet).
The single fields of the arrays contains of strings. (STILL)
| Source array | Array to hand over | index | consists of | Comments |
| pattern length_of_pattern |
PAT_DATA (The data are delimited by {:}) |
[0 .. 3] | PAT ID PAT ID nr complete PAT PAT length |
data for each different PAT |
| sequence Sequence_with_pattern |
SEQ_DATA (The data are delimited by {:} and {;}) |
[0 .. 6] | SEQ name SEQ length PAT ID PAT ID nr PAT Start Position PAT length Nr of all PAT |
data for each Sequence data for for each discovered Pattern |
| Variables | Meaning | important for |
| nr_diff_patterns | Number of different Pattern | Pattern part |
| mark_nr max_SEQ_length |
Number of marks for the ruler (max_seq_length div 100) Length of the longest Sequence |
Ruler |
| seq_nr max_nr_of_patterns_one_seq |
Number of Sequences maximum Number of Pattern in One Sequence |
Sequence part |
| Parameter from the CGI | Variables in the Applet | Meaning |
| nr_diff_patterns | difPATNumber | Number of different Patterns for the loops in the Pattern part |
| seq_nr | SEQNumber | Number of Sequences for the loops in the Sequence part |
| max_nr_of_patterns_one_seq | MaxPATNumber | maximal number of Pattern in one Sequences for the loops in the Sequence part |
| mark_nr | Marknr | Number of marks to measure the length for the Ruler part |
| max_SEQ_length | MaxSEQLength | Length of the longest Sequence to draw the Ruler for the Ruler part |
| Image part | Parameter arrays | index | Meaning |
| Pattern | IDNumberOfdifPAT | [0 .. difPATNumber] | ID-Number of different Patterns |
| IDOfPAT | -"- | ID-Letter of different Patterns | |
| FullPAT | -"- | complete Pattern structure | |
| difPATLength | -"- | Length of different Patterns | |
| PATshow | -"- | boolean variable to activate or deactivate Pattern in the image | |
| Sequence | SEQName | [0 .. SEQNumber] | Name of all Sequences |
| SEQLength | -"- | Length of all Sequences | |
| SEQHeight | -"- | Height of all Sequences | |
| PATNumber | -"- | Number of Patterns in every Sequence | |
| SEQStartPos | -"- | absolute start position to draw the Sequence | |
| IDOfPattern | [0 .. SEQNumber] [0 .. difPATNumber] |
ID-Number of all Patterns in every Sequence | |
| PositionOfPattern | -"- | Position of all Patterns in every Sequence | |
| LengthOfPattern | -"- | Length of all Patterns in every Sequence | |
| HeightPosOfPattern | -"- | Overlap position of all Patterns in every Sequence | |
| general Drawing | SEQStartWidth SEQStartHeight SEQEndWidth SEQEndHeight |
No array [0 .. SEQNumber] -"- -"- |
Variables for the dimension of the Sequences |
| Variable | Meaning |
| DATA | help variable for Parameter input / Buffer |
| PatternHeight PatternWidth PatternStartX PatternStartY |
Variables for the dimension of the Patterns in the image / the value will be set before drawing |
| Modul | variables | Meaning | Parent | Children | Explanation |
| MouseEnter | Event e int x int y |
Event expl X Y |
GetPatID showStatus |
handler for mouse events, JAVA library | |
| MouseMove | Event e int x int y |
-"- | GetPatID showStatus |
-"- | |
| MouseExit | Event e int x int y |
-"- | showStatus | -"- | |
| MouseDown | Event e int x int y |
-"- | SetPATStatus | -"- | |
| GetPatID | int posX int posY |
X Y |
MouseEnter MouseMove MouseDown |
Compares the handed over coordinates with the coordinates of all Pattern and returns with the Pattern ID number | |
| SetPATStatus | int posX int posY |
X Y |
MouseDown | Sets the status of Pattern at shown or hidden, draws the Sequences new and returns with the Pattern ID number | |
| drawPATStatus | int l Graphics g |
ID Number of diff Pattern Graphic variable |
paint | draws a mark (black circle) in front of every Pattern in the Pattern overview, which is shown at this time | |
| getSeqID | int posX int posY |
X Y |
MouseEnter MouseMove MouseDown |
returns the Sequence ID Number on the position of the mouse cursor | |
| setPatColor | int IDnumber | ID of Pattern | paint | Chooses color for the Pattern | |
| PrintPattern- Information | int patID int seqID |
ID of Pattern ID of Sequence |
MouseDown | shows in the Status line the both ID number under the mouse cursor | |
| setNew- SequenceStartPos | MouseDown | setSEQStartPos | recalculates the overlap positions of each Patterns and the Start position of each Sequence after repainting (show/hide Pattern) | ||
| setSEQStartPos | init setNew- SequenceStartPos |
sets the dimensions for the Sequeence, represented by a line |